downloading reverse dependencies ‘aroma.affymetrix’, ‘aroma.core’, ‘cramR’, ‘dataquieR’, ‘eoffice’, ‘inDAGO’, ‘inpdfr’, ‘PointedSDMs’, ‘babel’, ‘biplotEZ’, ‘matrixStats’, ‘metabodecon’, ‘PSCBS’, ‘R.rsp’ trying URL 'file:///data/Repositories/CRAN/src/contrib/aroma.affymetrix_3.2.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/aroma.core_3.3.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/cramR_0.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/dataquieR_2.5.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/eoffice_0.2.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/inDAGO_1.0.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/inpdfr_0.1.12.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/PointedSDMs_2.1.4.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/babel_0.3-0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/biplotEZ_2.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/matrixStats_1.5.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/metabodecon_1.6.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/PSCBS_0.68.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/R.rsp_0.46.0.tar.gz' installing dependencies ‘affxparser’, ‘affy’, ‘AffymetrixDataTestFiles’, ‘affyPLM’, ‘aroma.apd’, ‘aroma.core’, ‘aroma.light’, ‘ascii’, ‘bigtabulate’, ‘dbx’, ‘dChipIO’, ‘entropart’, ‘expectile’, ‘flexsiteboard’, ‘gcrma’, ‘ggvenn’, ‘GLAD’, ‘HaarSeg’, ‘harrypotter’, ‘HTSFilter’, ‘INLA’, ‘inlabru’, ‘MassSpecWavelet’, ‘mdrb’, ‘metacom’, ‘mpcbs’, ‘MultinomialCI’, ‘oligo’, ‘oligoClasses’, ‘palr’, ‘pdInfoBuilder’, ‘PSCBS’, ‘qmrparser’, ‘R.devices’, ‘R.filesets’, ‘rankICC’, ‘readJDX’, ‘Rsubread’, ‘sfit’, ‘ShortRead’, ‘speaq’, ‘spocc’, ‘spsComps’, ‘textutils’, ‘toscutil’, ‘upsetjs’ Warning: packages ‘sfit’, ‘expectile’, ‘HaarSeg’, ‘mpcbs’, ‘INLA’, ‘mdrb’ are not available for this version of R Versions of these packages for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘awsMethods’, ‘R.huge’, ‘affyio’, ‘aws’, ‘biganalytics’, ‘shinytoastr’, ‘hwriter’, ‘EntropyEstimation’, ‘rebird’, ‘rvertnet’, ‘ridigbio’ begin installing package ‘awsMethods’ begin installing package ‘R.huge’ begin installing package ‘affyio’ begin installing package ‘biganalytics’ begin installing package ‘shinytoastr’ begin installing package ‘hwriter’ begin installing package ‘EntropyEstimation’ begin installing package ‘rebird’ begin installing package ‘rvertnet’ begin installing package ‘ridigbio’ begin installing package ‘affxparser’ begin installing package ‘R.filesets’ begin installing package ‘aroma.light’ begin installing package ‘AffymetrixDataTestFiles’ begin installing package ‘dChipIO’ begin installing package ‘MultinomialCI’ begin installing package ‘qmrparser’ begin installing package ‘flexsiteboard’ begin installing package ‘ggvenn’ begin installing package ‘dbx’ begin installing package ‘rankICC’ begin installing package ‘upsetjs’ begin installing package ‘harrypotter’ begin installing package ‘HTSFilter’ begin installing package ‘palr’ begin installing package ‘Rsubread’ begin installing package ‘metacom’ begin installing package ‘inlabru’ * installing *source* package ‘MultinomialCI’ ... ** this is package ‘MultinomialCI’ version ‘1.2’ ** package ‘MultinomialCI’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MultinomialCI) begin installing package ‘readJDX’ * installing *source* package ‘dChipIO’ ... ** this is package ‘dChipIO’ version ‘0.1.5’ ** package ‘dChipIO’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dChipIO) begin installing package ‘toscutil’ * installing *source* package ‘flexsiteboard’ ... ** this is package ‘flexsiteboard’ version ‘0.0.7’ ** package ‘flexsiteboard’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flexsiteboard) begin installing package ‘MassSpecWavelet’ * installing *source* package ‘awsMethods’ ... ** this is package ‘awsMethods’ version ‘1.1-1’ ** package ‘awsMethods’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpWV0U5r/R.INSTALL3dd9bb488b193b/awsMethods/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c omp_funcs.c -o omp_funcs.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o awsMethods.so init.o omp_funcs.o -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWV0U5r/R.INSTALL3dd9bb488b193b/awsMethods/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-awsMethods/00new/awsMethods/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (awsMethods) begin installing package ‘ascii’ * installing *source* package ‘palr’ ... ** this is package ‘palr’ version ‘0.4.0’ ** package ‘palr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (palr) begin installing package ‘R.devices’ * installing *source* package ‘rankICC’ ... ** this is package ‘rankICC’ version ‘1.0.2’ ** package ‘rankICC’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rankICC) begin installing package ‘textutils’ * installing *source* package ‘EntropyEstimation’ ... ** this is package ‘EntropyEstimation’ version ‘1.2.1’ ** package ‘EntropyEstimation’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLE4OEz/R.INSTALL3dd9eb5d6dbe33/EntropyEstimation/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c EntropEst.c -o EntropEst.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o EntropyEstimation.so EntropEst.o init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLE4OEz/R.INSTALL3dd9eb5d6dbe33/EntropyEstimation/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-EntropyEstimation/00new/EntropyEstimation/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EntropyEstimation) begin installing package ‘aws’ * installing *source* package ‘hwriter’ ... ** this is package ‘hwriter’ version ‘1.3.2.1’ ** package ‘hwriter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hwriter) begin installing package ‘entropart’ * installing *source* package ‘dbx’ ... ** this is package ‘dbx’ version ‘0.4.0’ ** package ‘dbx’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dbx) begin installing package ‘ShortRead’ * installing *source* package ‘ridigbio’ ... ** this is package ‘ridigbio’ version ‘0.4.1’ ** package ‘ridigbio’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ridigbio) * installing *source* package ‘qmrparser’ ... ** this is package ‘qmrparser’ version ‘0.1.6’ ** package ‘qmrparser’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (qmrparser) * installing *source* package ‘AffymetrixDataTestFiles’ ... ** this is package ‘AffymetrixDataTestFiles’ version ‘0.48.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AffymetrixDataTestFiles) * installing *source* package ‘shinytoastr’ ... ** this is package ‘shinytoastr’ version ‘2.2.0’ ** package ‘shinytoastr’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (shinytoastr) begin installing package ‘spsComps’ * installing *source* package ‘R.huge’ ... ** this is package ‘R.huge’ version ‘0.10.1’ ** package ‘R.huge’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function nrow to nrow.default, which was defined in environment R.huge. Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function ncol to ncol.default, which was defined in environment R.huge. Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function rownames to rownames.default, which was defined in environment R.huge. Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function colnames to colnames.default, which was defined in environment R.huge. ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R.huge) begin installing package ‘aroma.apd’ * installing *source* package ‘upsetjs’ ... ** this is package ‘upsetjs’ version ‘1.11.1’ ** package ‘upsetjs’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (upsetjs) * installing *source* package ‘textutils’ ... ** this is package ‘textutils’ version ‘0.4-3’ ** package ‘textutils’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (textutils) * installing *source* package ‘toscutil’ ... ** this is package ‘toscutil’ version ‘2.8.0’ ** package ‘toscutil’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (toscutil) * installing *source* package ‘rebird’ ... ** this is package ‘rebird’ version ‘1.3.0’ ** package ‘rebird’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rebird) * installing *source* package ‘readJDX’ ... ** this is package ‘readJDX’ version ‘0.6.4’ ** package ‘readJDX’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (readJDX) * installing *source* package ‘aroma.light’ ... ** this is package ‘aroma.light’ version ‘3.40.0’ ** package ‘aroma.light’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aroma.light) begin installing package ‘PSCBS’ * installing *source* package ‘MassSpecWavelet’ ... ** this is package ‘MassSpecWavelet’ version ‘1.76.0’ ** package ‘MassSpecWavelet’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4IhEwF/R.INSTALL3de0916ac8761a/MassSpecWavelet/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c find_local_maximum.c -o find_local_maximum.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o MassSpecWavelet.so find_local_maximum.o init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4IhEwF/R.INSTALL3de0916ac8761a/MassSpecWavelet/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-MassSpecWavelet/00new/MassSpecWavelet/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MassSpecWavelet) begin installing package ‘speaq’ * installing *source* package ‘R.devices’ ... ** this is package ‘R.devices’ version ‘2.17.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R.devices) * installing *source* package ‘harrypotter’ ... ** this is package ‘harrypotter’ version ‘2.1.1’ ** package ‘harrypotter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (harrypotter) * installing *source* package ‘aroma.apd’ ... ** this is package ‘aroma.apd’ version ‘0.7.1’ ** package ‘aroma.apd’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location Warning in .requireBiocPackage("affxparser", neededBy = pkgname) : Package 'affxparser' could not be loaded. Without it aroma.apd will not work. Please install it from Bioconductor, cf. https://www.bioconductor.org/ ** testing if installed package can be loaded from final location Warning in .requireBiocPackage("affxparser", neededBy = pkgname) : Package 'affxparser' could not be loaded. Without it aroma.apd will not work. Please install it from Bioconductor, cf. https://www.bioconductor.org/ ** testing if installed package keeps a record of temporary installation path * DONE (aroma.apd) * installing *source* package ‘ggvenn’ ... ** this is package ‘ggvenn’ version ‘0.1.19’ ** package ‘ggvenn’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggvenn) * installing *source* package ‘rvertnet’ ... ** this is package ‘rvertnet’ version ‘0.8.4’ ** package ‘rvertnet’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rvertnet) begin installing package ‘spocc’ * installing *source* package ‘R.filesets’ ... ** this is package ‘R.filesets’ version ‘2.15.1’ ** package ‘R.filesets’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (R.filesets) * installing *source* package ‘metacom’ ... ** this is package ‘metacom’ version ‘1.5.3’ ** package ‘metacom’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (metacom) * installing *source* package ‘spsComps’ ... ** this is package ‘spsComps’ version ‘0.3.4.0’ ** package ‘spsComps’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spsComps) * installing *source* package ‘affyio’ ... ** this is package ‘affyio’ version ‘1.80.0’ ** package ‘affyio’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc-15 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-15 accepts -g... yes checking for gcc-15 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc-15 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for main in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes checking for pthread_create in -lpthread... yes checking if we can use pthreads... yes checking if PTHREAD_STACK_MIN is defined... yes configure: Enabling threading for affyio configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQbYzzG/R.INSTALL3dd9c15d691e71/affyio/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fread_functions.c -o fread_functions.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init_package.c -o init_package.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_abatch.c -o read_abatch.o read_abatch.c: In function ‘read_cel_file_intensities’: read_abatch.c:656:176: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:656:182: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 656 | Rprintf("Warning: found an empty line where not expected in %s.\nThis means that there is a cel intensity missing from the cel file.\nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:146: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:665:152: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:677:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:689:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function ‘read_cel_file_stddev’: read_abatch.c:764:178: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:764:184: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 764 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:774:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 774 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:785:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 785 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:795:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 795 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:805:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 805 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function ‘read_cel_file_npixels’: read_abatch.c:870:178: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:870:184: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 870 | Rprintf("Warning: found an empty line where not expected in %s.\n This means that there is a cel intensity missing from the cel file.\n Sucessfully read to cel intensity %d of %d expected\n", filename, i-1, i); | ~^ ~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:879:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 879 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:890:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 890 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:901:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 901 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:913:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 913 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:924:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 924 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function ‘read_gzcel_file_intensities’: read_abatch.c:1567:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1567:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1567 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1578:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1578 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1589:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1589 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function ‘read_gzcel_file_stddev’: read_abatch.c:1665:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1665:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1665 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1677:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1677 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1689:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1689 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1701:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1701 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function ‘read_gzcel_file_npixels’: read_abatch.c:1769:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1769:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1769 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1780:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1780 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1791:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1791 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1801:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1801 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:145: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c:1811:151: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1811 | Rprintf("Warning: found an incomplete line where not expected in %s.\nThe CEL file may be truncated. \nSucessfully read to cel intensity %d of %d expected\n", filename, i-1, rows); | ~^ ~~~~ | | | | int size_t {aka long unsigned int} | %ld read_abatch.c: In function ‘gzbinary_get_detailed_header_info’: read_abatch.c:3410:3: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 3410 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^ read_abatch.c:3410:65: note: length computed here 3410 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ read_abatch.c: In function ‘binary_get_detailed_header_info’: read_abatch.c:2661:3: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-truncation] 2661 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^ read_abatch.c:2661:65: note: length computed here 2661 | strncpy(header_info->AlgorithmParameters,my_header->alg_param,strlen(my_header->alg_param)-1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_bpmap.c -o read_bpmap.o read_bpmap.c: In function ‘ReadBPMAPFileIntoRList’: read_bpmap.c:849:39: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘SEXP’ {aka ‘struct SEXPREC *’} [-Wformat=] 849 | error("Unable to open the file %s",filename); | ~^ ~~~~~~~~ | | | | | SEXP {aka struct SEXPREC *} | char * read_bpmap.c:698:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 698 | sprintf(buf, "%d", j+1); | ^ In file included from /usr/include/stdio.h:970, from /home/hornik/tmp/R-d-gcc-15/include/R.h:44, from read_bpmap.c:23: In function ‘sprintf’, inlined from ‘readBPMAPSeqIdPositionInfo’ at read_bpmap.c:698:4, inlined from ‘ReadBPMAPFileIntoRList’ at read_bpmap.c:873:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function ‘ReadBPMAPFileIntoRList’: read_bpmap.c:655:27: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 655 | sprintf(buf, "%d", j+1); | ^ In function ‘sprintf’, inlined from ‘readBPMAPSeqIdPositionInfo’ at read_bpmap.c:655:4, inlined from ‘ReadBPMAPFileIntoRList’ at read_bpmap.c:873:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ read_bpmap.c: In function ‘ReadBPMAPFileIntoRList’: read_bpmap.c:603:25: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] 603 | sprintf(buf, "%d", j+1); | ^ In function ‘sprintf’, inlined from ‘readBPMAPSeqIdPositionInfo’ at read_bpmap.c:603:2, inlined from ‘ReadBPMAPFileIntoRList’ at read_bpmap.c:873:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 2 and 11 bytes into a destination of size 10 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_cdf_xda.c -o read_cdf_xda.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_cdffile2.c -o read_cdffile2.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_celfile_generic.c -o read_celfile_generic.o read_celfile_generic.c: In function ‘generic_get_detailed_header_info’: read_celfile_generic.c:272:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 272 | strncpy(header_info->AlgorithmParameters,"Percentile:",11); | ^ read_celfile_generic.c:294:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 294 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); | ^ read_celfile_generic.c:315:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 315 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); | ^ read_celfile_generic.c:336:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 336 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); | ^ read_celfile_generic.c:357:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 357 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); | ^ read_celfile_generic.c:378:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] 378 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); | ^ read_celfile_generic.c:399:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] 399 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); | ^ read_celfile_generic.c:420:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 420 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); | ^ read_celfile_generic.c:441:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] 441 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); | ^ read_celfile_generic.c:464:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 464 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); | ^ read_celfile_generic.c:488:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 488 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); | ^ read_celfile_generic.c:510:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 510 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); | ^ read_celfile_generic.c:532:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 532 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); | ^ read_celfile_generic.c:553:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] 553 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); | ^ read_celfile_generic.c:575:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 575 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); | ^ read_celfile_generic.c:597:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] 597 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); | ^ read_celfile_generic.c: In function ‘gzgeneric_get_detailed_header_info’: read_celfile_generic.c:1270:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1270 | strncpy(header_info->AlgorithmParameters,"Percentile:",11); | ^ read_celfile_generic.c:1292:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1292 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"CellMargin:",11); | ^ read_celfile_generic.c:1313:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 1313 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierHigh:",12); | ^ read_celfile_generic.c:1334:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1334 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"OutlierLow:",11); | ^ read_celfile_generic.c:1355:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1355 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"AlgVersion:",11); | ^ read_celfile_generic.c:1376:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 14 bytes from a string of the same length [-Wstringop-truncation] 1376 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FixedCellSize:",14); | ^ read_celfile_generic.c:1397:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 17 bytes from a string of the same length [-Wstringop-truncation] 1397 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureWidth:",17); | ^ read_celfile_generic.c:1418:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 1418 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FullFeatureHeight:",18); | ^ read_celfile_generic.c:1439:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 26 bytes from a string of the same length [-Wstringop-truncation] 1439 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"IgnoreOutliersInShiftRows:",26); | ^ read_celfile_generic.c:1462:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 18 bytes from a string of the same length [-Wstringop-truncation] 1462 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"FeatureExtraction:",18); | ^ read_celfile_generic.c:1486:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 1486 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolWidthExtenstion:",20); | ^ read_celfile_generic.c:1508:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation] 1508 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"PoolHeightExtension:",20); | ^ read_celfile_generic.c:1530:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 12 bytes from a string of the same length [-Wstringop-truncation] 1530 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"UseSubgrids:",12); | ^ read_celfile_generic.c:1551:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 16 bytes from a string of the same length [-Wstringop-truncation] 1551 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"RandomizePixels:",16); | ^ read_celfile_generic.c:1573:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 11 bytes from a string of the same length [-Wstringop-truncation] 1573 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"ErrorBasis:",11); | ^ read_celfile_generic.c:1595:3: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 8 bytes from a string of the same length [-Wstringop-truncation] 1595 | strncpy(&header_info->AlgorithmParameters[algorithm_paramsize],"StdMult:",8); | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_clf.c -o read_clf.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_generic.c -o read_generic.o read_generic.c: In function ‘print_decode_nvt_triplet’: read_generic.c:1293:37: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘int’ [-Wformat=] 1293 | Rprintf("Its a float value is %f\n",temp32); | ~^ ~~~~~~ | | | | | int | double | %d gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_pgf.c -o read_pgf.o read_pgf.c:363:12: warning: ‘token_ends_with’ defined but not used [-Wunused-function] 363 | static int token_ends_with(char *token, char *ends_in){ | ^~~~~~~~~~~~~~~ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQbYzzG/R.INSTALL3dd9c15d691e71/affyio/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-affyio/00new/affyio/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affyio) begin installing package ‘affy’ begin installing package ‘oligoClasses’ * installing *source* package ‘entropart’ ... ** this is package ‘entropart’ version ‘1.6-16’ ** package ‘entropart’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (entropart) * installing *source* package ‘ascii’ ... ** this is package ‘ascii’ version ‘2.6’ ** package ‘ascii’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ascii) * installing *source* package ‘spocc’ ... ** this is package ‘spocc’ version ‘1.2.4’ ** package ‘spocc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spocc) * installing *source* package ‘speaq’ ... ** this is package ‘speaq’ version ‘2.7.0’ ** package ‘speaq’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (speaq) * installing *source* package ‘PSCBS’ ... ** this is package ‘PSCBS’ version ‘0.68.0’ ** package ‘PSCBS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PSCBS) begin installing package ‘aroma.core’ * installing *source* package ‘inlabru’ ... ** this is package ‘inlabru’ version ‘2.13.0’ ** package ‘inlabru’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (inlabru) * installing *source* package ‘affy’ ... ** this is package ‘affy’ version ‘1.88.0’ ** package ‘affy’ successfully unpacked and MD5 sums checked ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... gcc-15 -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwrzMhu/R.INSTALL3de9ad448db999/affy/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c chipbackground.c -o chipbackground.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c getall_locations.c -o getall_locations.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mas5calls.c -o mas5calls.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rma2.c -o rma2.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rma_common.c -o rma_common.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwrzMhu/R.INSTALL3de9ad448db999/affy/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-affy/00new/affy/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affy) begin installing package ‘gcrma’ * installing *source* package ‘biganalytics’ ... ** this is package ‘biganalytics’ version ‘1.1.22’ ** package ‘biganalytics’ successfully unpacked and MD5 sums checked ** using staged installation checking for Sun Studio compiler... no checking for OS... Linux ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbiM9xW/R.INSTALL3dd9ce2371c40a/biganalytics/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c biganalytics_init.c -o biganalytics_init.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c binit.cpp -o binit.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from binit.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hash.cpp -o hash.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from hash.cpp:2: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kmeans.cpp -o kmeans.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from kmeans.cpp:32: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../include -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c summary_stat.cpp -o summary_stat.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from summary_stat.cpp:7: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o biganalytics.so biganalytics_init.o binit.o hash.o kmeans.o summary_stat.o -lrt -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbiM9xW/R.INSTALL3dd9ce2371c40a/biganalytics/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biganalytics/00new/biganalytics/libs ** R ** byte-compile and prepare package for lazy loading Creating a generic function for ‘apply’ from package ‘base’ in package ‘biganalytics’ ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biganalytics) begin installing package ‘bigtabulate’ * installing *source* package ‘aws’ ... ** this is package ‘aws’ version ‘2.5-6’ ** package ‘aws’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp4IBCKD/R.INSTALL3de247c935436/aws/src' gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ICIsmooth.f -o ICIsmooth.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rentries.c -o Rentries.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awslp.f -o awslp.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awswghts.f -o awswghts.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c caws.f -o caws.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cawsmask.f -o cawsmask.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c esiglike.f -o esiglike.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c estimateComplexSigma.f -o estimateComplexSigma.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.f -o misc.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nlmeans.f -o nlmeans.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c pcaws.f -o pcaws.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c segment.f -o segment.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smooth3d.f -o smooth3d.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smse3.f -o smse3.o gfortran-15 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c varest.f -o varest.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o aws.so ICIsmooth.o Rentries.o awslp.o awswghts.o caws.o cawsmask.o esiglike.o estimateComplexSigma.o init.o misc.o nlmeans.o pcaws.o segment.o smooth3d.o smse3.o varest.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4IBCKD/R.INSTALL3de247c935436/aws/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-aws/00new/aws/libs ** R ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aws) begin installing package ‘GLAD’ * installing *source* package ‘HTSFilter’ ... ** this is package ‘HTSFilter’ version ‘1.50.0’ ** package ‘HTSFilter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (HTSFilter) * installing *source* package ‘gcrma’ ... ** this is package ‘gcrma’ version ‘2.82.0’ ** package ‘gcrma’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLG889r/R.INSTALL3deca37bf407c7/gcrma/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c baseProfile.c -o baseProfile.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c computeAffinities.c -o computeAffinities.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c postmean.c -o postmean.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o gcrma.so baseProfile.o computeAffinities.o postmean.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLG889r/R.INSTALL3deca37bf407c7/gcrma/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-gcrma/00new/gcrma/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gcrma) begin installing package ‘affyPLM’ * installing *source* package ‘bigtabulate’ ... ** this is package ‘bigtabulate’ version ‘1.1.9’ ** package ‘bigtabulate’ successfully unpacked and MD5 sums checked ** using staged installation checking for Sun Studio compiler... no checking for OS... Linux ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9RlDqM/R.INSTALL3decaf51c9dff4/bigtabulate/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bigtabulate.cpp -o bigtabulate.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from bigtabulate.cpp:7: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:23: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/sp_counted_impl.hpp:23: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = BreakMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:130:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper]’ 130 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = BreakMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = BreakMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:438:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = double; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 438 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 439 | new BreakMapper( breaks[i][0], breaks[i][1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 | breaks[i][2], INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:772:24: required from here 772 | return TAPPLY( MatrixAccessor( REAL(numericMatrix), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 773 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 774 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 775 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘BreakMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = IndexMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:130:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper]’ 130 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = IndexMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = IndexMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:445:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = double; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 445 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 446 | new IndexMapper( RData(vec), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 | RData(vec) + vecLen, INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:772:24: required from here 772 | return TAPPLY( MatrixAccessor( REAL(numericMatrix), | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 773 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 774 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 775 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘IndexMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = BreakMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:130:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = BreakMapper]’ 130 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = BreakMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = BreakMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:438:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = int; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 438 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 439 | new BreakMapper( breaks[i][0], breaks[i][1], | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 440 | breaks[i][2], INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:782:21: required from here 782 | return TAPPLY( MatrixAccessor( INTEGER(numericMatrix), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 783 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 784 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 785 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘BreakMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp: In instantiation of ‘void boost::checked_delete(T*) [with T = IndexMapper]’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:130:34: required from ‘boost::detail::shared_count::shared_count(Y*) [with Y = IndexMapper]’ 130 | boost::checked_delete( p ); | ~~~~~~~~~~~~~~~~~~~~~^~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:205:20: required from ‘void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, shared_count&) [with T = Mapper; Y = IndexMapper]’ 205 | boost::detail::shared_count( p ).swap( pn ); | ^~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:283:44: required from ‘boost::shared_ptr::shared_ptr(Y*) [with Y = IndexMapper; T = Mapper]’ 283 | boost::detail::sp_pointer_construct( this, p, pn ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ bigtabulate.cpp:445:26: required from ‘SEXPREC* TAPPLY(MatrixAccessorType, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP) [with RType = int; MatrixAccessorType = MatrixAccessor; SEXP = SEXPREC*]’ 445 | mappers.push_back( MapperPtr( | ^~~~~~~~~~ 446 | new IndexMapper( RData(vec), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 | RData(vec) + vecLen, INTEGER(useNA)[0] > 0 ) ) ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bigtabulate.cpp:782:21: required from here 782 | return TAPPLY( MatrixAccessor( INTEGER(numericMatrix), | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 783 | static_cast(Rf_nrows(numericMatrix)) ), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 784 | columns, breaks, returnTable, useNA, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 785 | returnSummary, processColumns, summaryNARM, splitcol, splitlist ); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/core/checked_delete.hpp:44:5: warning: deleting object of polymorphic class type ‘IndexMapper’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 44 | delete x; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DLINUX -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bigtabulate_init.c -o bigtabulate_init.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o bigtabulate.so bigtabulate.o bigtabulate_init.o -lrt -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9RlDqM/R.INSTALL3decaf51c9dff4/bigtabulate/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bigtabulate/00new/bigtabulate/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bigtabulate) * installing *source* package ‘GLAD’ ... ** this is package ‘GLAD’ version ‘2.74.0’ ** package ‘GLAD’ successfully unpacked and MD5 sums checked ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes GSL has been found on the operating system operating system: Linux configure: creating ./config.status config.status: creating src/Makevars src/Makevars file PKG_LIBS = -lgsl -lgslcblas -lm PKG_CPPFLAGS = -I/usr/local/include ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQ5SzKe/R.INSTALL3dedf130070b6d/GLAD/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BkpInfo.cpp -o BkpInfo.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HaarSeg.cpp -o HaarSeg.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MoveBkp.cpp -o MoveBkp.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c OutliersGNL.cpp -o OutliersGNL.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c chrBreakpoints.cpp -o chrBreakpoints.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cutree.cpp -o cutree.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c daglad.cpp -o daglad.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distance.cpp -o distance.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c filterBkp.cpp -o filterBkp.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c findCluster.cpp -o findCluster.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glad-utils.cpp -o glad-utils.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hclust.cpp -o hclust.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c laws.c -o laws.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c loopRemove.cpp -o loopRemove.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpQ5SzKe/R.INSTALL3dedf130070b6d/GLAD/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GLAD/00new/GLAD/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GLAD) * installing *source* package ‘aroma.core’ ... ** this is package ‘aroma.core’ version ‘3.3.2’ ** package ‘aroma.core’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function write to write.default, which was defined in environment aroma.core. ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (aroma.core) * installing *source* package ‘oligoClasses’ ... ** this is package ‘oligoClasses’ version ‘1.72.0’ ** package ‘oligoClasses’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (oligoClasses) * installing *source* package ‘Rsubread’ ... ** this is package ‘Rsubread’ version ‘2.24.0’ ** package ‘Rsubread’ successfully unpacked and MD5 sums checked ** using staged installation @@@@@ The operating system is Linux. ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZiokCK/R.INSTALL3dda2145d6f771/Rsubread/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c HelperFunctions.c -o HelperFunctions.o HelperFunctions.c: In function ‘get_contig_fasta’: HelperFunctions.c:236:74: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 236 | unsigned int this_size = HashTableGet( tab -> size_table, chro ) - NULL; | ^ HelperFunctions.c: In function ‘read_contig_fasta’: HelperFunctions.c:310:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 310 | HashTablePut(tab -> size_table , mem_chro, NULL + inner_cursor); | ^ HelperFunctions.c: In function ‘IVT_createNode’: HelperFunctions.c:3157:35: warning: format ‘%p’ expects argument of type ‘void *’, but argument 3 has type ‘IVT_IntervalTreeNode *’ [-Wformat=] 3157 | if(0) fprintf(stderr,"MEMTEST %p ALLOC\n", node); | ~^ ~~~~ | | | | void * IVT_IntervalTreeNode * HelperFunctions.c: In function ‘IVT_freeTree’: HelperFunctions.c:3291:35: warning: format ‘%p’ expects argument of type ‘void *’, but argument 3 has type ‘IVT_IntervalTreeNode *’ [-Wformat=] 3291 | if(0) fprintf(stderr,"MEMTEST %p FREE\n", root); | ~^ ~~~~ | | | | void * IVT_IntervalTreeNode * gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMbase-index.c -o LRMbase-index.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMchro-event.c -o LRMchro-event.o LRMchro-event.c: In function ‘LRMevents_build_entries’: LRMchro-event.c:87:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 87 | int * entries_list = LRMHashTableGet(context -> events_realignment, NULL+sidepos); | ^ LRMchro-event.c:97:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 97 | LRMHashTablePut(context -> events_realignment , NULL+sidepos, entries_list); | ^ LRMchro-event.c:120:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 120 | LRMHashTablePut(context -> events_realignment, NULL+sidepos, entries_list); | ^ LRMchro-event.c: In function ‘LRMevents_search’: LRMchro-event.c:213:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 213 | int * event_here = LRMHashTableGet(context -> events_realignment, NULL + testing_pos); | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMfile-io.c -o LRMfile-io.o LRMfile-io.c: In function ‘LRMgenerate_bam_record’: LRMfile-io.c:275:89: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 275 | int chro_number = LRMHashTableGet(context->sam_bam_chromosome_table, chro_name) - NULL; | ^ LRMfile-io.c: In function ‘LRMwrite_chunk_compress_bam_block’: LRMfile-io.c:349:22: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 349 | bam_buf[9] = 0xff; // OS | ^~~~ LRMfile-io.c: In function ‘LRMload_offsets’: LRMfile-io.c:437:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 437 | LRMHashTablePut(context->sam_bam_chromosome_table, chro_name, NULL + chromosome_no + 1); | ^ LRMfile-io.c:437:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 437 | LRMHashTablePut(context->sam_bam_chromosome_table, chro_name, NULL + chromosome_no + 1); | ^ LRMfile-io.c:440:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 440 | LRMHashTablePut(context->chromosome_size_table, chro_name, NULL + (this_offset - last_end + 16 - context->current_index_padding * 2)); | ^ LRMfile-io.c:441:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 441 | LRMArrayListPush(context->chromosome_size_list, NULL + this_offset); | ^ LRMfile-io.c: In function ‘LRMsambam_write_header’: LRMfile-io.c:477:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 477 | int chro_length = LRMHashTableGet(context -> chromosome_size_table, chro_name) - NULL; | ^ LRMfile-io.c:513:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 513 | int chro_length = LRMHashTableGet(context -> chromosome_size_table, chro_name) - NULL; | ^ LRMfile-io.c: In function ‘LRMlocate_gene_position’: LRMfile-io.c:611:112: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 611 | while(n+jump_ns < total_offsets && LRMArrayListGet(context->chromosome_size_list, n + jump_ns) - NULL <= linear) | ^ LRMfile-io.c:619:73: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 619 | if ( (LRMArrayListGet(context->chromosome_size_list, n) - NULL) > linear) | ^ LRMfile-io.c:622:94: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 622 | if(n>0)(*pos) -= (LRMArrayListGet(context->chromosome_size_list, n-1)-NULL); | ^ LRMfile-io.c: In function ‘LRMlocate_chro_length’: LRMfile-io.c:640:112: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 640 | while(n+jump_ns < total_offsets && LRMArrayListGet(context->chromosome_size_list, n + jump_ns) - NULL <= linear) | ^ LRMfile-io.c:648:73: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 648 | if ( (LRMArrayListGet(context->chromosome_size_list, n) - NULL) > linear) { | ^ LRMfile-io.c:650:88: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 650 | (* end_pos) = LRMArrayListGet(context->chromosome_size_list, n)-NULL; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMhashtable.c -o LRMhashtable.o LRMhashtable.c: In function ‘LRMpointerHashFunction’: LRMhashtable.c:737:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 737 | return ((srUInt_64)( pointer - NULL )) ; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMhelper.c -o LRMhelper.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMseek-zlib.c -o LRMseek-zlib.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LRMsorted-hashtable.c -o LRMsorted-hashtable.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_wrapper.c -o R_wrapper.o R_wrapper.c: In function ‘R_try_cell_barcode_wrapper’: R_wrapper.c:119:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 119 | int rv = (void*)c_argv[7]-NULL; | ^ R_wrapper.c:120:44: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 120 | int tested_reads = (void*)c_argv[8]-NULL; | ^ R_wrapper.c:121:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 121 | int sample_good_reads = (void*)c_argv[9]-NULL; | ^ R_wrapper.c:122:48: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 122 | int cell_good_reads = (void*)c_argv[10]-NULL; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RsimReads.c -o RsimReads.o RsimReads.c: In function ‘Rgen_one_read_here’: RsimReads.c:71:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 71 | int trans_len = HashTableGet(grc->transcript_lengths, seq_name)-NULL-1; | ^ RsimReads.c: In function ‘Rgrc_put_new_trans’: RsimReads.c:114:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 114 | HashTablePut( grc->transcript_lengths, strdup(seq_name) , NULL+lbuf_len +1); | ^ RsimReads.c:114:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 114 | HashTablePut( grc->transcript_lengths, strdup(seq_name) , NULL+lbuf_len +1); | ^ RsimReads.c: In function ‘init_grc_by_file’: RsimReads.c:144:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 144 | HashTablePut(grc -> expression_levels, strdup(input_order_transcript_names[xk1]), NULL +1); | ^ RsimReads.c:155:125: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 155 | int ov = HashTableGet( grc -> expression_levels, input_order_transcript_names[input_order_transcript_per_read[xk1]-1] ) -NULL; | ^ RsimReads.c:158:125: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 158 | HashTablePutReplace(grc -> expression_levels, input_order_transcript_names[input_order_transcript_per_read[xk1]-1], NULL+ov, 0); | ^ RsimReads.c:183:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 183 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ RsimReads.c:185:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 185 | if(seq_exp>1)HashTablePut(seq_duplicate_tab, md5mem, 1+NULL); | ^ RsimReads.c:241:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 241 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c SNPCalling.c -o SNPCalling.o SNPCalling.c: In function ‘put_hash_to_pile’: SNPCalling.c:229:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 229 | int base_N_qual = cursor->value - NULL; | ^ SNPCalling.c:230:51: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 230 | int POI_pos = cursor->key - NULL - 100; | ^ SNPCalling.c: In function ‘read_tmp_block’: SNPCalling.c:383:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 383 | unsigned int original_value = HashTableGet(merge_table,NULL+POI_pos)-NULL; | ^ SNPCalling.c:383:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 383 | unsigned int original_value = HashTableGet(merge_table,NULL+POI_pos)-NULL; | ^ SNPCalling.c:388:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 388 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:388:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 388 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:403:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 403 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c:403:101: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 403 | HashTablePut(merge_table, NULL+POI_pos, NULL+base_N_qual); | ^ SNPCalling.c: In function ‘process_snp_votes’: SNPCalling.c:939:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 939 | long long int indel_no = HashTableGet(parameters -> cigar_event_table, event_token) - NULL; | ^ SNPCalling.c:943:114: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 943 | long long int tmpv = HashTableGet(parameters -> cigar_event_table, event_token2) - NULL; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c aligner.c -o aligner.o aligner.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c atgcContent.c -o atgcContent.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c build-sam-index.c -o build-sam-index.o build-sam-index.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cell-counts.c -o cell-counts.o In file included from cell-counts.c:20: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ cell-counts.c: In function ‘cellCounts_cell_barcode_tabel_destroy’: cell-counts.c:475:15: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 475 | if(((a-NULL) & 0xfffffffff0000000llu ) ==IMPOSSIBLE_MEMORY_SPACE )return; | ^ cell-counts.c: In function ‘cellCounts_make_barcode_HT_table’: cell-counts.c:494:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 494 | HashTablePut(cct_context -> cell_barcode_head_tail_table, strdup(bc), NULL+xx1+IMPOSSIBLE_MEMORY_SPACE); | ^ cell-counts.c:494:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 494 | HashTablePut(cct_context -> cell_barcode_head_tail_table, strdup(bc), NULL+xx1+IMPOSSIBLE_MEMORY_SPACE); | ^ cell-counts.c:507:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 507 | ArrayListPush(array_of_codes, NULL+xx1); | ^ cell-counts.c: In function ‘sheet_convert_ss_to_arr’: cell-counts.c:893:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 893 | hashed_arr -> appendix1 = NULL+ cct_context -> sample_id_to_name -> numOfElements; // One-based | ^ cell-counts.c:902:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 902 | push_arr[0] = NULL + lane_sample_int; | ^ cell-counts.c:903:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 903 | push_arr[1] = NULL + cct_context -> sample_id_to_name -> numOfElements; | ^ cell-counts.c:905:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 905 | push_arr[3] = NULL + (sbc_lane_sample[1]!=NULL && strlen(sbc_lane_sample[1])>12); | ^ cell-counts.c:907:78: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 907 | HashTablePut(cct_context -> lineno1B_to_sampleno1B_tab , NULL+line_no_in_sheet, NULL + cct_context -> sample_id_to_name -> numOfElements); | ^ cell-counts.c:907:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 907 | HashTablePut(cct_context -> lineno1B_to_sampleno1B_tab , NULL+line_no_in_sheet, NULL + cct_context -> sample_id_to_name -> numOfElements); | ^ cell-counts.c: In function ‘cellCounts_sample_SamBam_writers_new_files’: cell-counts.c:1022:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1022 | HashTablePut(fp_tab, NULL+x1+1 , wtrptr); | ^ cell-counts.c:1022:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1022 | HashTablePut(fp_tab, NULL+x1+1 , wtrptr); | ^ cell-counts.c: In function ‘cellCounts_write_one_chroEvent’: cell-counts.c:1130:86: warning: ordered comparison of pointer with integer zero [-Wpedantic] 1130 | if(ce->event_type == chroEvent_t_TYPE_JUNCTION && ce -> step2_supported_reads>0){ | ^ cell-counts.c:1138:56: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1138 | int pos2 = pos1 + ( (void*) ce->length - NULL ) +1; | ^ cell-counts.c: In function ‘cellCounts_write_junction_sumtable’: cell-counts.c:1147:16: warning: unused variable ‘params’ [-Wunused-variable] 1147 | void * params [5]; | ^~~~~~ cell-counts.c: In function ‘cellCounts_set_chroEvent_details’: cell-counts.c:1159:107: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1159 | chroEvent_t * old_or_new_env = HashTableGet( cct_context -> chroEvent_detail_table[sample_i], NULL+envkey); | ^ cell-counts.c:1165:117: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1165 | if( old_or_new_env -> n_events == 1 ) oldlen = (void *)( old_or_new_env -> length ) - NULL; | ^ cell-counts.c:1174:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1174 | int old_length = (void *)( old_or_new_env -> length ) - NULL; | ^ cell-counts.c:1199:55: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1199 | old_or_new_env -> length = (void*)NULL+(tlen); // "tlen" is the number before "N" in cigar. | ^ cell-counts.c:1202:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1202 | HashTablePut(cct_context -> chroEvent_detail_table[sample_i], NULL+envkey, old_or_new_env); | ^ cell-counts.c: In function ‘cellCounts_add_or_update_chroEvent_in_table’: cell-counts.c:1222:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1222 | LR_roots[0]=IVT_insert(LR_roots[0], l, l, NULL+r); | ^ cell-counts.c:1223:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1223 | LR_roots[1]=IVT_insert(LR_roots[1], r, r, NULL+l); | ^ cell-counts.c:1228:23: warning: variable ‘new_details’ set but not used [-Wunused-but-set-variable] 1228 | chroEvent_t * new_details = NULL; | ^~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_junction_in_table’: cell-counts.c:1256:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1256 | for(x2=0; x2attr == NULL+r ){known=1;break; } | ^ cell-counts.c: In function ‘cellCounts_copy_txn_to_juncs’: cell-counts.c:1282:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1282 | srInt_64 ve = ArrayListGet(my_exons, x1)-NULL; | ^ cell-counts.c:1267:28: warning: variable ‘last_start’ set but not used [-Wunused-but-set-variable] 1267 | int last_end = -1, last_start = -1; | ^~~~~~~~~~ cell-counts.c: In function ‘features_load_one_line’: cell-counts.c:1397:37: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1397 | ArrayListPush(txn_exons,NULL+((start-1)*1LLU<<32)+end-1); | ^ cell-counts.c:1397:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1397 | ArrayListPush(txn_exons,NULL+((start-1)*1LLU<<32)+end-1); | ^ cell-counts.c:1397:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1397 | ArrayListPush(txn_exons,NULL+((start-1)*1LLU<<32)+end-1); | ^ cell-counts.c:1400:101: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1400 | int access_n = HashTableGet(cct_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ cell-counts.c: In function ‘cellCounts_register_junc_feature’: cell-counts.c:1483:30: warning: unused variable ‘sample_i’ [-Wunused-variable] 1483 | int xk1, edge_tab_i, sample_i; | ^~~~~~~~ cell-counts.c: In function ‘cellCounts_find_or_insert_gene_name’: cell-counts.c:1566:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1566 | srInt_64 gene_number = HashTableGet(genetable, feature_name) - NULL; | ^ cell-counts.c:1571:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1571 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ cell-counts.c:1571:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1571 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ cell-counts.c: In function ‘cellCounts_load_annotations’: cell-counts.c:1874:128: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1874 | chro_stub -> chro_number = HashTableGet(cct_context -> chromosome_table.read_name_to_index, seq_name ) - NULL -1; | ^ cell-counts.c: In function ‘cellCounts_chroEvent_freebuff’: cell-counts.c:1987:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1987 | int inslen = (de -> n_events>1)? de -> length[0] :((void*)(de -> length) - NULL); | ^ cell-counts.c: In function ‘cellCounts_get_cellbarcode_no’: cell-counts.c:2354:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2354 | srInt_64 xint = xrawarr - NULL; | ^ cell-counts.c:2365:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2365 | int bcno = ArrayListGet(rawarr, xx2)-NULL; | ^ cell-counts.c:2368:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2368 | if(ArrayListGet(ret, xx3)==NULL+bcno){ | ^ cell-counts.c:2374:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2374 | if(!found)ArrayListPush(ret, NULL+bcno); | ^ cell-counts.c:2383:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2383 | int tbcn = ArrayListGet(ret,xx1)-NULL; | ^ cell-counts.c: In function ‘cellCounts_build_read_bin’: cell-counts.c:2420:107: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2420 | if(chro_name) refID = HashTableGet(cct_context -> chromosome_table.read_name_to_index, chro_name) - NULL - 1; | ^ cell-counts.c: In function ‘cellCounts_vote_and_add_count’: cell-counts.c:2644:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2644 | }else sample_bam_2fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+(sample_no-1) + 1); // sample_id-1: 0,1,2,... | ^ cell-counts.c:2644:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2644 | }else sample_bam_2fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+(sample_no-1) + 1); // sample_id-1: 0,1,2,... | ^ cell-counts.c:2605:139: warning: unused variable ‘testi’ [-Wunused-variable] 2605 | char * sample_seq=NULL, *sample_qual=NULL, *BC_qual=NULL, *BC_seq=NULL, *UMI_seq=NULL, *UMI_qual=NULL, *lane_str=NULL, *RG=NULL, *testi; | ^~~~~ cell-counts.c: In function ‘cellCounts_run_in_thread’: cell-counts.c:2732:38: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2732 | int thread_no = parameters[1]-NULL; | ^ cell-counts.c:2733:33: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2733 | int task = parameters[2]-NULL; | ^ cell-counts.c: In function ‘cellCounts_run_maybe_threads’: cell-counts.c:2782:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2782 | thr_parameters[1] = NULL+current_thread_no; | ^ cell-counts.c:2783:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2783 | thr_parameters[2] = NULL+task; | ^ cell-counts.c: In function ‘cellCounts_chroEvent_locks_opt’: cell-counts.c:3157:29: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3157 | srInt_64 vn = entity-NULL; | ^ cell-counts.c: In function ‘cellCounts_convert_stack_to_cigar_str’: cell-counts.c:3170:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3170 | if(stack[stack_depth].event_details == NULL+IMPOSSIBLE_MEMORY_SPACE)break; | ^ cell-counts.c:3193:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3193 | if(event_details -> n_events == 1) Nlen = (void*) event_details -> length -NULL; | ^ cell-counts.c:3167:37: warning: unused variable ‘thread_context’ [-Wunused-variable] 3167 | cellcounts_align_thread_t * thread_context = cct_context -> all_thread_contexts + thread_no; | ^~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_end_build_candidature_from_stacks’: cell-counts.c:3256:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3256 | if( HashTableGet(thread_context -> alignment_repating_table, NULL+hkey) )continue; | ^ cell-counts.c:3257:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3257 | HashTablePut(thread_context -> alignment_repating_table, NULL+hkey, NULL+1); | ^ cell-counts.c:3257:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3257 | HashTablePut(thread_context -> alignment_repating_table, NULL+hkey, NULL+1); | ^ cell-counts.c:3248:29: warning: unused variable ‘cigar_rlen’ [-Wunused-variable] 3248 | int cigar_rlen = cellCounts_reduce_Cigar(cigar_end5,final_cigar); | ^~~~~~~~~~ cell-counts.c:3215:29: warning: unused variable ‘x_candidate’ [-Wunused-variable] 3215 | int x_3end, x_5end, x_candidate; | ^~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_build_junction_read_finalise_current_stack’: cell-counts.c:3352:204: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3352 | if( thread_context -> realignment_event_stack_current_depth < JUNCTION_REALIGNMENT_MAX_DEPTH ) stack_copy_ptr[thread_context -> realignment_event_stack_current_depth].event_details = NULL+IMPOSSIBLE_MEMORY_SPACE; | ^ cell-counts.c: In function ‘cellCounts_tree_iterative_search’: cell-counts.c:3449:63: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3449 | int evbposright = evb -> attr - NULL; | ^ cell-counts.c:3455:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3455 | chroEvent_t * envdtl = HashTableGet( cct_context -> chroEvent_detail_table[sample_i], NULL+ envkey); | ^ cell-counts.c:3459:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3459 | int remote_first_matching_base_chro = evb -> attr - NULL, x2; | ^ cell-counts.c:3464:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3464 | else inslen = (void*)envdtl -> length - NULL; | ^ cell-counts.c:3427:21: warning: unused variable ‘read_for_testing_len’ [-Wunused-variable] 3427 | int read_for_testing_len = edge_region_end - edge_region_start +1; | ^~~~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_add_covered_indels_in_table’: cell-counts.c:3793:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 3793 | if(1) cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_INDEL , chro_name, chro_pos -1, rposv, inslen_negative, 0); // thread safe | ^~ cell-counts.c:3794:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 3794 | if(nch=='D') chro_cursor += tmpi; | ^~ cell-counts.c:3775:13: warning: unused variable ‘retlen’ [-Wunused-variable] 3775 | int retlen = general_dynamic_align_moves_to_cigar(result_buffer, moved_len, result_cigar); | ^~~~~~ cell-counts.c: In function ‘cellCounts_call_juncs_put_in_tab’: cell-counts.c:3825:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3825 | HashTablePut(iijj_to_chro_ptr , NULL+1+iijj, tstchro); | ^ cell-counts.c:3825:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3825 | HashTablePut(iijj_to_chro_ptr , NULL+1+iijj, tstchro); | ^ cell-counts.c:3828:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3828 | ArrayListPush( jstub_potential_mainhalf_list,NULL+iijj ); | ^ cell-counts.c:3844:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3844 | srInt_64 maiijj = ArrayListGet( jstub_potential_mainhalf_list , mainhalf_i ) - NULL; | ^ cell-counts.c:3863:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3863 | char * tstchro = HashTableGet(iijj_to_chro_ptr, NULL+1+iijj); | ^ cell-counts.c:3863:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3863 | char * tstchro = HashTableGet(iijj_to_chro_ptr, NULL+1+iijj); | ^ cell-counts.c:3890:45: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable] 3890 | int rgap = -1; | ^~~~ cell-counts.c:3923:110: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3923 | srInt_64 maiijj= ArrayListGet(jstub_potential_mainhalf_list, best_major_half)-NULL; | ^ cell-counts.c:3964:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3964 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:3964:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3964 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:3965:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3965 | HashTablePut(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:3965:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3965 | HashTablePut(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:3965:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3965 | HashTablePut(indel_dp_exed, NULL+1+(tstiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:3955:37: warning: unused variable ‘is_update’ [-Wunused-variable] 3955 | int is_update = cellCounts_add_or_update_chroEvent_in_table(cct_context, sample_i, chroEvent_t_TYPE_JUNCTION, machro, mapos, tstpos, 0, 0);//mapos and tstpos are just borrowed variables. | ^~~~~~~~~ cell-counts.c:3943:37: warning: variable ‘rgap’ set but not used [-Wunused-but-set-variable] 3943 | int rgap = -1; | ^~~~ cell-counts.c:3930:37: warning: unused variable ‘manegative’ [-Wunused-variable] 3930 | int manegative = votetab -> masks[mai][maj]; | ^~~~~~~~~~ cell-counts.c:3969:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3969 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:3969:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3969 | if(NULL==HashTableGet(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu))){ | ^ cell-counts.c:3970:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3970 | HashTablePut(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:3970:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3970 | HashTablePut(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:3970:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3970 | HashTablePut(indel_dp_exed, NULL+1+(maiijj & 0xffffffffffffllu), NULL+1); | ^ cell-counts.c:3842:29: warning: variable ‘best_GTAG_negative’ set but not used [-Wunused-but-set-variable] 3842 | int best_GTAG_negative = -1; | ^~~~~~~~~~~~~~~~~~ cell-counts.c:3839:29: warning: variable ‘best_misma_no’ set but not used [-Wunused-but-set-variable] 3839 | int best_misma_no = -1; | ^~~~~~~~~~~~~ cell-counts.c:3810:38: warning: unused variable ‘distinct_vote_number_i’ [-Wunused-variable] 3810 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:3810:17: warning: unused variable ‘reverse_text_offset’ [-Wunused-variable] 3810 | int i,j,reverse_text_offset, distinct_vote_number_i; | ^~~~~~~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_add_supported_unsupported_reads_from_cigar’: cell-counts.c:4040:110: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4040 | oneitem = HashTableGet( cct_context -> chroEvent_detail_table[sample_i], NULL+ envkey); | ^ cell-counts.c:4050:114: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4050 | }else oneitem -> step2_supported_reads = (void*) oneitem -> step2_supported_reads+1; | ^ cell-counts.c:4053:37: warning: variable ‘on_chro_len’ set but not used [-Wunused-but-set-variable] 4053 | int on_chro_len = tmpi +1; | ^~~~~~~~~~~ cell-counts.c:4079:137: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4079 | chroEvent_t * exed = HashTableGet(cct_context -> chroEvent_detail_table [sample_i], NULL+envkey); | ^ cell-counts.c:4091:118: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4091 | exed -> step2_supported_reads = (void*) exed -> step2_supported_reads+1; | ^ cell-counts.c:4084:66: warning: variable ‘x2_not_matter’ set but not used [-Wunused-but-set-variable] 4084 | int is_the_last, x2_not_matter; | ^~~~~~~~~~~~~ cell-counts.c:4118:81: warning: array subscript has type ‘char’ [-Wchar-subscripts] 4118 | IVT_IntervalTreeNode * myroot = LR_roots[LRi]; | ^ cell-counts.c:4126:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4126 | int evbposright = evb -> attr - NULL; | ^ cell-counts.c:4133:137: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4133 | chroEvent_t * uned = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , NULL+envkey); | ^ cell-counts.c:4136:146: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4136 | if(nch == 'N' && !(uned -> left_edge >= linear_cur && uned -> left_edge + ((void*) uned -> length-NULL) <= linear_env_R )) continue; // fly-over exons must be entirely in the "N" part. | ^ cell-counts.c:4142:153: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4142 | if(!is_the_last) uned -> step2_non_supported_reads = (void *) uned -> step2_non_supported_reads +1 ; | ^ cell-counts.c:4010:41: warning: unused variable ‘x3’ [-Wunused-variable] 4010 | int nch, tmpi=0, x1=0, b1off=0, x3; | ^~ cell-counts.c: In function ‘cellCounts_get_sample_no_from_rname’: cell-counts.c:4650:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4650 | sample_no = HashTableGet(cct_context -> lineno1B_to_sampleno1B_tab, NULL+lineno)-NULL; | ^ cell-counts.c:4650:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4650 | sample_no = HashTableGet(cct_context -> lineno1B_to_sampleno1B_tab, NULL+lineno)-NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_cell’: cell-counts.c:5176:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5176 | int sample_id = app1[3]-NULL; | ^ cell-counts.c:5164:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5185:41: note: in expansion of macro ‘ADD_count_hash’ 5185 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5185:41: note: in expansion of macro ‘ADD_count_hash’ 5185 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:164: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5185:41: note: in expansion of macro ‘ADD_count_hash’ 5185 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:166: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5185:41: note: in expansion of macro ‘ADD_count_hash’ 5185 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:194: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5185:41: note: in expansion of macro ‘ADD_count_hash’ 5185 | ADD_count_hash(str1->cellbc, str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5200:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5200 | HashTablePut(filtered_CGU_table, strdup(replaced_key), NULL-1); | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_UMI_merge_one_step’: cell-counts.c:5164:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5332:66: note: in expansion of macro ‘ADD_count_hash’ 5332 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5332:66: note: in expansion of macro ‘ADD_count_hash’ 5332 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:164: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5332:66: note: in expansion of macro ‘ADD_count_hash’ 5332 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:166: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5332:66: note: in expansion of macro ‘ADD_count_hash’ 5332 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c:5164:194: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5164 | #define ADD_count_hash(bc,gn,no) { HashTablePut(cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn) ), HashTableGet( cellBCp0_genep0_P1_to_UMIs, NULL +1+(((1LLU*(bc))<<32)| (gn))) +(no) );\ | ^ cell-counts.c:5332:66: note: in expansion of macro ‘ADD_count_hash’ 5332 | else if(is_UMI_step2 && str1->cellbc>=0) ADD_count_hash(str1->cellbc,str1->gene_no,1); | ^~~~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_do_one_batch_tab_to_struct_list_compare’: cell-counts.c:5389:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5389 | int sort_by_geneid_then_umi = app1[1] - NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_tab_to_struct_list’: cell-counts.c:5417:29: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5417 | int supp_reads = val-NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch_write_UMIs’: cell-counts.c:5439:20: warning: wrong type argument to decrement [-Wpointer-arith] 5439 | vcell_gene --; | ^~ cell-counts.c: In function ‘cellCounts_merge_batches_worker’: cell-counts.c:5449:35: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5449 | int my_worker_id = vpp[2] - NULL; | ^ cell-counts.c: In function ‘cellCounts_do_one_batch’: cell-counts.c:5629:143: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5629 | srInt_64 this_batch_size_and_no = ArrayListGet(file_size_list, file_size_list->numOfElements-1 -this_batch_sorted_idx)-NULL; | ^ cell-counts.c:5607:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5607 | srInt_64 supp_reads = HashTableGet(supp_reads_SCGU, my_key)-NULL; \ | ^ cell-counts.c:5680:41: note: in expansion of macro ‘ADD_key_struct’ 5680 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5608:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5608 | if(1>supp_reads) HashTablePut(supp_reads_SCGU, strdup(my_key), NULL+1); \ | ^ cell-counts.c:5680:41: note: in expansion of macro ‘ADD_key_struct’ 5680 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5609:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5609 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5680:41: note: in expansion of macro ‘ADD_key_struct’ 5680 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5609:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5609 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5680:41: note: in expansion of macro ‘ADD_key_struct’ 5680 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5607:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5607 | srInt_64 supp_reads = HashTableGet(supp_reads_SCGU, my_key)-NULL; \ | ^ cell-counts.c:5685:33: note: in expansion of macro ‘ADD_key_struct’ 5685 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5608:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5608 | if(1>supp_reads) HashTablePut(supp_reads_SCGU, strdup(my_key), NULL+1); \ | ^ cell-counts.c:5685:33: note: in expansion of macro ‘ADD_key_struct’ 5685 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5609:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5609 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5685:33: note: in expansion of macro ‘ADD_key_struct’ 5685 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5609:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5609 | else HashTablePutReplaceEx(supp_reads_SCGU, my_key, NULL+supp_reads+1, 0,0,0); } | ^ cell-counts.c:5685:33: note: in expansion of macro ‘ADD_key_struct’ 5685 | ADD_key_struct; | ^~~~~~~~~~~~~~ cell-counts.c:5713:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5713 | app1[1] = NULL+1; | ^ cell-counts.c:5720:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5720 | app1[1] = NULL+0; | ^ cell-counts.c:5764:39: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5764 | if(umi == NULL-1) umi="-----------------------------------------"; | ^ cell-counts.c:5785:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5785 | return NULL + removed_UMIs; | ^ cell-counts.c: In function ‘cellCounts_save_BAM_result’: cell-counts.c:5798:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5798 | void ** fps = HashTableGet(cct_context -> sample_BAM_writers, NULL+sample_id); | ^ cell-counts.c: In function ‘cellCounts_merged_write_sparse_unique_genes’: cell-counts.c:5831:26: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5831 | int cellbcP1 = ky-NULL; | ^ cell-counts.c:5832:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5832 | if(used_cellnoP1_tab && !HashTableGet(used_cellnoP1_tab, NULL+cellbcP1))return; | ^ cell-counts.c:5838:131: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5838 | if(!HashTableGet(unique_geneno1B_tab, ArrayListGet(g2ul,x1))) HashTablePut(unique_geneno1B_tab, geneno1B_ptr, NULL+1); | ^ cell-counts.c: In function ‘cellCounts_merged_write_sparse_matrix’: cell-counts.c:5878:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5878 | int gene_index_0B = ArrayListGet(unique_NZ_genenosP1_list, x2) - NULL-1; | ^ cell-counts.c:5884:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5884 | srInt_64 cellno = ArrayListGet(used_cell_barcodes, x1)-NULL; | ^ cell-counts.c:5890:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5890 | srInt_64 cellno = ArrayListGet(used_cell_barcodes, x1)-NULL; | ^ cell-counts.c:5891:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5891 | HashTable * geneno1B_to_UMIs = HashTableGet(cellP1_to_geneP1_to_umis_tab, NULL+1+cellno); | ^ cell-counts.c:5891:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5891 | HashTable * geneno1B_to_UMIs = HashTableGet(cellP1_to_geneP1_to_umis_tab, NULL+1+cellno); | ^ cell-counts.c:5894:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5894 | int geneno1B = ArrayListGet(unique_NZ_genenosP1_list, x2)-NULL; | ^ cell-counts.c:5895:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5895 | int this_umis = HashTableGet(geneno1B_to_UMIs, NULL+geneno1B) -NULL; | ^ cell-counts.c:5895:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5895 | int this_umis = HashTableGet(geneno1B_to_UMIs, NULL+geneno1B) -NULL; | ^ cell-counts.c: In function ‘cellCounts_merged_45K_to_90K_sum_SUM_Level2’: cell-counts.c:5909:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5909 | HashTablePut(summed_gene_to_umis, GeneNo1B, vUMIs + (HashTableGet(summed_gene_to_umis, GeneNo1B)-NULL)); | ^ cell-counts.c:5909:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5909 | HashTablePut(summed_gene_to_umis, GeneNo1B, vUMIs + (HashTableGet(summed_gene_to_umis, GeneNo1B)-NULL)); | ^ cell-counts.c: In function ‘cellCounts_merged_45K_to_90K_sum_WRT’: cell-counts.c:5926:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5926 | unsigned char * gene_name = cct_context -> gene_name_array[ kyGeneID - NULL-1 ]; | ^ cell-counts.c:5927:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5927 | fprintf(ofp, "%s\t%u\n", gene_name, (unsigned int) (valUMIs-NULL)); | ^ cell-counts.c: In function ‘cellCounts_merged_write_nozero_geneids_WRT’: cell-counts.c:5958:71: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5958 | unsigned char* gene_symbol = cct_context -> gene_name_array [k-NULL-1]; | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write_build_UMIcount_in’: cell-counts.c:5977:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5977 | tab -> counter1 += (val-NULL); | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write_build_UMIcounts’: cell-counts.c:5982:25: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5982 | int cell_no = ky-NULL-1; | ^ cell-counts.c:5987:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5987 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c:5987:50: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5987 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c:5987:64: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5987 | HashTablePut(cellbcP1_to_umis_tab, NULL+1+cell_no, NULL+geneP1_to_counts_tab -> counter1); | ^ cell-counts.c: In function ‘cellCounts_merged_ambient_rescure’: cell-counts.c:6003:129: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6003 | srInt_64 median_umis = HashTableGet(cellnoP1_to_umis_tab, ArrayListGet(sorted_bcno_p1 , (high_conf_cells-1)/2))-NULL; | ^ cell-counts.c:6010:100: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6010 | srInt_64 this_bc_umis = HashTableGet(cellnoP1_to_umis_tab, this_bc_pnt_p1) - NULL; | ^ cell-counts.c:6017:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6017 | ArrayListPush(this_sample_ambient_rescure_candi, this_bc_pnt_p1-1); | ^ cell-counts.c:6022:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6022 | ArrayListPush(this_sample_45k_90k_barcode_no_P0, ArrayListGet(sorted_bcno_p1 , x1)-1 ); | ^ cell-counts.c: In function ‘cellCounts_merged_bootstrap_a_sample’: cell-counts.c:6045:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6045 | srInt_64 this_umis = HashTableGet(cellnoP1_to_umis_tab, cellbc_p1_ptr )-NULL; | ^ cell-counts.c:6047:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6047 | ArrayListPush(highconf_cellbc_list, ArrayListGet( sorted_idx, x1 ) - 1 ); | ^ cell-counts.c:6058:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6058 | srInt_64 this_umis = HashTableGet( cellnoP1_to_umis_tab, cellbc_p1_ptr )-NULL; | ^ cell-counts.c:6059:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6059 | ArrayListPush(resampled_list_of_umis,NULL+this_umis); | ^ cell-counts.c:6062:159: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6062 | srInt_64 UMIs_30th_div10 = ArrayListGet(resampled_list_of_umis, resampled_list_of_umis -> numOfElements - SCRNA_BOOTSTRAP_HIGH_INDEX) -NULL; | ^ cell-counts.c:6067:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6067 | srInt_64 this_umis = ArrayListGet(resampled_list_of_umis, lli)-NULL; | ^ cell-counts.c:6079:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6079 | ArrayListPush(highconf_cellbc_list, last_ptr - 1 ); | ^ cell-counts.c:6081:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6081 | last_umi_no = HashTableGet(cellnoP1_to_umis_tab ,last_ptr)-NULL; | ^ cell-counts.c: In function ‘cellCounts_merged_to_tables_write’: cell-counts.c:6119:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6119 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6119:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6119 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6119:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6119 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6119:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6119 | HashTablePut(sorted_order_p1_to_i_p1_tab, NULL+ feature1->sorted_order+1 , NULL+xk1+1 ); | ^ cell-counts.c:6124:126: warning: wrong type argument to decrement [-Wpointer-arith] 6124 | for(xk1=0; xk1numOfElements; xk1++) all_barcode_index_list->elementList[xk1]--; | ^~ cell-counts.c: In function ‘cellCounts_do_cellbc_batches’: cell-counts.c:6190:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6190 | ArrayListPush(file_size_list, NULL+( batchsize<<20 | xk1)); | ^ cell-counts.c:6212:31: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6212 | vpp[1] = NULL + xk1; | ^ cell-counts.c:6221:39: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6221 | removed_umis += (pret - NULL); | ^ cell-counts.c:6262:31: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6262 | vpp[2] = NULL + xk1; | ^ cell-counts.c:6287:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6287 | HashTable *gene_tab = HashTableGet(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1); | ^ cell-counts.c:6287:122: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6287 | HashTable *gene_tab = HashTableGet(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1); | ^ cell-counts.c:6290:98: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6290 | HashTablePut(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1, gene_tab); | ^ cell-counts.c:6290:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6290 | HashTablePut(cellnoP1_to_genenoP1_to_UMIs[sample_i], NULL+cellbc_no+1, gene_tab); | ^ cell-counts.c:6292:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6292 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c:6292:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6292 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c:6292:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6292 | HashTablePut(gene_tab, NULL+gene_no0B+1 , NULL+umis); | ^ cell-counts.c: In function ‘cellCounts_determine_jcount_gene_transcript_report’: cell-counts.c:6632:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6632 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ cell-counts.c:6632:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6632 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ cell-counts.c:6635:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6635 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6635:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6635 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6660:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6660 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ cell-counts.c:6660:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6660 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ cell-counts.c:6663:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6663 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6663:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6663 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ cell-counts.c:6673:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6673 | int edge1_ptr = HashTableGet(edge1P1_table, edge1_txnid)-NULL; | ^ cell-counts.c:6675:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6675 | int edge2_ptr = HashTableGet(edge2P1_table, edge1_txnid)-NULL; | ^ cell-counts.c:6677:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6677 | int exonno_1 = HashTableGet(edge1exonNo_table, edge1_txnid)-NULL-1; | ^ cell-counts.c:6678:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6678 | int exonno_2 = HashTableGet(edge2exonNo_table, edge1_txnid)-NULL-1; | ^ cell-counts.c:6690:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6690 | HashTablePut(out_gene_tab, txnptr -> gene_name, NULL+1); | ^ cell-counts.c:6691:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6691 | HashTablePut(out_txn_tab, txnptr -> transcript_id, NULL+1); | ^ cell-counts.c:6722:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6722 | srInt_64 edge_dist = HashTableGet(this_side_olay_tab, this_side_txn_id)-NULL; | ^ cell-counts.c:6725:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6725 | HashTablePut(this_side_reported_genes, txn_ptr -> gene_name, NULL+1); | ^ cell-counts.c: In function ‘cellCounts_find_nearest_gene_dist’: cell-counts.c:6815:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6815 | HashTablePut(gene_name_tab, gene_name, NULL+1); | ^ cell-counts.c: In function ‘cellCounts_copy_junc_table_to_output_table’: cell-counts.c:6854:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6854 | locate_gene_position(ed -> left_edge + ((void*)ed -> length-NULL) +1, &cct_context -> chromosome_table, &chro, &pos_large); | ^ cell-counts.c:6863:59: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6863 | srInt_64 cck = (void*)ed -> step2_supported_reads - NULL + report_0_junc; | ^ cell-counts.c:6864:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6864 | cck = cck << 32 |((void*)ed -> step2_non_supported_reads - NULL); | ^ cell-counts.c: In function ‘cellCounts_write_final_other_events’: cell-counts.c:6891:62: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6891 | envlen = (void*)ed -> length - NULL; | ^ cell-counts.c:6892:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6892 | nsupp = (void*)ed -> step2_supported_reads - NULL; | ^ cell-counts.c:6893:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6893 | nonsupp = (void*)ed -> step2_non_supported_reads - NULL; | ^ cell-counts.c: In function ‘cellCounts_write_final_junctions’: cell-counts.c:6961:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 6961 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ cell-counts.c:6940:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 6940 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:6940:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 6940 | int ky_i1, ky_i2; | ^~~~~ cell-counts.c:6938:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 6938 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ cell-counts.c:6904:13: warning: unused variable ‘infile_i’ [-Wunused-variable] 6904 | int infile_i, disk_is_full = 0, sample_i; | ^~~~~~~~ cell-counts.c: In function ‘cellCounts_find_hits_for_mapped_section’: cell-counts.c:2237:19: warning: ‘search_start’ may be used uninitialized [-Wmaybe-uninitialized] 2237 | if(search_start>0xffffff00) return; | ^ cell-counts.c:2226:30: note: ‘search_start’ was declared here 2226 | unsigned int search_start, search_end, search_block_id; | ^~~~~~~~~~~~ cell-counts.c: In function ‘cellCounts_write_final_other_events’: cell-counts.c:6871:40: warning: array subscript -999 is below array bounds of ‘HashTable *[41]’ [-Warray-bounds=] 6871 | ArrayList * small_large_keys = HashTableKeys(cct_context -> chroEvent_detail_table[sample_i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:322:27: note: while referencing ‘chroEvent_detail_table’ 322 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1]; | ^~~~~~~~~~~~~~~~~~~~~~ cell-counts.c:6876:86: warning: array subscript -999 is below array bounds of ‘HashTable *[41]’ [-Warray-bounds=] 6876 | chroEvent_t * ed = HashTableGet(cct_context -> chroEvent_detail_table[sample_i] , ArrayListGet(small_large_keys,x1)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ cell-counts.c:322:27: note: while referencing ‘chroEvent_detail_table’ 322 | HashTable * chroEvent_detail_table[MAX_SCRNA_SAMPLE_NUMBER+1]; | ^~~~~~~~~~~~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-bigtable.c -o core-bigtable.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-indel.c -o core-indel.o In file included from core-indel.c:34: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ core-indel.c: In function ‘anti_support_thread_run’: core-indel.c:223:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:223:136: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:223:141: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 223 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:225:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:225:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:225:125: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut( atcont -> result_tab , NULL+small_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:247:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:247:144: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:247:149: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 247 | long long cur_count = HashTableGet(atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 ) - NULL; | ^ core-indel.c:249:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:249:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c:249:133: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 249 | HashTablePut( atcont -> result_tab , NULL+large_side_ordered_event_ids[x1]+1 , NULL+cur_count ); | ^ core-indel.c: In function ‘anti_support_add_count’: core-indel.c:263:21: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 263 | int eno = ky-NULL-1; | ^ core-indel.c:265:51: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 265 | event_body -> anti_supporting_reads+= (va - NULL); | ^ core-indel.c: In function ‘remove_neighbour’: core-indel.c:579:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 579 | unsigned int * res = HashTableGet(event_table, NULL+pos); | ^ core-indel.c:590:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 590 | HashTableRemove(event_table, NULL+pos); | ^ core-indel.c: In function ‘localPointerCmp_forEventEntry’: core-indel.c:609:50: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 609 | unsigned int v1 = (unsigned int)(pointer1-NULL); | ^ core-indel.c:610:50: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 610 | unsigned int v2 = (unsigned int)(pointer2-NULL); | ^ core-indel.c: In function ‘localPointerHashFunction_forEventEntry’: core-indel.c:616:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 616 | unsigned int v = (pointer-NULL); | ^ core-indel.c: In function ‘init_indel_tables’: core-indel.c:672:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 672 | indel_context -> local_reassembly_pileup_files -> appendix1 = NULL + max_open_file * 2/ 3; | ^ core-indel.c: In function ‘sort_junction_entry_table’: core-indel.c:920:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 920 | HashTablePut(indel_context -> event_entry_table, NULL + last_scannping_pos, id_list); | ^ core-indel.c: In function ‘do_juncs_add_feature’: core-indel.c:1240:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1240 | int access_n = HashTableGet( global_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ core-indel.c: In function ‘put_new_event’: core-indel.c:1397:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1397 | unsigned int * id_list = HashTableGet(event_table, NULL+sides[xk1]); | ^ core-indel.c:1403:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1403 | HashTablePut(event_table , NULL+sides[xk1] , id_list); | ^ core-indel.c: In function ‘search_event’: core-indel.c:1439:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1439 | unsigned int * res = HashTableGet(event_table, NULL+pos); | ^ core-indel.c: In function ‘insert_pileup_read’: core-indel.c:2550:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2550 | unsigned int next_jump_array = HashTableGet(current_table ,NULL+next_key_prefix) - NULL; | ^ core-indel.c:2550:106: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2550 | unsigned int next_jump_array = HashTableGet(current_table ,NULL+next_key_prefix) - NULL; | ^ core-indel.c:2558:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2558 | HashTablePut(current_table, NULL + next_key_prefix , NULL + next_jump_array); | ^ core-indel.c:2558:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2558 | HashTablePut(current_table, NULL + next_key_prefix , NULL + next_jump_array); | ^ core-indel.c: In function ‘finalise_db_graph’: core-indel.c:2587:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2587 | next_moves = HashTableGet(de_brujin_graph , NULL + current_key) - NULL; | ^ core-indel.c:2587:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2587 | next_moves = HashTableGet(de_brujin_graph , NULL + current_key) - NULL; | ^ core-indel.c: In function ‘rectify_read_text’: core-indel.c:2814:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2814 | char * neighbour_read_text = HashTableGet(block_context->read_sequence_table,NULL+neighbour_read_key); | ^ core-indel.c: In function ‘search_window_once’: core-indel.c:2903:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2903 | char * start_read_txt = HashTableGet(block_context->read_sequence_table,NULL+starter_read_key); | ^ core-indel.c:2907:83: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2907 | int start_read_pos = HashTableGet(block_context->read_position_table, NULL+starter_read_key) - NULL ; | ^ core-indel.c:2907:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2907 | int start_read_pos = HashTableGet(block_context->read_position_table, NULL+starter_read_key) - NULL ; | ^ core-indel.c:2976:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2976 | int next_read_pos = HashTableGet(block_context->read_position_table, NULL+test_next_read_key) - NULL; | ^ core-indel.c:2976:127: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2976 | int next_read_pos = HashTableGet(block_context->read_position_table, NULL+test_next_read_key) - NULL; | ^ core-indel.c:2991:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2991 | char * next_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_next_read_key); | ^ core-indel.c:3034:127: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3034 | +(unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3034:147: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3034 | +(unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3056:128: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3056 | + (unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3056:148: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3056 | + (unsigned int)(HashTableGet(block_context -> read_quality_table, NULL+test_next_read_key)-NULL)/10 - wrong_bases * 20000; | ^ core-indel.c:3089:140: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3089 | char *prev_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_prev_read_key); | ^ core-indel.c:3179:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3179 | char * next_read_txt = HashTableGet(block_context->read_sequence_table,NULL+test_next_read_key); | ^ core-indel.c: In function ‘finalise_pileup_file’: core-indel.c:3981:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3981:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3981:110: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3981 | HashTablePut(read_position_table, NULL + read_hashed_key, NULL+first_base_pos+1); | ^ core-indel.c:3982:64: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3982 | HashTablePut(read_sequence_table, NULL + read_hashed_key, sequence_for_hash); | ^ core-indel.c:3983:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3983 | HashTablePut(read_quality_table, NULL + read_hashed_key, NULL + qual_of_this_read); | ^ core-indel.c:3983:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3983 | HashTablePut(read_quality_table, NULL + read_hashed_key, NULL + qual_of_this_read); | ^ core-indel.c:4052:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4052 | char * start_read_txt = HashTableGet(block_context.read_sequence_table,NULL+starter_read_key); | ^ core-indel.c: In function ‘destroy_pileup_table’: core-indel.c:4316:38: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4316 | if(fp != NULL+1) | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-interface-aligner.c -o core-interface-aligner.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-interface-subjunc.c -o core-interface-subjunc.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core-junction.c -o core-junction.o In file included from core-junction.c:32: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ core-junction.c: In function ‘find_donor_receptor’: core-junction.c:2099:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2099 | if(0&& FIXLENstrcmp("V0112_0155:7:1101:12618:2466#ACTTGA", rname) == 0) | ^~ core-junction.c:2103:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2103 | if( (end_site_mismatches + start_site_mismatches) * 500 + insertion_in_between_i < best_testing_score ){ | ^~ core-junction.c: In function ‘find_translocation_brk_PQR’: core-junction.c:5725:59: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5725 | int event_no = event_ptr_list_A1[candA1i] - NULL; | ^ core-junction.c:5738:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5738 | unsigned int event_no_P = event_ptr_list_A1[candBrkPi] - NULL; | ^ core-junction.c:5761:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5761 | unsigned int event_no_Q = event_ptr_list_Q[candQi] - NULL; | ^ core-junction.c:5779:84: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5779 | unsigned int event_no_R = event_ptr_list_R[candRi] - NULL; | ^ core-junction.c: In function ‘finalise_translocations’: core-junction.c:6025:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6025 | subread_read_number_t frag_S_no = (s_ptrs[cand_i] - NULL)/ 2; | ^ core-junction.c:6026:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6026 | int frag_S_is_read_B = (s_ptrs[cand_i] - NULL) % 2; | ^ core-junction.c: In function ‘finalise_inversions’: core-junction.c:6210:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6210 | subread_read_number_t frag_S_no = (s_ptrs[cand_i] - NULL)/2; | ^ core-junction.c:6211:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6211 | int frag_S_larger_read = (s_ptrs[cand_i] - NULL)%2; | ^ core-junction.c:6295:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6295 | int event_no_Y = s1_ptrs[cand_Y] - NULL; | ^ core-junction.c:6305:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 6305 | int event_no_Z = s1_ptrs[cand_Z] - NULL; | ^ core-junction.c: In function ‘build_breakpoint_tables’: core-junction.c:6479:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6479 | if(index_table) bktable_append(index_table, chro_name_left, chro_pos_left, NULL + xk1); | ^ core-junction.c:6480:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 6480 | if(index_table) bktable_append(index_table, chro_name_right, chro_pos_right, NULL + xk1); | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c core.c -o core.o In file included from core.c:55: core-junction.h:111:9: warning: struct has no members [-Wpedantic] 111 | typedef struct{ | ^~~~~~ core.c: In function ‘write_single_fragment’: core.c:1909:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1909 | bktable_append(&global_context -> funky_table_BC, rec1 -> chro, rec1 -> offset , NULL + (2*pair_number)); | ^ core.c:1910:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1910 | bktable_append(&global_context -> funky_table_BC, rec2 -> chro, rec2 -> offset , NULL + (2*pair_number+1)); | ^ core.c:1914:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1914 | bktable_append(&global_context -> funky_table_DE, rec1 -> chro, rec1 -> offset , NULL + (2*pair_number + (rec1 -> offset > rec2 -> offset ? 1:0))); | ^ core.c:1915:111: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1915 | bktable_append(&global_context -> funky_table_DE, rec2 -> chro, rec2 -> offset , NULL + (2*pair_number + (rec1 -> offset < rec2 -> offset ? 1:0))); | ^ core.c: In function ‘do_anno_bitmap_add_feature’: core.c:3927:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3927 | HashTablePut(global_context -> annotation_chro_table, memstrcpy( chro_name ), NULL+1); | ^ core.c:3930:105: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3930 | int access_n = HashTableGet( global_context -> chromosome_table.read_name_to_index, chro_name ) - NULL; | ^ core.c: In function ‘test_PE_and_same_chro_align’: core.c:4816:16: warning: ISO C forbids ‘return’ with expression, in function returning void [-Wpedantic] 4816 | return test_PE_and_same_chro_cigars(global_context, res1 -> first_base_position, res2 -> first_base_position, is_exonic_regions, is_PE_distance, is_same_chromosome , read_len_1 , read_len_2, res1 -> cigar_string, res2 -> cigar_string, read_name, res_tlen); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ core.c:4815:6: note: declared here 4815 | void test_PE_and_same_chro_align(global_context_t * global_context , realignment_result_t * res1, realignment_result_t * res2, int * is_exonic_regions, int * is_PE_distance, int * is_same_chromosome, int read_len_1, int read_len_2, char * read_name, int *res_tlen){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c detection-calls.c -o detection-calls.o detection-calls.c: In function ‘DTCload_fasta’: detection-calls.c:95:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 95 | HashTablePut(context -> chro_length_table, curr_chro_mem , NULL + base_current_chro_len); | ^ detection-calls.c:136:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 136 | HashTablePut(context -> chro_length_table, curr_chro_mem , NULL + base_current_chro_len); | ^ detection-calls.c: In function ‘DTCprint_lentab_items’: detection-calls.c:160:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 160 | SUBREADprintf("%s => %ld\n", (char*)key, (long)(hashed_obj - NULL)); | ^ detection-calls.c: In function ‘DTCtotal_GC_bases’: detection-calls.c:168:82: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 168 | unsigned int chro_len = HashTableGet(context -> chro_length_table, chro) - NULL; | ^ detection-calls.c:175:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 175 | chro_len = HashTableGet(context -> chro_length_table, tna) - NULL; | ^ detection-calls.c:182:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 182 | chro_len = HashTableGet(context -> chro_length_table, tna) - NULL; | ^ detection-calls.c: In function ‘DTCparse_GTF_and_Genome’: detection-calls.c:413:148: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 413 | DTCanno_fill_gap(context, current_chro_name_in_anno, top_end + 1, HashTableGet(context -> chro_length_table, current_chro) - NULL - 1); | ^ detection-calls.c: In function ‘DTCwrite_annotations’: detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:109: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ detection-calls.c:155:9: warning: dangling pointer ‘gc_2int’ to an unnamed temporary may be used [-Wdangling-pointer=] 155 | DTCadd_annotation(context, gene_name, chro_name, start, end, is_negative_strand, gc_2int[0], gc_2int[1], 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ detection-calls.c:154:48: note: unnamed temporary defined here 154 | if(!gc_2int) gc_2int = (unsigned int[]){0,0,0}; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c detectionCall.c -o detectionCall.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c detectionCallAnnotation.c -o detectionCallAnnotation.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c exon-algorithms.c -o exon-algorithms.o exon-algorithms.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c exon-align-indel.c -o exon-align-indel.o exon-align-indel.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c exon-align.c -o exon-align.o exon-align.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c flattenAnnotations.c -o flattenAnnotations.o flattenAnnotations.c: In function ‘flatAnno_do_anno_chop_one_array’: flattenAnnotations.c:167:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 167 | if(ArrayListGet(edge_before_me_List,findi)-NULL == search_tag){ | ^ flattenAnnotations.c:172:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 172 | if(0==found) ArrayListPush(edge_before_me_List, NULL+search_tag); | ^ flattenAnnotations.c:180:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 180 | int an_edge_before_me = edge_before_me_List-> elementList[i]-NULL; | ^ flattenAnnotations.c:215:68: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 215 | curr_2i[0] = edge_before_me_List -> elementList[i] -NULL; | ^ flattenAnnotations.c:216:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 216 | curr_2i[1] = edge_before_me_List -> elementList[i+1] -NULL-1; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fullscan.c -o fullscan.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fusion-align.c -o fusion-align.o fusion-align.c:2: warning: ISO C forbids an empty translation unit [-Wpedantic] gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gen_rand_reads.c -o gen_rand_reads.o gen_rand_reads.c: In function ‘gen_a_read_from_one_transcript’: gen_rand_reads.c:206:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 206 | int actual_transcript_len = HashTableGet(grc->transcript_lengths, trans_name) - NULL; | ^ gen_rand_reads.c: In function ‘calc_N_from_M’: gen_rand_reads.c:299:132: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 299 | unsigned long long space_end = ArrayListGet(grc->transcript_hitting_space, grc->transcript_hitting_space->numOfElements -1)-NULL; | ^ gen_rand_reads.c:303:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 303 | unsigned long long thisv = ArrayListGet(grc->transcript_hitting_space, ti) - NULL; | ^ gen_rand_reads.c: In function ‘convert_hitting_space_to_num_of_reads’: gen_rand_reads.c:339:132: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 339 | unsigned long long space_end = ArrayListGet(grc->transcript_hitting_space, grc->transcript_hitting_space->numOfElements -1)-NULL; | ^ gen_rand_reads.c:349:87: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 349 | int seq_len = HashTableGet(grc-> transcript_lengths, seq_name)-NULL; | ^ gen_rand_reads.c:350:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 350 | unsigned long long thisv = ArrayListGet(grc->transcript_hitting_space, read_i) - NULL; | ^ gen_rand_reads.c:366:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 366 | ArrayListPush(rescure_hitting_space, NULL+to_rescure_read_top); | ^ gen_rand_reads.c:367:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 367 | ArrayListPush(num_of_frags_per_transcript, NULL+expected_reads); | ^ gen_rand_reads.c:382:122: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 382 | unsigned long long expected_reads = ArrayListGet(num_of_frags_per_transcript, this_transcript_no)-NULL; | ^ gen_rand_reads.c:384:92: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 384 | num_of_frags_per_transcript->elementList[this_transcript_no] = NULL+expected_reads; | ^ gen_rand_reads.c: In function ‘grc_gen’: gen_rand_reads.c:412:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 412 | int seq_len = HashTableGet(grc-> transcript_lengths, seq_name)-NULL; | ^ gen_rand_reads.c:413:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 413 | unsigned long long expected_reads = ArrayListGet(num_of_frags_per_transcript, read_i)-NULL; | ^ gen_rand_reads.c:423:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 423 | ArrayListPush(per_transcript_reads_hitting_space, NULL+total_read_top); | ^ gen_rand_reads.c: In function ‘grc_summary_fasta’: gen_rand_reads.c:531:85: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 531 | long dupval = HashTableGet(seq_duplicate_tab,md5mem)-NULL; | ^ gen_rand_reads.c:533:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 533 | HashTablePutReplace( seq_duplicate_tab, md5mem, NULL+dupval , 0); | ^ gen_rand_reads.c:540:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 540 | HashTablePut( seq_length_tab, seq_name, NULL+seq_len); | ^ gen_rand_reads.c:562:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 562 | HashTablePut(name_duplicate_tab, seq_name, NULL+1); | ^ gen_rand_reads.c:581:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 581 | long dupval = HashTableGet(seq_duplicate_tab,md5mem)-NULL; | ^ gen_rand_reads.c:583:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 583 | HashTablePutReplace( seq_duplicate_tab, md5mem, NULL+dupval ,0); | ^ gen_rand_reads.c:592:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 592 | HashTablePut( seq_length_tab, seq_name, NULL+seq_len); | ^ gen_rand_reads.c:601:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 601 | long md5repeated = HashTableGet(seq_duplicate_tab, md5str) - NULL; | ^ gen_rand_reads.c:603:66: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 603 | long seqlen = HashTableGet(seq_length_tab,seqnam)-NULL; | ^ gen_rand_reads.c:605:51: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 605 | HashTablePut(reprs_tab,md5str,NULL+1); | ^ gen_rand_reads.c: In function ‘grc_put_new_trans’: gen_rand_reads.c:627:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 627 | HashTablePut(grc-> transcript_lengths, seq_name, NULL+ seq_len); | ^ gen_rand_reads.c:628:95: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 628 | unsigned long long this_seq_exp_10000 = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gen_rand_reads.c:636:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 636 | ArrayListPush(grc->transcript_hitting_space, NULL+*linear_space_top); | ^ gen_rand_reads.c: In function ‘grc_load_env’: gen_rand_reads.c:696:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 696 | HashTablePut(grc->expression_levels, seqname_buf, NULL+seqexp_int+1); | ^ gen_rand_reads.c:696:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 696 | HashTablePut(grc->expression_levels, seqname_buf, NULL+seqexp_int+1); | ^ gen_rand_reads.c:771:94: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 771 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gen_rand_reads.c:773:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 773 | if(seq_exp>1)HashTablePut(seq_duplicate_tab, md5mem, 1+NULL); | ^ gen_rand_reads.c:829:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 829 | long seq_exp = HashTableGet(grc->expression_levels, seq_name)-NULL; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gene-algorithms.c -o gene-algorithms.o gene-algorithms.c: In function ‘linear_gene_position’: gene-algorithms.c:425:67: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 425 | n = HashTableGet(offsets -> read_name_to_index, chro_name)-NULL; | ^ gene-algorithms.c: In function ‘find_and_explain_indel’: gene-algorithms.c:768:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 768 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xff ; | ^~~~ gene-algorithms.c: In function ‘explain_indel_in_middle’: gene-algorithms.c:918:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘253’ to ‘-3’ [-Woverflow] 918 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfd; | ^~~~ gene-algorithms.c:945:93: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘254’ to ‘-2’ [-Woverflow] 945 | *(allvote -> max_indel_recorder + qid * allvote -> indel_recorder_length) = 0xfe ; | ^~~~ gene-algorithms.c: In function ‘load_offsets’: gene-algorithms.c:1355:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1355 | HashTablePut(offsets->read_name_to_index, read_name_mem , NULL + 1 + n); | ^ gene-algorithms.c:1355:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1355 | HashTablePut(offsets->read_name_to_index, read_name_mem , NULL + 1 + n); | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gene-value-index.c -o gene-value-index.o gene-value-index.c: In function ‘is_offset_in_chro’: gene-value-index.c:85:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 85 | if( pos < chros -> padding || pos >= ( chros->read_offsets[n] - chros->read_offsets[n-1] - chros -> padding )) | ^~ In file included from gene-value-index.h:24, from gene-value-index.c:25: subread.h:153:24: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 153 | #define SUBREADprintf msgqu_printf | ^~~~~~~~~~~~ gene-value-index.c:87:41: note: in expansion of macro ‘SUBREADprintf’ 87 | SUBREADprintf("INCHRO:%d ; POS:%d\n", ret, pos); | ^~~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hashtable.c -o hashtable.o hashtable.c: In function ‘ArrayListToLookupTable_Int’: hashtable.c:43:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c:43:99: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c:43:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 43 | for(x1 = 0; x1 < arr->numOfElements; x1++) HashTablePut(ret, ArrayListGet(arr, x1)+1, NULL+x1+1); | ^ hashtable.c: In function ‘ArrayListSort_compare’: hashtable.c:169:75: warning: ISO C forbids initialization between function pointer and ‘void *’ [-Wpedantic] 169 | int (*comp_elems)(void * L_elem, void * R_elem, ArrayList * me) = sortdata[1]; | ^~~~~~~~ hashtable.c: In function ‘ArrayListSort_merge’: hashtable.c:188:75: warning: ISO C forbids initialization between function pointer and ‘void *’ [-Wpedantic] 188 | int (*comp_elems)(void * L_elem, void * R_elem, ArrayList * me) = sortdata[1]; | ^~~~~~~~ hashtable.c: In function ‘ArrayListSort’: hashtable.c:214:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 214 | sortdata[1] = compare_L_minus_R?compare_L_minus_R:ArrayListSort_comp_pntr; | ^ hashtable.c: In function ‘ArrayListLLUComparison’: hashtable.c:227:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 227 | srUInt_64 lint = L_elem-NULL; | ^ hashtable.c:228:32: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 228 | srUInt_64 rint = R_elem-NULL; | ^ hashtable.c: In function ‘ArrayListFindNextDent’: hashtable.c:236:35: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 236 | if( list -> elementList[h]- NULL <= value_less_than_dent )return -1l; | ^ hashtable.c:239:55: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 239 | srUInt_64 mv = list -> elementList[m] - NULL; | ^ hashtable.c:247:46: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 247 | for(; m>=0 && list -> elementList[m] - NULL >= value_less_than_dent; m--); | ^ hashtable.c:250:44: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 250 | if( list -> elementList[m] - NULL > value_less_than_dent )return m; | ^ hashtable.c: In function ‘HashTableInc’: hashtable.c:321:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 321 | HashTablePut(tab, key, oldv+1); | ^ hashtable.c:322:21: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 322 | return oldv - NULL+1; | ^ hashtable.c: In function ‘pointerHashFunction’: hashtable.c:987:36: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 987 | return (srUInt_64)(pointer - NULL); | ^ hashtable.c: In function ‘HashTableSortedIndexes’: hashtable.c:1089:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1089 | appx[1]=NULL+larger_value_first; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c index-builder.c -o index-builder.o index-builder.c: In function ‘save_none_informative’: index-builder.c:78:40: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 78 | unsigned int subread_int = key - NULL; | ^ index-builder.c:79:34: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 79 | int repeats = hashed_obj - NULL; | ^ index-builder.c: In function ‘build_gene_index’: index-builder.c:349:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c:349:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c:349:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 349 | int is_no_info = HashTableGet(huge_table, NULL+1+int_key)-NULL; | ^ index-builder.c: In function ‘scan_gene_index’: index-builder.c:678:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ index-builder.c:678:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ index-builder.c:678:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 678 | HashTablePut(huge_table,NULL+1+ current_bucket -> item_keys[j], NULL+current_bucket -> item_values [j]); | ^ index-builder.c: In function ‘check_and_convert_FastA’: index-builder.c:905:90: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 905 | int is_exist = HashTableGet(rep_name_table , line_buf+1) - NULL; | ^ index-builder.c:915:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 915 | HashTablePut(rep_name_table, keymem, NULL+1); | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c input-blc.c -o input-blc.o input-blc.c: In function ‘iBLC_guess_scan’: input-blc.c:128:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 128 | ArrayListPush(tilelist, NULL+tmpi); | ^ input-blc.c:149:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 149 | scancon -> cbcl_tile_numbers[ii] = ArrayListGet(tilelist,ii) - NULL; | ^ input-blc.c: In function ‘iCache_continuous_read_lanes’: input-blc.c:508:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 508 | ArrayListPush(tfp -> list_mapped_qscore, NULL+tov); | ^ input-blc.c:520:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 520 | HashTablePut(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit, NULL+seek_start); | ^ input-blc.c:520:135: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 520 | HashTablePut(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit, NULL+seek_start); | ^ input-blc.c:521:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:521:127: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:521:129: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 521 | HashTablePut(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit, NULL+1+reads_in_tile); | ^ input-blc.c:537:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 537 | int this_tile_reads = HashTableGet(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit) - NULL -1; | ^ input-blc.c:537:129: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 537 | int this_tile_reads = HashTableGet(tfp -> digit4_to_total_read_no_P1, NULL+tile_4digit) - NULL -1; | ^ input-blc.c:538:132: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 538 | srInt_64 next_tile_start_off = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit) - NULL; | ^ input-blc.c:538:146: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 538 | srInt_64 next_tile_start_off = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+tile_4digit) - NULL; | ^ input-blc.c:558:130: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 558 | nch = (nch & 3) | (4*(tfp -> list_mapped_qscore -> elementList[ nch >>2 ]-NULL)); | ^ input-blc.c:577:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 577 | np1 = HashTableGet(tfp -> digit4_to_compressed_start_of_next, NULL+new_4digit); | ^ input-blc.c:580:59: warning: unused variable ‘npos’ [-Wunused-variable] 580 | long long npos = lseek(tfp -> cbcl_bin_fd, next_tile_start_off , SEEK_SET); | ^~~~ input-blc.c: In function ‘input_BLC_parse_SampleSheet’: input-blc.c:1002:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1002 | entry[0] = NULL + lane_no; | ^ input-blc.c:1004:41: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1004 | entry[2] = NULL + stat1_line; // the N-th line in the file , 1 based | ^ input-blc.c: In function ‘iCache_write_supIdx_result’: input-blc.c:1126:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1126 | fprintf(ofp, "%s\t%d\n", (char*)ky, (int)(va-NULL)); | ^ input-blc.c: In function ‘iCache_copy_sample_table_2_list’: input-blc.c:1139:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1139 | push_arr[0] = NULL + lane_sample_int; | ^ input-blc.c:1140:36: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1140 | push_arr[1] = NULL + cbclist -> numOfElements+1; | ^ input-blc.c:1140:62: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1140 | push_arr[1] = NULL + cbclist -> numOfElements+1; | ^ input-blc.c: In function ‘iCache_get_cell_no’: input-blc.c:1171:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1171 | srInt_64 xint = xrawarr - NULL; | ^ input-blc.c:1182:77: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1182 | int bcno = ArrayListGet(rawarr, xx2)-NULL; | ^ input-blc.c:1185:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1185 | if(ArrayListGet(ret, xx3)==NULL+bcno){ | ^ input-blc.c:1191:74: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1191 | if(!found)ArrayListPush(ret, NULL+bcno); | ^ input-blc.c:1200:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1200 | int tbcn = ArrayListGet(ret,xx1)-NULL; | ^ input-blc.c: In function ‘iCache_delete_bcb_key’: input-blc.c:1218:15: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1218 | if(((k-NULL) & 0xFFFFFFFFF0000000llu)!= IMPOSSIBLE_MEMORY_ADDRESS) ArrayListDestroy(k); | ^ input-blc.c: In function ‘do_R_try_cell_barcode_files’: input-blc.c:1248:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1248 | argv[7]=NULL+rv; | ^ input-blc.c:1249:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1249 | argv[8]=NULL+tested_reads; | ^ input-blc.c:1250:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1250 | argv[9]=NULL+valid_sample_index; | ^ input-blc.c:1251:22: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1251 | argv[10]=NULL+valid_cell_barcode; | ^ input-blc.c: In function ‘cacheBCL_quality_test’: input-blc.c:1425:70: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1425 | HashTablePut(cell_barcode_table, strdup(bcbstr), NULL+IMPOSSIBLE_MEMORY_ADDRESS+xx1); | ^ input-blc.c:1425:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1425 | HashTablePut(cell_barcode_table, strdup(bcbstr), NULL+IMPOSSIBLE_MEMORY_ADDRESS+xx1); | ^ input-blc.c:1440:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1440 | ArrayListPush(array_of_codes, NULL+xx1); | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c input-files.c -o input-files.o input-files.c: In function ‘get_temp_file_pointer’: input-files.c:1536:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1536 | if(temp_file_pointer == NULL || temp_file_pointer == NULL + 1) { | ^ input-files.c:1550:64: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1550 | int maximum_open_file = fp_table -> appendix1 - NULL; | ^ input-files.c:1555:72: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1555 | HashTablePut(fp_table, key_name , NULL + 1); | ^ input-files.c: In function ‘my_fclose’: input-files.c:1565:28: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1565 | if(fp && fp != NULL+1) | ^ input-files.c: In function ‘add_cigar_indel_event’: input-files.c:1681:76: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1681 | int exist_indel_count = HashTableGet(event_table_ptr, event_token) - NULL; | ^ input-files.c:1688:85: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1688 | srInt_64 t64v = (HashTableGet(event_table_ptr, event_token)-NULL); | ^ input-files.c:1708:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1708 | memset(event_table_ptr->appendix2 + event_space_max_size * sizeof(short), 0, sizeof(short) * event_space_max_size); | ^ input-files.c:1718:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1718 | HashTablePut(event_table_ptr, token_1, NULL+1); | ^ input-files.c:1722:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1722 | HashTablePutReplace(event_table_ptr, event_token, NULL+exist_indel_count+1, 0); | ^ input-files.c:1722:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1722 | HashTablePutReplace(event_table_ptr, event_token, NULL+exist_indel_count+1, 0); | ^ input-files.c:1731:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1731 | HashTablePut(event_table_ptr, token_2, NULL + ((0xff & (0x80 + indels)) | ((indel_event_id_long&0xffffff) << 8))); | ^ input-files.c: In function ‘destroy_cigar_event_table’: input-files.c:1758:57: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1758 | srInt_64 tmpv = cursor -> value - NULL; | ^ input-files.c: In function ‘break_SAM_file’: input-files.c:1885:38: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1885 | fp_table -> appendix1 = NULL + max_open_file * 2/ 3; | ^ input-files.c: In function ‘SAM_pairer_create’: input-files.c:2609:22: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 2609 | old_sig_TERM = signal (SIGTERM, REPAIR_SIGINT_hook); | ^ input-files.c:2610:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 2610 | old_sig_INT = signal (SIGINT, REPAIR_SIGINT_hook); | ^ input-files.c: In function ‘SAM_pairer_destroy’: input-files.c:2699:26: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 2699 | signal (SIGTERM, old_sig_TERM); | ^~~~~~~~~~~~ In file included from input-files.c:21: /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c:2700:25: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 2700 | signal (SIGINT, old_sig_INT); | ^~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c: In function ‘SAM_pairer_get_next_read_BIN’: input-files.c:3126:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3126 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c:3126:116: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3126 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c: In function ‘online_register_contig’: input-files.c:3169:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3169 | signed int refId = HashTableGet(pairer->sam_contig_number_table, ref) - NULL - 1; | ^ input-files.c:3176:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3176 | HashTablePut(pairer->sam_contig_number_table, mem_ref, NULL + refId + 1); | ^ input-files.c:3176:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3176 | HashTablePut(pairer->sam_contig_number_table, mem_ref, NULL + refId + 1); | ^ input-files.c: In function ‘reduce_SAM_to_BAM’: input-files.c:3228:79: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3228 | signed int refID = HashTableGet(pairer->sam_contig_number_table, ref) - NULL - 1; | ^ input-files.c:3252:86: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3252 | mate_refID = HashTableGet(pairer->sam_contig_number_table, mate_ref) - NULL - 1; | ^ input-files.c:3277:39: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3277 | bin_tmp[bin_ptr ++] = 0xff; | ^~~~ input-files.c:3278:39: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3278 | bin_tmp[bin_ptr ++] = 0xff; | ^~~~ input-files.c:3244:13: warning: unused variable ‘seq_len’ [-Wunused-variable] 3244 | int seq_len = qual - seq - 1; | ^~~~~~~ input-files.c: In function ‘SAM_pairer_make_dummy’: input-files.c:3683:37: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 3683 | out_bin2[36 + len_name+1] = 0xff; | ^~~~ input-files.c: In function ‘SAM_pairer_rescure_orphants_max_FP’: input-files.c:4236:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4236 | int thread_no = (int)(param_ptr[1]-NULL); | ^ input-files.c: In function ‘SAM_pairer_thread_run’: input-files.c:4523:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4523 | int thread_no = (int)(param_ptr[1]-NULL), is_disk_full = 0; | ^ input-files.c: In function ‘SAM_pairer_finish_margins’: input-files.c:4597:34: warning: wrong type argument to increment [-Wpointer-arith] 4597 | tab -> appendix2 ++; | ^~ input-files.c:4616:32: warning: wrong type argument to decrement [-Wpointer-arith] 4616 | }else tab -> appendix2 --; | ^~ input-files.c: In function ‘SAM_pairer_run_once’: input-files.c:4647:47: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4647 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c:4668:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4668 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c: In function ‘SAM_pairer_fix_format’: input-files.c:4863:50: warning: variable ‘readname’ set but not used [-Wunused-but-set-variable] 4863 | char tmpfname [MAX_FILE_NAME_LENGTH+14], readname[256]; | ^~~~~~~~ input-files.c: In function ‘SAM_nosort_thread_run’: input-files.c:5159:43: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5159 | int thread_no = (int)(param_ptr[1]-NULL); | ^ input-files.c: In function ‘SAM_nosort_run_once’: input-files.c:5271:47: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5271 | init_params[1] = (void *)(NULL+x1); | ^ input-files.c:5437:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5437 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c:5437:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5437 | HashTablePut(pairer -> sam_contig_number_table , mem_contig_name, NULL + 1 + header_contigs); | ^ input-files.c: In function ‘sort_SAM_create’: input-files.c:5678:22: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 5678 | old_sig_TERM = signal (SIGTERM, SAM_SORT_SIGINT_hook); | ^ input-files.c:5679:21: warning: ISO C forbids assignment between function pointer and ‘void *’ [-Wpedantic] 5679 | old_sig_INT = signal (SIGINT, SAM_SORT_SIGINT_hook); | ^ input-files.c: In function ‘sort_SAM_finalise’: input-files.c:5817:65: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 5817 | old_line_mem[0]=0xff; | ^~~~ input-files.c:6048:26: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 6048 | signal (SIGTERM, old_sig_TERM); | ^~~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ input-files.c:6049:25: warning: ISO C forbids passing argument 2 of ‘signal’ between function pointer and ‘void *’ [-Wpedantic] 6049 | signal (SIGINT, old_sig_INT); | ^~~~~~~~~~~ /usr/include/signal.h:88:57: note: expected ‘__sighandler_t’ {aka ‘void (*)(int)’} but argument is of type ‘void *’ 88 | extern __sighandler_t signal (int __sig, __sighandler_t __handler) | ~~~~~~~~~~~~~~~^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c interval_merge.c -o interval_merge.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c long-hashtable.c -o long-hashtable.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c longread-mapping.c -o longread-mapping.o longread-mapping.c: In function ‘LRM_thread_runner’: longread-mapping.c:350:27: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 350 | int thid = argv[1]-NULL; | ^ longread-mapping.c:351:27: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 351 | int task = argv[2]-NULL; | ^ longread-mapping.c: In function ‘LRMstart_thread’: longread-mapping.c:391:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 391 | th_args[1] = NULL + th_id; | ^ longread-mapping.c:392:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 392 | th_args[2] = NULL + task; | ^ longread-mapping.c: In function ‘LRMis_gap_in_used_gap’: longread-mapping.c:636:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 636 | unsigned int used_start = LRMArrayListGet(iteration_context -> chain_used_gaps, xxi) - NULL; | ^ longread-mapping.c:637:102: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 637 | unsigned int used_end = LRMArrayListGet(iteration_context -> chain_used_gaps, xxi+1) - NULL; | ^ longread-mapping.c: In function ‘LRMbuild_chains’: longread-mapping.c:968:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 968 | LRMArrayListPush(iteration_context -> chain_used_gaps, NULL+this_gap_start_corr); | ^ longread-mapping.c:969:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 969 | LRMArrayListPush(iteration_context -> chain_used_gaps, NULL+this_gap_end_corr); | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mergeVCF.c -o mergeVCF.o mergeVCF.c: In function ‘do_find_common’: mergeVCF.c:219:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 219 | int repeat_times = HashTableGet(extra_count_table, ky) - NULL; | ^ mergeVCF.c:222:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 222 | HashTablePut(extra_count_table, ky, NULL+1); | ^ mergeVCF.c:225:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut(extra_qual_table, ky, NULL + qual + 1); | ^ mergeVCF.c:225:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 225 | HashTablePut(extra_qual_table, ky, NULL + qual + 1); | ^ mergeVCF.c:235:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 235 | int repeat_times = HashTableGet(extra_count_table, ky) - NULL; | ^ mergeVCF.c:238:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 238 | int old_qual = HashTableGet(extra_qual_table, ky) - NULL - 1; | ^ mergeVCF.c:240:97: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 240 | HashTablePutReplace(extra_count_table, ky, NULL + repeat_times, 0); | ^ mergeVCF.c:251:104: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 251 | HashTablePutReplace(extra_qual_table, ky, NULL + 1 + qual, 0); | ^ mergeVCF.c:251:108: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 251 | HashTablePutReplace(extra_qual_table, ky, NULL + 1 + qual, 0); | ^ mergeVCF.c:277:54: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 277 | int counts = cursor -> value - NULL; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c processExons.c -o processExons.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c propmapped.c -o propmapped.o propmapped.c: In function ‘get_FP_by_read_name’: propmapped.c:248:66: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 248 | FILE * ret = HashTableGet(context -> split_fp_table, NULL+1+(int)(hash_key)); | ^ propmapped.c:248:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 248 | FILE * ret = HashTableGet(context -> split_fp_table, NULL+1+(int)(hash_key)); | ^ propmapped.c:258:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 258 | HashTablePut(context -> split_fp_table, NULL+1+(int)(hash_key), ret); | ^ propmapped.c:258:63: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 258 | HashTablePut(context -> split_fp_table, NULL+1+(int)(hash_key), ret); | ^ propmapped.c: In function ‘prop_PE’: propmapped.c:409:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 409 | int old_OK = HashTableGet(rname_table, read_name) - NULL; | ^ propmapped.c:416:98: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 416 | HashTablePut(rname_table, read_name, NULL+2); | ^ propmapped.c:419:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 419 | HashTablePut(rname_table, read_name, NULL + new_OK + 1); | ^ propmapped.c:419:100: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 419 | HashTablePut(rname_table, read_name, NULL + new_OK + 1); | ^ propmapped.c:435:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 435 | if(cursor -> value == NULL+2) context -> mapped_reads++; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qualityScores.c -o qualityScores.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read-repair.c -o read-repair.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c readSummary.c -o readSummary.o readSummary.c: In function ‘load_feature_info’: readSummary.c:1260:134: warning: non-ISO-standard escape sequence, ‘\E’ [-Wpedantic] 1260 | SUBREADprintf("\Error: the feature on the %d-th line has zero coordinate or zero lengths\n\n", lineno); | ^ readSummary.c: In function ‘find_or_insert_gene_name’: readSummary.c:1409:70: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1409 | srInt_64 gene_number = HashTableGet(genetable, feature_name) - NULL; | ^ readSummary.c:1415:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1415 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ readSummary.c:1415:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1415 | HashTablePut(genetable, feature_name, NULL+gene_number+1); | ^ readSummary.c: In function ‘add_bin_new_tags’: readSummary.c:2644:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2644 | int intv = vals[tagi] - NULL; | ^ readSummary.c: In function ‘compress_read_detail_BAM’: readSummary.c:2706:38: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘255’ to ‘-1’ [-Woverflow] 2706 | bam_buf[9] = 0xff; // OS | ^~~~ readSummary.c: In function ‘write_read_details_FP’: readSummary.c:2799:29: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2799 | vals[1]=NULL+feature_count; | ^ readSummary.c: In function ‘warning_anno_BAM_chromosomes’: readSummary.c:2830:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2830 | HashTablePut(BAM_chro_tab, BAM_chro, NULL+1); | ^ readSummary.c:2838:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2838 | HashTablePut(ANNO_chro_tab, global_context -> exontable_chr[x1], NULL+1); | ^ readSummary.c: In function ‘add_fragment_supported_junction’: readSummary.c:3463:49: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3463 | srInt_64 count_junc = count_ptr - NULL; | ^ readSummary.c:3464:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3464 | HashTablePut(junction_counting_table, this_key, NULL+count_junc + 1); | ^ readSummary.c:3464:81: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3464 | HashTablePut(junction_counting_table, this_key, NULL+count_junc + 1); | ^ readSummary.c:3475:48: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 3475 | count_junc = count_ptr - NULL; | ^ readSummary.c:3476:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3476 | HashTablePut(splicing_point_table, lr_key, NULL + count_junc + 1); | ^ readSummary.c:3476:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 3476 | HashTablePut(splicing_point_table, lr_key, NULL + count_junc + 1); | ^ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3900:58: warning: variable ‘assignment_target_number’ set but not used [-Wunused-but-set-variable] 3900 | srInt_64 assignment_target_number = tmp_voter_id; | ^~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘fc_thread_merge_results’: readSummary.c:4046:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4046 | globval += (cursor -> value - NULL); | ^ readSummary.c:4046:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4046 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4064:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4064 | globval += (cursor -> value - NULL); | ^ readSummary.c:4064:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4064 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4123:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4123 | globval += (cursor -> value - NULL); | ^ readSummary.c:4123:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4123 | globval += (cursor -> value - NULL); | ^~ readSummary.c:4143:69: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 4143 | globval += (cursor -> value - NULL); | ^ readSummary.c:4143:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 4143 | globval += (cursor -> value - NULL); | ^~ readSummary.c:3970:32: warning: unused variable ‘sample_i’ [-Wunused-variable] 3970 | int xk1, xk2, ret = 0, sample_i; | ^~~~~~~~ readSummary.c: In function ‘determine_jcount_gene_transcript_report’: readSummary.c:5420:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5420 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ readSummary.c:5420:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5420 | HashTablePut(edge1P1_table, txp_ptr -> transcript_id, NULL+1+edge1_dist); | ^ readSummary.c:5423:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5423 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5423:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5423 | HashTablePut(edge1exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5448:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5448 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ readSummary.c:5448:93: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5448 | HashTablePut(edge2P1_table, txp_ptr -> transcript_id, NULL+1+edge2_dist); | ^ readSummary.c:5451:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5451 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5451:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5451 | HashTablePut(edge2exonNo_table, txp_ptr -> transcript_id, NULL+1+exactly_matched_exon_no); | ^ readSummary.c:5461:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5461 | int edge1_ptr = HashTableGet(edge1P1_table, edge1_txnid)-NULL; | ^ readSummary.c:5463:81: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5463 | int edge2_ptr = HashTableGet(edge2P1_table, edge1_txnid)-NULL; | ^ readSummary.c:5465:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5465 | int exonno_1 = HashTableGet(edge1exonNo_table, edge1_txnid)-NULL-1; | ^ readSummary.c:5466:92: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5466 | int exonno_2 = HashTableGet(edge2exonNo_table, edge1_txnid)-NULL-1; | ^ readSummary.c:5478:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5478 | HashTablePut(out_gene_tab, txnptr -> gene_name, NULL+1); | ^ readSummary.c:5479:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5479 | HashTablePut(out_txn_tab, txnptr -> transcript_id, NULL+1); | ^ readSummary.c:5510:104: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5510 | srInt_64 edge_dist = HashTableGet(this_side_olay_tab, this_side_txn_id)-NULL; | ^ readSummary.c:5513:106: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5513 | HashTablePut(this_side_reported_genes, txn_ptr -> gene_name, NULL+1); | ^ readSummary.c: In function ‘find_nearest_gene_dist’: readSummary.c:5603:84: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5603 | HashTablePut(gene_name_tab, gene_name, NULL+1); | ^ readSummary.c: In function ‘fc_write_final_junctions’: readSummary.c:5651:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5651 | unsigned int old_supp = HashTableGet(merged_splicing_table, ky) - NULL; | ^ readSummary.c:5652:62: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5652 | old_supp += (cursor -> value - NULL); | ^ readSummary.c:5653:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5653 | HashTablePut(merged_splicing_table, ky, NULL+old_supp); | ^ readSummary.c:5671:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 5671 | HashTablePut(merged_junction_table, ky, NULL+1); | ^ readSummary.c:5831:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 5831 | srInt_64 count = HashTableGet(junc_table, key_list[ky_i]) - NULL; | ^ readSummary.c:5724:21: warning: unused variable ‘unique_junctions’ [-Wunused-variable] 5724 | int unique_junctions = 0; | ^~~~~~~~~~~~~~~~ readSummary.c:5700:20: warning: unused variable ‘ky_i2’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5700:13: warning: unused variable ‘ky_i1’ [-Wunused-variable] 5700 | int ky_i1, ky_i2; | ^~~~~ readSummary.c:5698:81: warning: unused variable ‘gene_name_tail’ [-Wunused-variable] 5698 | char * gene_names = malloc(max_junction_genes * FEATURE_NAME_LENGTH), * gene_name_tail; | ^~~~~~~~~~~~~~ readSummary.c: In function ‘readSummary’: readSummary.c:5971:52: warning: variable ‘scrna_total_BAM_no’ set but not used [-Wunused-but-set-variable] 5971 | int isGTF, n_input_files=0,is_dual_index, scrna_total_BAM_no; | ^~~~~~~~~~~~~~~~~~ readSummary.c: In function ‘vote_and_add_count’: readSummary.c:3833:66: warning: ‘longest_overlap_score’ may be used uninitialized [-Wmaybe-uninitialized] 3833 | if(longest_overlap_score > scoring_numbers[score_x1]) scoring_numbers[score_x1] = 0; | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ readSummary.c:3602:51: note: ‘longest_overlap_score’ was declared here 3602 | int scoring_count = 0, score_x1, longest_overlap_score; | ^~~~~~~~~~~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c removeDupReads.c -o removeDupReads.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sam2bed.c -o sam2bed.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sambam-file.c -o sambam-file.o sambam-file.c: In function ‘SamBam_writer_write_header’: sambam-file.c:1282:85: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1282 | char * chro_name = HashTableGet(writer -> chromosome_id_table, NULL + 1 + header_ptr); | ^ sambam-file.c:1282:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1282 | char * chro_name = HashTableGet(writer -> chromosome_id_table, NULL + 1 + header_ptr); | ^ sambam-file.c:1283:91: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c:1283:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c:1283:109: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1283 | unsigned int chro_len = HashTableGet(writer -> chromosome_len_table, NULL + 1 + header_ptr) - NULL - 1; | ^ sambam-file.c: In function ‘SamBam_writer_add_chromosome’: sambam-file.c:1408:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1408 | HashTablePut(writer -> chromosome_name_table, chro_name_space, NULL+1+chro_id); | ^ sambam-file.c:1408:78: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1408 | HashTablePut(writer -> chromosome_name_table, chro_name_space, NULL+1+chro_id); | ^ sambam-file.c:1409:57: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1409 | HashTablePut(writer -> chromosome_id_table, NULL+1+chro_id, chro_name_space); | ^ sambam-file.c:1409:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1409 | HashTablePut(writer -> chromosome_id_table, NULL+1+chro_id, chro_name_space); | ^ sambam-file.c:1410:58: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:75: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c:1410:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1410 | HashTablePut(writer -> chromosome_len_table, NULL+1+chro_id, NULL + 1 + chro_length); | ^ sambam-file.c: In function ‘SamBam_writer_add_read’: sambam-file.c:1746:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1746 | int refID = HashTableGet(writer -> chromosome_name_table, chro_name) - NULL - 1; | ^ sambam-file.c:1752:91: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1752 | nextRefID = HashTableGet(writer -> chromosome_name_table, next_chro_name) - NULL - 1; | ^ sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM_test_bins’: sambam-file.c:1946:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1946 | ArrayListPush(win16k_list, NULL+ this_Vpos); | ^ sambam-file.c:1950:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1950 | ArrayList * this_bin_chunks = HashTableGet(bin_tab, NULL+binno+1); | ^ sambam-file.c:1950:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1950 | ArrayList * this_bin_chunks = HashTableGet(bin_tab, NULL+binno+1); | ^ sambam-file.c:1953:43: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1953 | HashTablePut(bin_tab, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:1953:49: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1953 | HashTablePut(bin_tab, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:1954:45: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1954 | ArrayListPush(bin_list, NULL+binno); | ^ sambam-file.c:1962:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1962 | diff -=(this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] - NULL)>>16; | ^ sambam-file.c:1964:101: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1964:112: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1964:123: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1964 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements -1] = NULL+this_Vpos + block_len+4; | ^ sambam-file.c:1972:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1972 | ArrayListPush(this_bin_chunks, NULL + this_Vpos); | ^ sambam-file.c:1973:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c:1973:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c:1973:76: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 1973 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + block_len+4); | ^ sambam-file.c: In function ‘SamBam_writer_sorted_compress’: sambam-file.c:1981:37: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 1981 | int this_thread_no = vptr[1]-NULL; | ^ sambam-file.c: In function ‘SamBam_thread_wait_merge_write’: sambam-file.c:2015:69: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ sambam-file.c:2015:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ sambam-file.c:2015:126: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2015 | HashTablePut(writer -> block_no_p1_to_vpos_tab, NULL+1+writer -> writer_threads[thread_no].bam_block_no, NULL+fpos); | ^ sambam-file.c: In function ‘SamBam_writer_merge_chunks’: sambam-file.c:2173:45: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2173 | ll[0] = ArrayListGet(chs, i)-NULL; | ^ sambam-file.c:2174:47: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2174 | ll[1] = ArrayListGet(chs, i+1)-NULL; | ^ sambam-file.c:2181:32: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2181 | ArrayListPush(chs, NULL+ll0[0]); | ^ sambam-file.c:2182:32: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2182 | ArrayListPush(chs, NULL+ll0[1]); | ^ sambam-file.c:2185:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2185 | long long last_end = ArrayListGet(chs, chs -> numOfElements-1) -NULL; | ^ sambam-file.c:2192:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2192 | chs-> elementList[chs -> numOfElements-1] = NULL+max(ll_this[1],last_end); | ^ sambam-file.c:2194:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2194 | ArrayListPush(chs, NULL+ll_this[0]); | ^ sambam-file.c:2195:48: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2195 | ArrayListPush(chs, NULL+ll_this[1]); | ^ sambam-file.c: In function ‘SamBam_writer_optimize_bins_level’: sambam-file.c:2211:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2211 | int binno = ArrayListGet(bin_arr, i)-NULL; | ^ sambam-file.c:2213:77: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2213 | ArrayList * old_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2213:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2213 | ArrayList * old_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2215:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2215 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(old_bin_arr)); | ^ sambam-file.c:2215:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2215 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(old_bin_arr)); | ^ sambam-file.c:2216:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2216 | ArrayListPush(new_arrs, NULL+binno); | ^ sambam-file.c:2224:53: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2224 | int binno = ArrayListGet(bin_arr, i)-NULL; | ^ sambam-file.c:2226:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2226 | ArrayList * small_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2226:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2226 | ArrayList * small_bin_arr = HashTableGet(bin_tab, NULL+1+binno); | ^ sambam-file.c:2233:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2233 | long long this_start = ArrayListGet(small_bin_arr, j)-NULL; | ^ sambam-file.c:2234:78: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2234 | long long this_end = ArrayListGet(small_bin_arr, j+1)-NULL; | ^ sambam-file.c:2243:80: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2243 | ArrayList * parent_bin_arr = HashTableGet(new_tab, NULL+1+parent_binno); | ^ sambam-file.c:2243:82: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2243 | ArrayList * parent_bin_arr = HashTableGet(new_tab, NULL+1+parent_binno); | ^ sambam-file.c:2246:59: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2246 | HashTablePut(new_tab, NULL+1+parent_binno, parent_bin_arr); | ^ sambam-file.c:2246:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2246 | HashTablePut(new_tab, NULL+1+parent_binno, parent_bin_arr); | ^ sambam-file.c:2247:61: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2247 | ArrayListPush(new_arrs, NULL+parent_binno); | ^ sambam-file.c:2253:51: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2253 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(small_bin_arr)); | ^ sambam-file.c:2253:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2253 | HashTablePut(new_tab, NULL+1+binno, ArrayListDuplicate(small_bin_arr)); | ^ sambam-file.c:2254:54: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2254 | ArrayListPush(new_arrs, NULL + binno); | ^ sambam-file.c:2260:54: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2260 | int binno = ArrayListGet(new_arrs, i)-NULL; | ^ sambam-file.c:2262:71: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2262 | ArrayList * large_bin_arr = HashTableGet(new_tab, NULL+1+binno); | ^ sambam-file.c:2262:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2262 | ArrayList * large_bin_arr = HashTableGet(new_tab, NULL+1+binno); | ^ sambam-file.c: In function ‘SamBam_write_BAI_for_1chr’: sambam-file.c:2317:60: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2317 | int bin_no = ArrayListGet(*bins_list, bini)-NULL; | ^ sambam-file.c:2318:79: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2318 | ArrayList * chunks_list = HashTableGet(*bin_chunks_table, NULL+ bin_no+1); | ^ sambam-file.c:2318:87: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2318 | ArrayList * chunks_list = HashTableGet(*bin_chunks_table, NULL+ bin_no+1); | ^ sambam-file.c:2325:84: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2325 | long long int Voff_st = ArrayListGet(chunks_list, chunk_i) - NULL; | ^ sambam-file.c:2326:86: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2326 | long long int Voff_en = ArrayListGet(chunks_list, chunk_i+1) - NULL; | ^ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2327:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2327 | SAMBAM_Block2Vpos(Voff_st); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2328:25: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2328 | SAMBAM_Block2Vpos(Voff_en); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2336:72: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2336 | long long int Voff = ArrayListGet(*win16k_list , bini) - NULL; | ^ sambam-file.c:2298:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:96: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c:2298:99: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2298 | #define SAMBAM_Block2Vpos(v) (v)=((HashTableGet(writer -> block_no_p1_to_vpos_tab, NULL+(v>>16)+1)-NULL )<<16 )|(v & 0xffff); | ^ sambam-file.c:2337:17: note: in expansion of macro ‘SAMBAM_Block2Vpos’ 2337 | SAMBAM_Block2Vpos(Voff); | ^~~~~~~~~~~~~~~~~ sambam-file.c: In function ‘SamBam_writer_sort_bins_to_BAM’: sambam-file.c:2397:35: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2397 | thparam[1] = NULL + thread_i; | ^ sambam-file.c: In function ‘simple_bam_writer_update_index’: sambam-file.c:2531:107: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2531 | struct simple_bam_writer_index_per_chro * index_chro = HashTableGet(writer -> index_per_chro, NULL+chro_no+1); | ^ sambam-file.c:2531:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2531 | struct simple_bam_writer_index_per_chro * index_chro = HashTableGet(writer -> index_per_chro, NULL+chro_no+1); | ^ sambam-file.c:2534:60: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2534 | HashTablePut(writer -> index_per_chro, NULL+chro_no+1, index_chro); | ^ sambam-file.c:2534:68: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2534 | HashTablePut(writer -> index_per_chro, NULL+chro_no+1, index_chro); | ^ sambam-file.c:2546:56: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2546 | ArrayListPush(win16k_list, NULL+ this_Vpos); | ^ sambam-file.c:2549:89: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2549 | ArrayList * this_bin_chunks = HashTableGet(index_chro -> index_binP1_table, NULL+binno+1); | ^ sambam-file.c:2549:95: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2549 | ArrayList * this_bin_chunks = HashTableGet(index_chro -> index_binP1_table, NULL+binno+1); | ^ sambam-file.c:2552:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2552 | HashTablePut(index_chro -> index_binP1_table, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:2552:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2552 | HashTablePut(index_chro -> index_binP1_table, NULL+binno+1, this_bin_chunks); | ^ sambam-file.c:2553:67: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2553 | ArrayListPush(index_chro -> index_binP0_list, NULL+binno); | ^ sambam-file.c:2560:96: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2560 | diff -=(this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] - NULL)>>16; | ^ sambam-file.c:2562:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2562:113: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2562:122: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2562 | this_bin_chunks -> elementList [ this_bin_chunks -> numOfElements - 1] = NULL+this_Vpos + binlen + 4; | ^ sambam-file.c:2568:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2568 | ArrayListPush(this_bin_chunks, NULL + this_Vpos); | ^ sambam-file.c:2569:53: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c:2569:65: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c:2569:73: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2569 | ArrayListPush(this_bin_chunks, NULL + this_Vpos + binlen+4); | ^ sambam-file.c: In function ‘simple_bam_write_compressed_block’: sambam-file.c:2574:88: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c:2574:90: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c:2574:109: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2574 | if(block_number >= 0)HashTablePut(writer -> bam_blockP1_to_offset0B_table, NULL+1+block_number, NULL+ftello(writer -> bam_FP)); | ^ sambam-file.c: In function ‘simple_bam_write’: sambam-file.c:2591:21: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2591 | bin += concatinate_binlen; | ^~ sambam-file.c: In function ‘simple_bam_close’: sambam-file.c:2635:113: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2635 | struct simple_bam_writer_index_per_chro *this_idx = HashTableGet(writer -> index_per_chro , NULL+1+chri); | ^ sambam-file.c:2635:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2635 | struct simple_bam_writer_index_per_chro *this_idx = HashTableGet(writer -> index_per_chro , NULL+1+chri); | ^ sambam-file.c:2647:93: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2647 | int binno = ArrayListGet(this_idx -> index_binP0_list, bini)-NULL; | ^ sambam-file.c:2648:103: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2648 | ArrayList * bingaps = HashTableGet(this_idx -> index_binP1_table, NULL+1+binno); | ^ sambam-file.c:2648:105: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2648 | ArrayList * bingaps = HashTableGet(this_idx -> index_binP1_table, NULL+1+binno); | ^ sambam-file.c:2653:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2653 | srInt_64 rposone, vposone = ArrayListGet(bingaps , gapi)-NULL; | ^ sambam-file.c:2625:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:134: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2654:41: note: in expansion of macro ‘vpos_to_rpos’ 2654 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2661:106: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2661 | srInt_64 rposone, vposone = ArrayListGet(this_idx -> win16k_list , bini )-NULL; | ^ sambam-file.c:2625:115: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:117: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ sambam-file.c:2625:134: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 2625 | #define vpos_to_rpos rposone = (vposone & 0xffff ) + ( (HashTableGet(writer -> bam_blockP1_to_offset0B_table, NULL+1+(vposone >>16)) - NULL) << 16 ) | ^ sambam-file.c:2662:33: note: in expansion of macro ‘vpos_to_rpos’ 2662 | vpos_to_rpos; | ^~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seek-zlib.c -o seek-zlib.o seek-zlib.c: In function ‘seekgz_open’: seek-zlib.c:136:45: warning: overflow in conversion from ‘int’ to ‘char’ changes value from ‘139’ to ‘-117’ [-Woverflow] 136 | fp -> in_zipped_buffer[1] = 0x8b; | ^~~~ seek-zlib.c: In function ‘seekgz_load_1_block’: seek-zlib.c:327:75: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 327 | int zipped_data_used = (void *)fp -> stem.next_in - old_next_in; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sorted-hashtable.c -o sorted-hashtable.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sublog.c -o sublog.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 2.24.0\"" -g3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tx-unique.c -o tx-unique.o tx-unique.c: In function ‘txunique_process_gene_chro’: tx-unique.c:292:101: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 292 | int old_all_bases = HashTableGet(context -> result_table, hash_key) - NULL; | ^ tx-unique.c:294:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 294 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + total_bases); | ^ tx-unique.c:294:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 294 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + total_bases); | ^ tx-unique.c:298:97: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 298 | old_all_bases = HashTableGet(context -> result_table, hash_key) - NULL; | ^ tx-unique.c:300:86: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 300 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + unique_bases); | ^ tx-unique.c:300:102: warning: pointer of type ‘void *’ used in arithmetic [-Wpointer-arith] 300 | HashTablePut(context -> result_table, hash_key, NULL + old_all_bases + unique_bases); | ^ tx-unique.c: In function ‘txunique_process_write_gene’: tx-unique.c:320:80: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 320 | int all_bases = HashTableGet(context -> result_table, hash_key)-NULL-1; | ^ tx-unique.c:322:83: warning: pointer of type ‘void *’ used in subtraction [-Wpointer-arith] 322 | int unique_bases = HashTableGet(context -> result_table, hash_key)-NULL-1; | ^ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o cell-counts.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZiokCK/R.INSTALL3dda2145d6f771/Rsubread/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rsubread/00new/Rsubread/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rsubread) * installing *source* package ‘affyPLM’ ... ** this is package ‘affyPLM’ version ‘1.86.0’ ** package ‘affyPLM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpE5Ge7r/R.INSTALL3df0a64721b602/affyPLM/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LESN.c -o LESN.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PLM_avg_log.c -o PLM_avg_log.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PLM_biweight.c -o PLM_biweight.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PLM_log_avg.c -o PLM_log_avg.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PLM_medianPM.c -o PLM_medianPM.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PLM_median_logPM.c -o PLM_median_logPM.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PLM_medianpolish.c -o PLM_medianpolish.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c PLM_modelmatrix.c -o PLM_modelmatrix.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c SCAB.c -o SCAB.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c chipbackground.c -o chipbackground.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common_types.c -o common_types.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c do_PLMrlm.c -o do_PLMrlm.o do_PLMrlm.c: In function ‘do_PLM_rlm’: do_PLMrlm.c:620:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 620 | int first_ind; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c do_PLMrma.c -o do_PLMrma.o do_PLMrma.c: In function ‘do_PLMrma’: do_PLMrma.c:209:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 209 | int first_ind; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c do_PLMthreestep.c -o do_PLMthreestep.o do_PLMthreestep.c: In function ‘do_PLMthreestep’: do_PLMthreestep.c:118:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 118 | int first_ind; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c idealmismatch.c -o idealmismatch.o idealmismatch.c: In function ‘IdealMM_correct_single’: idealmismatch.c:71:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 71 | int first_ind; | ^~~~~~~~~ idealmismatch.c: In function ‘SpecificBiweightCorrect_single’: idealmismatch.c:183:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 183 | int first_ind; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_threestep.c -o lm_threestep.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c matrix_functions.c -o matrix_functions.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c nthLargestPM.c -o nthLargestPM.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c preprocess.c -o preprocess.o preprocess.c: In function ‘pp_background’: preprocess.c:158:7: warning: variable ‘which_lesn’ set but not used [-Wunused-but-set-variable] 158 | int which_lesn; | ^~~~~~~~~~ preprocess.c: In function ‘pp_bothstages’: preprocess.c:677:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable] 677 | int rows,cols; | ^~~~ preprocess.c:677:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable] 677 | int rows,cols; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c psi_fns.c -o psi_fns.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qnorm_probeset.c -o qnorm_probeset.o qnorm_probeset.c: In function ‘qnorm_probeset_c’: qnorm_probeset.c:110:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 110 | int first_ind; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read_rmaexpress.c -o read_rmaexpress.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rlm_PLM.c -o rlm_PLM.o rlm_PLM.c: In function ‘R_rlm_PLMset_c’: rlm_PLM.c:1481:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable] 1481 | int rows,cols; | ^~~~ rlm_PLM.c:1481:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable] 1481 | int rows,cols; | ^~~~ rlm_PLM.c: In function ‘rlm_PLMset_nameoutput’: rlm_PLM.c:870:32: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=] 870 | snprintf(tmp_str2,9,"%d",j+1); | ^~ rlm_PLM.c:870:31: note: directive argument in the range [1, 2147483647] 870 | snprintf(tmp_str2,9,"%d",j+1); | ^~~~ In file included from /usr/include/stdio.h:970, from /home/hornik/tmp/R-d-gcc-15/include/R.h:44, from preprocess.h:4, from rlm_PLM.c:71: In function ‘snprintf’, inlined from ‘rlm_PLMset_nameoutput’ at rlm_PLM.c:870:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 9 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ rlm_PLM.c: In function ‘rlm_PLMset_nameoutput’: rlm_PLM.c:868:32: warning: ‘%d’ directive output may be truncated writing between 1 and 10 bytes into a region of size 9 [-Wformat-truncation=] 868 | snprintf(tmp_str2,9,"%d",j+2); | ^~ rlm_PLM.c:868:31: note: directive argument in the range [2, 2147483647] 868 | snprintf(tmp_str2,9,"%d",j+2); | ^~~~ In function ‘snprintf’, inlined from ‘rlm_PLMset_nameoutput’ at rlm_PLM.c:868:4: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:10: note: ‘__builtin___snprintf_chk’ output between 2 and 11 bytes into a destination of size 9 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rlm_threestep.c -o rlm_threestep.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rmaPLM_pseudo.c -o rmaPLM_pseudo.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rma_PLM.c -o rma_PLM.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rma_common.c -o rma_common.o rma_common.c: In function ‘median’: rma_common.c:60:7: warning: unused variable ‘i’ [-Wunused-variable] 60 | int i; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c scaling.c -o scaling.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c threestep.c -o threestep.o threestep.c: In function ‘threestep_summary’: threestep.c:82:15: warning: variable ‘MM’ set but not used [-Wunused-but-set-variable] 82 | double *PM,*MM; | ^~ threestep.c: In function ‘R_threestep_c’: threestep.c:193:12: warning: variable ‘cols’ set but not used [-Wunused-but-set-variable] 193 | int rows,cols; | ^~~~ threestep.c:193:7: warning: variable ‘rows’ set but not used [-Wunused-but-set-variable] 193 | int rows,cols; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c threestep_PLM.c -o threestep_PLM.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c threestep_common.c -o threestep_common.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c threestep_summary.c -o threestep_summary.o threestep_summary.c: In function ‘do_3summary’: threestep_summary.c:73:7: warning: variable ‘first_ind’ set but not used [-Wunused-but-set-variable] 73 | int first_ind; | ^~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c threestep_summary_methods.c -o threestep_summary_methods.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c transfns.c -o transfns.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o affyPLM.so LESN.o PLM_avg_log.o PLM_biweight.o PLM_log_avg.o PLM_medianPM.o PLM_median_logPM.o PLM_medianpolish.o PLM_modelmatrix.o SCAB.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o lm_threestep.o matrix_functions.o nthLargestPM.o preprocess.o psi_fns.o qnorm_probeset.o read_rmaexpress.o rlm_PLM.o rlm_threestep.o rmaPLM_pseudo.o rma_PLM.o rma_common.o scaling.o threestep.o threestep_PLM.o threestep_common.o threestep_summary.o threestep_summary_methods.o transfns.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -lz -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpE5Ge7r/R.INSTALL3df0a64721b602/affyPLM/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-affyPLM/00new/affyPLM/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affyPLM) * installing *source* package ‘ShortRead’ ... ** this is package ‘ShortRead’ version ‘1.68.0’ ** package ‘ShortRead’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc-15 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-15 accepts -g... yes checking for gcc-15 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc-15 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqoJj9h/R.INSTALL3de271528ed3f8/ShortRead/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_ShortRead.c -o R_init_ShortRead.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alphabet.c -o alphabet.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c count.c -o count.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io.c -o io.o io.c: In function ‘read_prb_as_character’: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] 227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0))); | ~^ | | | double | %s io.c: In function ‘_read_solexa_export_file’: io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 658 | error("invalid 'strand' field '%s', %s:%d", | ~^ | | | char * | %d 659 | *elt[13], fname, lineno); | ~~~~~~~~ | | | int io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 676 | error("invalid 'filtering' field '%s', %s:%d", | ~^ | | | char * | %d 677 | *elt[21], fname, lineno); | ~~~~~~~~ | | | int gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_bowtie.c -o io_bowtie.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_soap.c -o io_soap.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_maq_map.cc -o read_maq_map.o In file included from read_maq_map.cc:13: maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sampler.c -o sampler.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trim.c -o trim.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xsnap.c -o xsnap.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqoJj9h/R.INSTALL3de271528ed3f8/ShortRead/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ShortRead/00new/ShortRead/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ShortRead) * installing *source* package ‘affxparser’ ... ** this is package ‘affxparser’ version ‘1.82.0’ ** package ‘affxparser’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpkZcUr6/R.INSTALL3dd9df7e3b35bc/affxparser/src' rm -f fusion/calvin_files/data/src/CDFData.o fusion/calvin_files/data/src/CDFProbeGroupInformation.o fusion/calvin_files/data/src/CDFProbeInformation.o fusion/calvin_files/data/src/CDFProbeSetInformation.o fusion/calvin_files/data/src/CDFQCProbeInformation.o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o fusion/calvin_files/data/src/CELData.o fusion/calvin_files/data/src/CHPBackgroundZone.o fusion/calvin_files/data/src/CHPData.o fusion/calvin_files/data/src/CHPExpressionEntry.o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPTilingData.o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPGenotypeEntry.o fusion/calvin_files/data/src/CHPUniversalEntry.o fusion/calvin_files/data/src/ColumnInfo.o fusion/calvin_files/data/src/DataGroup.o fusion/calvin_files/data/src/DataGroupHeader.o fusion/calvin_files/data/src/DataSet.o fusion/calvin_files/data/src/DataSetHeader.o fusion/calvin_files/data/src/FileHeader.o fusion/calvin_files/data/src/GenericData.o fusion/calvin_files/data/src/GenericDataHeader.o fusion/calvin_files/exception/src/ExceptionBase.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionBPMAPData.o fusion/calvin_files/fusion/src/FusionCDFData.o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion/calvin_files/fusion/src/FusionCELData.o fusion/calvin_files/fusion/src/FusionCHPData.o fusion/calvin_files/fusion/src/FusionProbeSetResults.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion/calvin_files/fusion/src/FusionCHPTilingData.o fusion/calvin_files/fusion/src/FusionCHPGenericData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion/calvin_files/parameter/src/ParameterNameValueType.o fusion/calvin_files/parsers/src/CDFFileReader.o fusion/calvin_files/parsers/src/CelFileReader.o fusion/calvin_files/parsers/src/CHPFileReader.o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion/calvin_files/parsers/src/CHPTilingFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o fusion/calvin_files/parsers/src/DataGroupReader.o fusion/calvin_files/parsers/src/DataSetHeaderReader.o fusion/calvin_files/parsers/src/DataSetReader.o fusion/calvin_files/parsers/src/FileHeaderReader.o fusion/calvin_files/parsers/src/FileInput.o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o fusion/calvin_files/parsers/src/GenericFileReader.o fusion/calvin_files/utils/src/AffymetrixGuid.o fusion/calvin_files/utils/src/DateTime.o fusion/calvin_files/utils/src/FileUtils.o fusion/calvin_files/utils/src/StringUtils.o fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o 000.init.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFData.cpp -o fusion/calvin_files/data/src/CDFData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeGroupInformation.cpp -o fusion/calvin_files/data/src/CDFProbeGroupInformation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeInformation.cpp -o fusion/calvin_files/data/src/CDFProbeInformation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFProbeSetInformation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFQCProbeInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeInformation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CDFQCProbeSetInformation.cpp -o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CELData.cpp -o fusion/calvin_files/data/src/CELData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPBackgroundZone.cpp -o fusion/calvin_files/data/src/CHPBackgroundZone.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPData.cpp -o fusion/calvin_files/data/src/CHPData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPExpressionEntry.cpp -o fusion/calvin_files/data/src/CHPExpressionEntry.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPMultiDataData.cpp -o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPMultiDataData.cpp: In member function ‘void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int32_t, const std::vector&, const std::wstring&)’: fusion/calvin_files/data/src/CHPMultiDataData.cpp:427:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 427 | else | ^~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp:429:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 429 | DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); | ^~~~~~~~~~~~~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp: In member function ‘void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int, int, int, const std::wstring&)’: fusion/calvin_files/data/src/CHPMultiDataData.cpp:457:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 457 | else | ^~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp:459:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 459 | DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); | ^~~~~~~~~~~~~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp: In member function ‘void affymetrix_calvin_io::CHPMultiDataData::SetEntryCount(affymetrix_calvin_io::MultiDataType, int32_t, int, int, int, int, const std::wstring&)’: fusion/calvin_files/data/src/CHPMultiDataData.cpp:482:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 482 | else | ^~~~ fusion/calvin_files/data/src/CHPMultiDataData.cpp:484:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 484 | DataGroupHeader* dgHdr = GetDataGroupHeader(dataTypeGroupNames[dataType]); | ^~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPTilingData.cpp -o fusion/calvin_files/data/src/CHPTilingData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPQuantificationData.cpp -o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationData.cpp: In member function ‘void affymetrix_calvin_io::CHPQuantificationData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)’: fusion/calvin_files/data/src/CHPQuantificationData.cpp:144:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 144 | else | ^~~~ fusion/calvin_files/data/src/CHPQuantificationData.cpp:146:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 146 | hdr.AddFloatColumn(QUANTIFICATION_QUANTIFICATION_NAME); | ^~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp -o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp: In member function ‘void affymetrix_calvin_io::CHPQuantificationDetectionData::AddColumns(affymetrix_calvin_io::DataSetHeader&, bool)’: fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp:151:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 151 | else | ^~~~ fusion/calvin_files/data/src/CHPQuantificationDetectionData.cpp:153:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 153 | hdr.AddFloatColumn(QUANTIFICATION_DETECTION_QUANTIFICATION_NAME); | ^~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPGenotypeEntry.cpp -o fusion/calvin_files/data/src/CHPGenotypeEntry.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/CHPUniversalEntry.cpp -o fusion/calvin_files/data/src/CHPUniversalEntry.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/ColumnInfo.cpp -o fusion/calvin_files/data/src/ColumnInfo.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataGroup.cpp -o fusion/calvin_files/data/src/DataGroup.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataGroupHeader.cpp -o fusion/calvin_files/data/src/DataGroupHeader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataSet.cpp -o fusion/calvin_files/data/src/DataSet.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/DataSetHeader.cpp -o fusion/calvin_files/data/src/DataSetHeader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/FileHeader.cpp -o fusion/calvin_files/data/src/FileHeader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/GenericData.cpp -o fusion/calvin_files/data/src/GenericData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/data/src/GenericDataHeader.cpp -o fusion/calvin_files/data/src/GenericDataHeader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/exception/src/ExceptionBase.cpp -o fusion/calvin_files/exception/src/ExceptionBase.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.cpp -o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.cpp -o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionBPMAPData.cpp -o fusion/calvin_files/fusion/src/FusionBPMAPData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCDFData.cpp -o fusion/calvin_files/fusion/src/FusionCDFData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp -o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCELData.cpp -o fusion/calvin_files/fusion/src/FusionCELData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPData.cpp -o fusion/calvin_files/fusion/src/FusionCHPData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionProbeSetResults.cpp -o fusion/calvin_files/fusion/src/FusionProbeSetResults.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp -o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.cpp -o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPLegacyData.cpp -o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.cpp -o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPMultiDataData.cpp -o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPTilingData.cpp -o fusion/calvin_files/fusion/src/FusionCHPTilingData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPGenericData.cpp -o fusion/calvin_files/fusion/src/FusionCHPGenericData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPQuantificationData.cpp -o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.cpp -o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parameter/src/ParameterNameValueType.cpp -o fusion/calvin_files/parameter/src/ParameterNameValueType.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CDFFileReader.cpp -o fusion/calvin_files/parsers/src/CDFFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CelFileReader.cpp -o fusion/calvin_files/parsers/src/CelFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPFileReader.cpp -o fusion/calvin_files/parsers/src/CHPFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPMultiDataFileReader.cpp -o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPTilingFileReader.cpp -o fusion/calvin_files/parsers/src/CHPTilingFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPQuantificationFileReader.cpp -o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.cpp -o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataGroupHeaderReader.cpp -o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataGroupReader.cpp -o fusion/calvin_files/parsers/src/DataGroupReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataSetHeaderReader.cpp -o fusion/calvin_files/parsers/src/DataSetHeaderReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/DataSetReader.cpp -o fusion/calvin_files/parsers/src/DataSetReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/FileHeaderReader.cpp -o fusion/calvin_files/parsers/src/FileHeaderReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/FileInput.cpp -o fusion/calvin_files/parsers/src/FileInput.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/GenericDataHeaderReader.cpp -o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/parsers/src/GenericFileReader.cpp -o fusion/calvin_files/parsers/src/GenericFileReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/AffymetrixGuid.cpp -o fusion/calvin_files/utils/src/AffymetrixGuid.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/DateTime.cpp -o fusion/calvin_files/utils/src/DateTime.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/FileUtils.cpp -o fusion/calvin_files/utils/src/FileUtils.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/StringUtils.cpp -o fusion/calvin_files/utils/src/StringUtils.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/calvin_files/utils/src/checksum.cpp -o fusion/calvin_files/utils/src/checksum.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/BPMAPFileData.cpp -o fusion/file/BPMAPFileData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/BPMAPFileWriter.cpp -o fusion/file/BPMAPFileWriter.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/CDFFileData.cpp -o fusion/file/CDFFileData.o fusion/file/CDFFileData.cpp: In member function ‘bool affxcdf::CCDFFileData::ReadTextFormat()’: fusion/file/CDFFileData.cpp:858:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 858 | else if ( strncmp( subStr, CDFVERSION6, strlen(CDFVERSION6)) == 0) | ^~ fusion/file/CDFFileData.cpp:861:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 861 | if (m_Header.m_Version >= 6) | ^~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/CELFileData.cpp -o fusion/file/CELFileData.o fusion/file/CELFileData.cpp: In member function ‘float affxcel::CCELFileData::GetIntensity(int)’: fusion/file/CELFileData.cpp:2409:41: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2409 | fIntensity=MmGetFloat_I(&m_pEntries[index].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2414:41: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2414 | fIntensity=MmGetFloat_I(&(m_pEntries[index].Intensity)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2419:42: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2419 | fIntensity=MmGetUInt16_N(&(m_pTransciptomeEntries[index].Intensity)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function ‘int affxcel::CCELFileData::GetIntensities(int, std::vector&)’: fusion/file/CELFileData.cpp:2445:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2445 | intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2451:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2451 | intensities[idx]=MmGetFloat_I(&m_pEntries[idx].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2457:38: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2457 | intensities[idx]=MmGetUInt16_N(&m_pTransciptomeEntries[idx].Intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function ‘float affxcel::CCELFileData::GetStdv(int)’: fusion/file/CELFileData.cpp:2506:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2506 | fStdev=MmGetFloat_I(&m_pEntries[index].Stdv); | ^~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2509:37: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2509 | fStdev=MmGetFloat_I(&(m_pEntries[index].Stdv)); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2512:38: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2512 | fStdev=MmGetUInt16_N(&(m_pTransciptomeEntries[index].Stdv)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function ‘short int affxcel::CCELFileData::GetPixels(int)’: fusion/file/CELFileData.cpp:2551:38: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2551 | sPixels=MmGetInt16_I(&m_pEntries[index].Pixels); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:2554:38: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 2554 | sPixels=MmGetInt16_I(&m_pEntries[index].Pixels); | ^~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function ‘void affxcel::CCELFileData::SetIntensity(int, float)’: fusion/file/CELFileData.cpp:3194:30: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 3194 | MmSetFloat_I(&m_pEntries[index].Intensity,intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:3199:30: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 3199 | MmSetFloat_I(&m_pEntries[index].Intensity,intensity); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:3204:31: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 3204 | MmSetUInt16_N(&m_pTransciptomeEntries[index].Intensity,s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function ‘void affxcel::CCELFileData::SetStdv(int, float)’: fusion/file/CELFileData.cpp:3251:31: warning: taking address of packed member of ‘affxcel::_CELFileTranscriptomeEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 3251 | MmSetUInt16_N(&m_pTransciptomeEntries[index].Stdv,s); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp:3255:30: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 3255 | MmSetFloat_I(&m_pEntries[index].Stdv,stdev); | ^~~~~~~~~~~~~~~~~~~~~~~ fusion/file/CELFileData.cpp: In member function ‘void affxcel::CCELFileData::SetPixels(int, short int)’: fusion/file/CELFileData.cpp:3294:42: warning: taking address of packed member of ‘affxcel::_CELFileEntryType’ may result in an unaligned pointer value [-Waddress-of-packed-member] 3294 | MmSetUInt16_I((uint16_t*)&m_pEntries[index].Pixels,(uint16_t)pixels); | ^~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/CHPFileData.cpp -o fusion/file/CHPFileData.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/FileIO.cpp -o fusion/file/FileIO.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/FileWriter.cpp -o fusion/file/FileWriter.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/TsvFile/ClfFile.cpp -o fusion/file/TsvFile/ClfFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/TsvFile/PgfFile.cpp -o fusion/file/TsvFile/PgfFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/file/TsvFile/TsvFile.cpp -o fusion/file/TsvFile/TsvFile.o fusion/file/TsvFile/TsvFile.cpp: In member function ‘void affx::TsvFile::dump_bindings()’: fusion/file/TsvFile/TsvFile.cpp:3918:20: warning: format ‘%p’ expects argument of type ‘void*’, but argument 3 has type ‘affx::TsvFileBinding*’ [-Wformat=] 3918 | printf("%3d : %p : bound to clvl=%2d cidx=%2d cname='%s')\n", | ~^ | | | void* 3919 | vi,var, | ~~~ | | | affx::TsvFileBinding* fusion/file/TsvFile/TsvFile.cpp: In static member function ‘static int affx::TsvFile::getLineCountInFile(const std::string&, bool)’: fusion/file/TsvFile/TsvFile.cpp:4921:20: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 4921 | catch (exception e) { | ^ fusion/file/TsvFile/TsvFile.cpp: In static member function ‘static int affx::TsvFile::replaceCharInFile(const std::string&, char, char, bool)’: fusion/file/TsvFile/TsvFile.cpp:4970:20: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 4970 | catch (exception e) { | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/AffxByteArray.cpp -o fusion/util/AffxByteArray.o fusion/util/AffxByteArray.cpp: In member function ‘const AffxByteArray& AffxByteArray::operator=(const AffxByteArray&)’: fusion/util/AffxByteArray.cpp:320:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 320 | if (this == &ba) | ^~ fusion/util/AffxByteArray.cpp:323:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 323 | empty(); | ^~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/AffxConv.cpp -o fusion/util/AffxConv.o fusion/util/AffxConv.cpp: In function ‘std::string getInt(int, bool)’: fusion/util/AffxConv.cpp:124:15: warning: self-comparison always evaluates to false [-Wtautological-compare] 124 | if (i != i) {return "nan";} | ~ ^~ ~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/MsgStream.cpp -o fusion/util/MsgStream.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/Util.cpp -o fusion/util/Util.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/Err.cpp -o fusion/util/Err.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/Fs.cpp -o fusion/util/Fs.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/Verbose.cpp -o fusion/util/Verbose.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/RowFile.cpp -o fusion/util/RowFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/TableFile.cpp -o fusion/util/TableFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c fusion/util/Convert.cpp -o fusion/util/Convert.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c R_affx_cdf_parser.cpp -o R_affx_cdf_parser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c R_affx_cdf_extras.cpp -o R_affx_cdf_extras.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c R_affx_bpmap_parser.cpp -o R_affx_bpmap_parser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c R_affx_clf_pgf_parser.cpp -o R_affx_clf_pgf_parser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-sign-compare -O0 -c R_affx_chp_parser.cpp -o R_affx_chp_parser.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -Ifusion/calvin_files/array/src -Ifusion/calvin_files/data/src -Ifusion/calvin_files/exception/src -Ifusion/calvin_files/fusion/src -Ifusion/calvin_files/fusion/src/GCOSAdapter -Ifusion/calvin_files/fusion/src/CalvinAdapter -Ifusion/calvin_files/parameter/src -Ifusion/calvin_files/parsers/src -Ifusion/calvin_files/portability/src -Ifusion/calvin_files/template/src -Ifusion/calvin_files/utils/src -Ifusion/calvin_files/writers/src -Ifusion/file -Ifusion/file/TsvFile -Ifusion/portability -Ifusion/util -Ifusion -D_USE_MEM_MAPPING_ -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c 000.init.c -o 000.init.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o affxparser.so fusion/calvin_files/data/src/CDFData.o fusion/calvin_files/data/src/CDFProbeGroupInformation.o fusion/calvin_files/data/src/CDFProbeInformation.o fusion/calvin_files/data/src/CDFProbeSetInformation.o fusion/calvin_files/data/src/CDFQCProbeInformation.o fusion/calvin_files/data/src/CDFQCProbeSetInformation.o fusion/calvin_files/data/src/CELData.o fusion/calvin_files/data/src/CHPBackgroundZone.o fusion/calvin_files/data/src/CHPData.o fusion/calvin_files/data/src/CHPExpressionEntry.o fusion/calvin_files/data/src/CHPMultiDataData.o fusion/calvin_files/data/src/CHPTilingData.o fusion/calvin_files/data/src/CHPQuantificationData.o fusion/calvin_files/data/src/CHPQuantificationDetectionData.o fusion/calvin_files/data/src/CHPGenotypeEntry.o fusion/calvin_files/data/src/CHPUniversalEntry.o fusion/calvin_files/data/src/ColumnInfo.o fusion/calvin_files/data/src/DataGroup.o fusion/calvin_files/data/src/DataGroupHeader.o fusion/calvin_files/data/src/DataSet.o fusion/calvin_files/data/src/DataSetHeader.o fusion/calvin_files/data/src/FileHeader.o fusion/calvin_files/data/src/GenericData.o fusion/calvin_files/data/src/GenericDataHeader.o fusion/calvin_files/exception/src/ExceptionBase.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o fusion/calvin_files/fusion/src/CalvinAdapter/CalvinCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionBPMAPData.o fusion/calvin_files/fusion/src/FusionCDFData.o fusion/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o fusion/calvin_files/fusion/src/FusionCELData.o fusion/calvin_files/fusion/src/FusionCHPData.o fusion/calvin_files/fusion/src/FusionProbeSetResults.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o fusion/calvin_files/fusion/src/GCOSAdapter/GCOSCHPDataAdapter.o fusion/calvin_files/fusion/src/FusionCHPLegacyData.o fusion/calvin_files/fusion/src/FusionCHPMultiDataAccessor.o fusion/calvin_files/fusion/src/FusionCHPMultiDataData.o fusion/calvin_files/fusion/src/FusionCHPTilingData.o fusion/calvin_files/fusion/src/FusionCHPGenericData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationData.o fusion/calvin_files/fusion/src/FusionCHPQuantificationDetectionData.o fusion/calvin_files/parameter/src/ParameterNameValueType.o fusion/calvin_files/parsers/src/CDFFileReader.o fusion/calvin_files/parsers/src/CelFileReader.o fusion/calvin_files/parsers/src/CHPFileReader.o fusion/calvin_files/parsers/src/CHPMultiDataFileReader.o fusion/calvin_files/parsers/src/CHPTilingFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationFileReader.o fusion/calvin_files/parsers/src/CHPQuantificationDetectionFileReader.o fusion/calvin_files/parsers/src/DataGroupHeaderReader.o fusion/calvin_files/parsers/src/DataGroupReader.o fusion/calvin_files/parsers/src/DataSetHeaderReader.o fusion/calvin_files/parsers/src/DataSetReader.o fusion/calvin_files/parsers/src/FileHeaderReader.o fusion/calvin_files/parsers/src/FileInput.o fusion/calvin_files/parsers/src/GenericDataHeaderReader.o fusion/calvin_files/parsers/src/GenericFileReader.o fusion/calvin_files/utils/src/AffymetrixGuid.o fusion/calvin_files/utils/src/DateTime.o fusion/calvin_files/utils/src/FileUtils.o fusion/calvin_files/utils/src/StringUtils.o fusion/calvin_files/utils/src/checksum.o fusion/file/BPMAPFileData.o fusion/file/BPMAPFileWriter.o fusion/file/CDFFileData.o fusion/file/CELFileData.o fusion/file/CHPFileData.o fusion/file/FileIO.o fusion/file/FileWriter.o fusion/file/TsvFile/ClfFile.o fusion/file/TsvFile/PgfFile.o fusion/file/TsvFile/TsvFile.o fusion/util/AffxByteArray.o fusion/util/AffxConv.o fusion/util/MsgStream.o fusion/util/Util.o fusion/util/Err.o fusion/util/Fs.o fusion/util/Verbose.o fusion/util/RowFile.o fusion/util/TableFile.o fusion/util/Convert.o R_affx_cel_parser.o R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o R_affx_clf_pgf_parser.o R_affx_chp_parser.o 000.init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpkZcUr6/R.INSTALL3dd9df7e3b35bc/affxparser/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-affxparser/00new/affxparser/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affxparser) begin installing package ‘oligo’ * installing *source* package ‘oligo’ ... ** this is package ‘oligo’ version ‘1.74.0’ ** package ‘oligo’ successfully unpacked and MD5 sums checked ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... gcc-15 -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpPOhySB/R.INSTALL3df46359f8d8e9/oligo/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c DABG.c -o DABG.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ParserGzXYS.c -o ParserGzXYS.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ParserXYS.c -o ParserXYS.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c baseProfile.c -o baseProfile.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c basecontent.c -o basecontent.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c chipbackground.c -o chipbackground.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mas5calls.c -o mas5calls.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rma2.c -o rma2.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rma_common.c -o rma_common.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/preprocessCore/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trimmed.c -o trimmed.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpPOhySB/R.INSTALL3df46359f8d8e9/oligo/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-oligo/00new/oligo/libs ** R ** inst ** byte-compile and prepare package for lazy loading Note: in method for ‘pm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" Note: in method for ‘mm<-’ with signature ‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’: expanding the signature to include omitted arguments in definition: subset = "missing", target = "missing" ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (oligo) begin installing package ‘pdInfoBuilder’ * installing *source* package ‘pdInfoBuilder’ ... ** this is package ‘pdInfoBuilder’ version ‘1.74.0’ ** package ‘pdInfoBuilder’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGKzI2Y/R.INSTALL3df5f81e119380/pdInfoBuilder/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pdInfoBuilder.c -o pdInfoBuilder.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o pdInfoBuilder.so pdInfoBuilder.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGKzI2Y/R.INSTALL3df5f81e119380/pdInfoBuilder/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pdInfoBuilder/00new/pdInfoBuilder/libs ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘pdInfoBuilder’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘pdInfoBuilder’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘pdInfoBuilder’ ** testing if installed package keeps a record of temporary installation path * DONE (pdInfoBuilder) checking R.devices_2.17.3.tar.gz ... checking aroma.core_3.3.2.tar.gz ... checking aroma.affymetrix_3.2.3.tar.gz ... checking cramR_0.1.1.tar.gz ... checking dataquieR_2.5.1.tar.gz ... checking eoffice_0.2.2.tar.gz ... checking inDAGO_1.0.3.tar.gz ... checking inpdfr_0.1.12.tar.gz ... checking PointedSDMs_2.1.4.tar.gz ... checking babel_0.3-0.tar.gz ... checking biplotEZ_2.2.tar.gz ... checking matrixStats_1.5.0.tar.gz ... checking metabodecon_1.6.2.tar.gz ... checking PSCBS_0.68.0.tar.gz ... checking R.rsp_0.46.0.tar.gz ... Depends: Package: R.devices Depends: R (>= 2.14.0) Imports: grDevices, R.methodsS3 (>= 1.8.1), R.oo (>= 1.24.0), R.utils (>= 2.10.1), base64enc (>= 0.1-2) Timings: user system elapsed R.devices 40.219 5.676 48.667 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 1 13 Check results summary: R.devices ... OK rdepends_aroma.affymetrix ... OK rdepends_aroma.core ... OK rdepends_babel ... OK rdepends_biplotEZ ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_cramR ... OK rdepends_dataquieR ... OK rdepends_eoffice ... OK rdepends_inDAGO ... OK rdepends_inpdfr ... OK rdepends_matrixStats ... OK rdepends_metabodecon ... OK rdepends_PointedSDMs ... OK rdepends_PSCBS ... OK rdepends_R.rsp ... OK Check results changes: Package: babel Check: CRAN incoming feasibility Old result: NOTE Package: inpdfr Check: CRAN incoming feasibility Old result: NOTE