downloading reverse dependencies ... downloading biplotbootGUI_1.3.tar.gz ... ok downloading cncaGUI_1.1.tar.gz ... ok downloading ConvergenceConcepts_1.2.3.tar.gz ... ok downloading forensim_4.3.3.tar.gz ... ok downloading idendr0_1.5.3.tar.gz ... ok downloading InterfaceqPCR_1.0.1.tar.gz ... ok downloading leem_0.2.0.tar.gz ... ok downloading multibiplotGUI_1.1.tar.gz ... ok downloading plfMA_2.0.tar.gz ... ok downloading RcmdrPlugin.PcaRobust_1.1.4.tar.gz ... ok downloading rriskDistributions_2.1.2.tar.gz ... ok downloading uHMM_1.0.tar.gz ... ok downloading ade4TkGUI_0.3.4.tar.gz ... ok downloading adehabitatHR_0.4.22.tar.gz ... ok downloading adehabitatHS_0.3.18.tar.gz ... ok downloading adehabitatLT_0.3.28.tar.gz ... ok downloading adehabitatMA_0.3.17.tar.gz ... ok downloading aplpack_1.3.5.tar.gz ... ok downloading asbio_1.11.tar.gz ... ok downloading baggingbwsel_1.1.tar.gz ... ok downloading biotools_4.3.tar.gz ... ok downloading dynBiplotGUI_1.1.6.tar.gz ... ok downloading FFD_1.0-9.tar.gz ... ok downloading fmri_1.9.12.1.tar.gz ... ok downloading geoelectrics_0.2.2.tar.gz ... ok downloading LogConcDEAD_1.6-12.tar.gz ... ok downloading maGUI_4.0.tar.gz ... ok downloading MareyMap_1.3.10.tar.gz ... ok downloading MCPtests_1.0.1.tar.gz ... ok downloading midrangeMCP_3.1.1.tar.gz ... ok downloading misc3d_0.9-1.tar.gz ... ok downloading mritc_0.5-3.tar.gz ... ok downloading RcmdrPlugin.RiskDemo_3.2.tar.gz ... ok downloading RcmdrPlugin.TeachingDemos_1.2-0.tar.gz ... ok downloading RcmdrPlugin.TeachStat_1.1.3.tar.gz ... ok downloading relMix_1.4.1.tar.gz ... ok downloading RHRV_5.0.0.tar.gz ... ok downloading rpanel_1.1-5.2.tar.gz ... ok downloading RSA_0.10.6.tar.gz ... ok downloading RSAtools_0.1.1.tar.gz ... ok downloading sm_2.2-6.0.tar.gz ... ok downloading smovie_1.1.6.tar.gz ... ok downloading sudoku_2.8.tar.gz ... ok downloading TeachingDemos_2.13.tar.gz ... ok downloading TextMiningGUI_0.3.tar.gz ... ok downloading TVMM_3.2.1.tar.gz ... ok installing dependencies ‘adehabitatHR’, ‘adimpro’, ‘affy’, ‘aws’, ‘beadarray’, ‘Category’, ‘corrr’, ‘demography’, ‘dendroextras’, ‘DendSer’, ‘denstrip’, ‘DescToolsAddIns’, ‘Familias’, ‘ftsa’, ‘GEOmetadb’, ‘GOstats’, ‘HMM’, ‘IndexNumR’, ‘kedd’, ‘KEGGgraph’, ‘lomb’, ‘lumi’, ‘nonlinearTseries’, ‘oligo’, ‘pdInfoBuilder’, ‘pedFamilias’, ‘RandomFields’, ‘randtests’, ‘rggobi’, ‘RSA’, ‘SMR’, ‘soilphysics’, ‘SpatialEpi’, ‘ssize’, ‘tkrplot’, ‘tkRplotR’ Warning: packages ‘rggobi’, ‘RandomFields’ 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 ‘scrime’, ‘TxDb.Hsapiens.UCSC.hg19.knownGene’, ‘bumphunter’, ‘beanplot’, ‘siggenes’, ‘FDb.InfiniumMethylation.hg19’, ‘minfi’, ‘base64’, ‘awsMethods’, ‘affxparser’, ‘oligoClasses’, ‘methylumi’, ‘affyio’, ‘BeadDataPackR’, ‘illuminaio’, ‘AnnotationForge’, ‘HMDHFDplus’ begin installing package ‘scrime’ begin installing package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ begin installing package ‘bumphunter’ begin installing package ‘beanplot’ begin installing package ‘base64’ begin installing package ‘awsMethods’ begin installing package ‘affxparser’ begin installing package ‘affyio’ begin installing package ‘BeadDataPackR’ begin installing package ‘AnnotationForge’ begin installing package ‘HMDHFDplus’ begin installing package ‘dendroextras’ begin installing package ‘DendSer’ begin installing package ‘tkRplotR’ begin installing package ‘HMM’ begin installing package ‘adehabitatHR’ begin installing package ‘kedd’ begin installing package ‘soilphysics’ begin installing package ‘SpatialEpi’ begin installing package ‘ssize’ begin installing package ‘GEOmetadb’ begin installing package ‘KEGGgraph’ begin installing package ‘Category’ begin installing package ‘SMR’ begin installing package ‘ftsa’ begin installing package ‘IndexNumR’ begin installing package ‘randtests’ begin installing package ‘Familias’ * installing *source* package ‘base64’ ... ** this is package ‘base64’ version ‘2.0.2’ ** package ‘base64’ 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 (base64) begin installing package ‘pedFamilias’ * installing *source* package ‘dendroextras’ ... ** this is package ‘dendroextras’ version ‘0.2.3’ ** package ‘dendroextras’ 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 (dendroextras) begin installing package ‘nonlinearTseries’ * installing *source* package ‘HMM’ ... ** this is package ‘HMM’ version ‘1.0.2’ ** package ‘HMM’ 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 (HMM) begin installing package ‘lomb’ * installing *source* package ‘ssize’ ... ** this is package ‘ssize’ version ‘1.82.0’ ** 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 (ssize) begin installing package ‘denstrip’ * 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-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBP68Jx/R.INSTALL6285d7c5e089/awsMethods/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o awsMethods.so init.o omp_funcs.o -fopenmp -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBP68Jx/R.INSTALL6285d7c5e089/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 ‘RSA’ * installing *source* package ‘randtests’ ... ** this is package ‘randtests’ version ‘1.0.2’ ** package ‘randtests’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (randtests) begin installing package ‘corrr’ * installing *source* package ‘beanplot’ ... ** this is package ‘beanplot’ version ‘1.3.1’ ** package ‘beanplot’ 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 (beanplot) begin installing package ‘DescToolsAddIns’ * installing *source* package ‘tkRplotR’ ... ** this is package ‘tkRplotR’ version ‘0.1.7’ ** package ‘tkRplotR’ 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 (tkRplotR) begin installing package ‘tkrplot’ * installing *source* package ‘BeadDataPackR’ ... ** this is package ‘BeadDataPackR’ version ‘1.60.0’ ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBQkPQT/R.INSTALL628583c6880c0/BeadDataPackR/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BeadDataPackR.c -o BeadDataPackR.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_BeadDataPackR.c -o R_init_BeadDataPackR.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o BeadDataPackR.so BeadDataPackR.o R_init_BeadDataPackR.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpBQkPQT/R.INSTALL628583c6880c0/BeadDataPackR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BeadDataPackR/00new/BeadDataPackR/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 (BeadDataPackR) begin installing package ‘illuminaio’ * installing *source* package ‘DendSer’ ... ** this is package ‘DendSer’ version ‘1.0.2’ ** package ‘DendSer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXkK6xR/R.INSTALL6288215811cb1/DendSer/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c DendSer_init.c -o DendSer_init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c carct.c -o carct.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cbar.c -o cbar.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c clpl.c -o clpl.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cpl.c -o cpl.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o DendSer.so DendSer_init.o carct.o cbar.o clpl.o cpl.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXkK6xR/R.INSTALL6288215811cb1/DendSer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DendSer/00new/DendSer/libs ** R ** demo ** byte-compile and prepare package for lazy loading Warning in seriation::set_criterion_method("dist", "BAR", criterion_method_dist_BAR, : Entry with name ‘BAR’ already exists! Modifying entry. ** 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 (DendSer) begin installing package ‘aws’ * installing *source* package ‘GEOmetadb’ ... ** this is package ‘GEOmetadb’ version ‘1.70.0’ ** 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 (GEOmetadb) begin installing package ‘adimpro’ * installing *source* package ‘IndexNumR’ ... ** this is package ‘IndexNumR’ version ‘0.6.0’ ** package ‘IndexNumR’ 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 (IndexNumR) * installing *source* package ‘denstrip’ ... ** this is package ‘denstrip’ version ‘1.5.5’ ** package ‘denstrip’ 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 (denstrip) * installing *source* package ‘illuminaio’ ... ** this is package ‘illuminaio’ version ‘0.50.0’ ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp63sSbX/R.INSTALL62f44672e5a7c/illuminaio/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -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 gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c des.c -o des.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c local_des.c -o local_des.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o illuminaio.so 000.init.o des.o local_des.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp63sSbX/R.INSTALL62f44672e5a7c/illuminaio/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-illuminaio/00new/illuminaio/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 (illuminaio) begin installing package ‘beadarray’ * installing *source* package ‘tkrplot’ ... ** this is package ‘tkrplot’ version ‘0.0-30’ ** using staged installation configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxlYHcZ/R.INSTALL62f00ba00ab6/tkrplot/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/include/tcl8.6 -I/usr/include/tcl8.6 -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tcltkimg.c -o tcltkimg.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o tkrplot.so tcltkimg.o -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -L/usr/lib/x86_64-linux-gnu -ltk8.6 -lX11 -lXss -lXext -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxlYHcZ/R.INSTALL62f00ba00ab6/tkrplot/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-tkrplot/00new/tkrplot/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 (tkrplot) * installing *source* package ‘scrime’ ... ** this is package ‘scrime’ version ‘1.3.5’ ** package ‘scrime’ 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 (scrime) begin installing package ‘siggenes’ * installing *source* package ‘HMDHFDplus’ ... ** this is package ‘HMDHFDplus’ version ‘2.0.6’ ** package ‘HMDHFDplus’ 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 (HMDHFDplus) * installing *source* package ‘corrr’ ... ** this is package ‘corrr’ version ‘0.4.4’ ** package ‘corrr’ 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 (corrr) * installing *source* package ‘KEGGgraph’ ... ** this is package ‘KEGGgraph’ version ‘1.68.0’ ** 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 (KEGGgraph) * installing *source* package ‘pedFamilias’ ... ** this is package ‘pedFamilias’ version ‘0.2.4’ ** package ‘pedFamilias’ 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 ** 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 (pedFamilias) * installing *source* package ‘SMR’ ... ** this is package ‘SMR’ version ‘2.1.0’ ** package ‘SMR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp6IxwpL/R.INSTALL628a6c54a461/SMR/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gausslegendre.cpp -o gausslegendre.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o SMR.so RcppExports.o gausslegendre.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp6IxwpL/R.INSTALL628a6c54a461/SMR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-SMR/00new/SMR/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 (SMR) * installing *source* package ‘lomb’ ... ** this is package ‘lomb’ version ‘2.5.0’ ** package ‘lomb’ 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 (lomb) * installing *source* package ‘affyio’ ... ** this is package ‘affyio’ version ‘1.78.0’ ** using staged installation checking for gcc... gcc-14 -std=gnu23 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-14 -std=gnu23 accepts -g... yes checking for gcc-14 -std=gnu23 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc-14 -std=gnu23 -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-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvtTO4N/R.INSTALL6284f6c1d61e3/affyio/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -shared -L/home/hornik/tmp/R/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/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpvtTO4N/R.INSTALL6284f6c1d61e3/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 ‘oligoClasses’ begin installing package ‘affy’ * installing *source* package ‘kedd’ ... ** this is package ‘kedd’ version ‘1.0.4’ ** package ‘kedd’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (kedd) * installing *source* package ‘adehabitatHR’ ... ** this is package ‘adehabitatHR’ version ‘0.4.22’ ** package ‘adehabitatHR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpsllmoo/R.INSTALL6288e1e9fd397/adehabitatHR/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tests.c -o tests.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o adehabitatHR.so init.o tests.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpsllmoo/R.INSTALL6288e1e9fd397/adehabitatHR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-adehabitatHR/00new/adehabitatHR/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 (adehabitatHR) * installing *source* package ‘DescToolsAddIns’ ... ** this is package ‘DescToolsAddIns’ version ‘1.12’ ** package ‘DescToolsAddIns’ 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 ** 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 (DescToolsAddIns) * installing *source* package ‘RSA’ ... ** this is package ‘RSA’ version ‘0.10.6’ ** package ‘RSA’ 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 ** 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 (RSA) * installing *source* package ‘adimpro’ ... ** this is package ‘adimpro’ version ‘0.9.7.2’ ** package ‘adimpro’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpPaoj1l/R.INSTALL632027be21d3c/adimpro/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c aniso.f -o aniso.o aniso.f:206:64: 206 | integer i1,i2,j1,j2,ja1,je1,ja2,je2,l,k,n,info,kdv,jx,jy,i, | 1 Warning: Unused variable ‘i’ declared at (1) [-Wunused-variable] gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awsimage.f -o awsimage.o awsimage.f:254:72: 254 | thnew(k,i1,i2)=FLOOR(swjy(k,thrednr)/swj) | ^ Warning: ‘thrednr’ may be used uninitialized [-Wmaybe-uninitialized] awsimage.f:198:47: 198 | integer ih,ih1,ii,i1,i2,j1,j2,k,n,thrednr, | ^ note: ‘thrednr’ was declared here gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awspimage.f -o awspimage.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c demosaic.f -o demosaic.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c edges.f -o edges.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.f -o misc.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c segment.f -o segment.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c shrink.f -o shrink.o shrink.f:279:72: 279 | call median3(z(1,1,thrednr),k,yy,tol) | ^ Warning: ‘thrednr’ may be used uninitialized [-Wmaybe-uninitialized] shrink.f:205:62: 205 | integer iy1,iy2,ja1,ja2,je1,je2,jx1,jx2,k,method,thrednr | ^ note: ‘thrednr’ was declared here shrink.f:190:72: 190 | call median1(z(1,thrednr),k,yy,tol) | ^ Warning: ‘thrednr’ may be used uninitialized [-Wmaybe-uninitialized] shrink.f:131:62: 131 | integer iy1,iy2,ja1,ja2,je1,je2,jx1,jx2,k,method,thrednr | ^ note: ‘thrednr’ was declared here gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smsensor.f -o smsensor.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o adimpro.so Rentries.o aniso.o awsimage.o awspimage.o demosaic.o edges.o init.o misc.o segment.o shrink.o smsensor.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpPaoj1l/R.INSTALL632027be21d3c/adimpro/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-adimpro/00new/adimpro/libs ** R ** demo ** 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 (adimpro) * installing *source* package ‘Familias’ ... ** this is package ‘Familias’ version ‘2.6.3’ ** package ‘Familias’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpK3FCrG/R.INSTALL628ad30fedbcb/Familias/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Element.cpp -o Element.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FamInterface.cpp -o FamInterface.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c GroupOfPersons.cpp -o GroupOfPersons.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Node.cpp -o Node.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Pedigree.cpp -o Pedigree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PedigreeList.cpp -o PedigreeList.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PedigreeSet.cpp -o PedigreeSet.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c aldata.cpp -o aldata.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c alsys.cpp -o alsys.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cutset.cpp -o cutset.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c family.cpp -o family.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c help.cpp -o help.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c main.cpp -o main.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c odds.cpp -o odds.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pater.cpp -o pater.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c person.cpp -o person.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c read.cpp -o read.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c special.cpp -o special.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c table.cpp -o table.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o Familias.so Element.o FamInterface.o GroupOfPersons.o Node.o Pedigree.o PedigreeList.o PedigreeSet.o aldata.o alsys.o cutset.o family.o help.o main.o odds.o pater.o person.o read.o registerDynamicSymbol.o special.o table.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpK3FCrG/R.INSTALL628ad30fedbcb/Familias/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Familias/00new/Familias/libs ** R ** data ** 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 (Familias) * installing *source* package ‘siggenes’ ... ** this is package ‘siggenes’ version ‘1.82.0’ ** 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 (siggenes) * installing *source* package ‘AnnotationForge’ ... ** this is package ‘AnnotationForge’ version ‘1.50.0’ ** 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 (AnnotationForge) * installing *source* package ‘affy’ ... ** this is package ‘affy’ version ‘1.86.0’ ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... gcc-14 -std=gnu23 -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-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGy6iBH/R.INSTALL634c17d9ff7e/affy/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGy6iBH/R.INSTALL634c17d9ff7e/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) * 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-14 (Debian 14.2.0-19) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZ6jaqL/R.INSTALL63009564d8bd7/aws/src' gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ICIsmooth.f -o ICIsmooth.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awslp.f -o awslp.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awswghts.f -o awswghts.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c caws.f -o caws.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cawsmask.f -o cawsmask.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c esiglike.f -o esiglike.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c estimateComplexSigma.f -o estimateComplexSigma.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.f -o misc.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nlmeans.f -o nlmeans.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c pcaws.f -o pcaws.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c segment.f -o segment.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smooth3d.f -o smooth3d.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smse3.f -o smse3.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c varest.f -o varest.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/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/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZ6jaqL/R.INSTALL63009564d8bd7/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) * installing *source* package ‘ftsa’ ... ** this is package ‘ftsa’ version ‘6.6’ ** package ‘ftsa’ 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 (ftsa) begin installing package ‘demography’ * installing *source* package ‘soilphysics’ ... ** this is package ‘soilphysics’ version ‘5.0’ ** package ‘soilphysics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (soilphysics) * installing *source* package ‘Category’ ... ** this is package ‘Category’ version ‘2.74.0’ ** 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 (Category) begin installing package ‘GOstats’ * installing *source* package ‘SpatialEpi’ ... ** this is package ‘SpatialEpi’ version ‘1.2.8’ ** package ‘SpatialEpi’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpP2QOhz/R.INSTALL628935967208d/SpatialEpi/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bayes_cluster.cpp -o bayes_cluster.o bayes_cluster.cpp: In function ‘Rcpp::List return_local_moves(Rcpp::NumericVector, Rcpp::List, Rcpp::NumericMatrix)’: bayes_cluster.cpp:399:23: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized] 399 | for(int z=start; z (m - *nmads*ma))){ | ~~~^~~~~~~~~~~~ findAllOutliers.c:155:16: note: ‘m’ was declared here 155 | double m, ma; | ^ findAllOutliers.c:189:15: warning: ‘ma’ may be used uninitialized [-Wmaybe-uninitialized] 189 | if(ma==0) { | ^ findAllOutliers.c:155:19: note: ‘ma’ was declared here 155 | double m, ma; | ^~ findAllOutliers.c: In function ‘findAllOutliers’: findAllOutliers.c:246:20: warning: ‘status’ may be used uninitialized [-Wmaybe-uninitialized] 246 | free(status->validInds); | ~~~~~~^~~~~~~~~~~ findAllOutliers.c:226:27: note: ‘status’ was declared here 226 | beadStatusStruct *status; | ^~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c imageProcessing.c -o imageProcessing.o imageProcessing.c: In function ‘illuminaBackground’: imageProcessing.c:88: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 88 | #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function ‘medianBackground’: imageProcessing.c:135: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 135 | #pragma omp parallel shared(nthreads, nbeads, imageHeight, pixelMatrix, coords) private(tid, start, end) imageProcessing.c: In function ‘illuminaSharpen’: imageProcessing.c:244: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 244 | #pragma omp parallel for private(i, j) shared(sharpened) num_threads(2) imageProcessing.c:251: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas] 251 | #pragma omp parallel for private(i, j, sum) shared(sharpened) num_threads(2) gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXalnLH/R.INSTALL632cd403419b2/beadarray/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-beadarray/00new/beadarray/libs ** 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 ** 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 (beadarray) * installing *source* package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ... ** this is package ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ version ‘3.2.2’ ** 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 (TxDb.Hsapiens.UCSC.hg19.knownGene) begin installing package ‘FDb.InfiniumMethylation.hg19’ * installing *source* package ‘bumphunter’ ... ** this is package ‘bumphunter’ version ‘1.50.0’ ** 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 (bumphunter) begin installing package ‘minfi’ * installing *source* package ‘demography’ ... ** this is package ‘demography’ version ‘2.0’ ** package ‘demography’ 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 (demography) * installing *source* package ‘oligoClasses’ ... ** this is package ‘oligoClasses’ version ‘1.70.0’ ** 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 ‘GOstats’ ... ** this is package ‘GOstats’ version ‘2.74.0’ ** 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 (GOstats) * installing *source* package ‘nonlinearTseries’ ... ** this is package ‘nonlinearTseries’ version ‘0.3.1’ ** package ‘nonlinearTseries’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOcFl66/R.INSTALL62c894c302dfa/nonlinearTseries/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c ANN.cpp -o ANN.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c DFA.cpp -o DFA.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c NN.cpp -o NN.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bd_fix_rad_search.cpp -o bd_fix_rad_search.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bd_pr_search.cpp -o bd_pr_search.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bd_search.cpp -o bd_search.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bd_tree.cpp -o bd_tree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c brute.cpp -o brute.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c corr_dim.cpp -o corr_dim.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c generic_functions.cpp -o generic_functions.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c information_dimension.cpp -o information_dimension.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kd_dump.cpp -o kd_dump.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kd_fix_rad_search.cpp -o kd_fix_rad_search.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kd_pr_search.cpp -o kd_pr_search.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kd_search.cpp -o kd_search.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kd_split.cpp -o kd_split.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kd_tree.cpp -o kd_tree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c kd_util.cpp -o kd_util.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c lyapunov_exponent.cpp -o lyapunov_exponent.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mutual_information.cpp -o mutual_information.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c neighbour_search.cpp -o neighbour_search.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c neighbour_search_wrapper.cpp -o neighbour_search_wrapper.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nonlinear_noise_reduction.cpp -o nonlinear_noise_reduction.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c poincare_map.cpp -o poincare_map.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rqa.cpp -o rqa.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c space_time_plot.cpp -o space_time_plot.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -IANN -DRANN -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/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o nonlinearTseries.so ANN.o DFA.o NN.o RcppExports.o bd_fix_rad_search.o bd_pr_search.o bd_search.o bd_tree.o brute.o corr_dim.o generic_functions.o information_dimension.o kd_dump.o kd_fix_rad_search.o kd_pr_search.o kd_search.o kd_split.o kd_tree.o kd_util.o lyapunov_exponent.o mutual_information.o neighbour_search.o neighbour_search_wrapper.o nonlinear_noise_reduction.o poincare_map.o rqa.o space_time_plot.o utils.o -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOcFl66/R.INSTALL62c894c302dfa/nonlinearTseries/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-nonlinearTseries/00new/nonlinearTseries/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 (nonlinearTseries) * installing *source* package ‘FDb.InfiniumMethylation.hg19’ ... ** this is package ‘FDb.InfiniumMethylation.hg19’ version ‘2.2.0’ ** using staged installation ** R ** data ** demo ** 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 (FDb.InfiniumMethylation.hg19) * installing *source* package ‘affxparser’ ... ** this is package ‘affxparser’ version ‘1.80.0’ ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDQd3c4/R.INSTALL628793e4b9499/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R/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/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDQd3c4/R.INSTALL628793e4b9499/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 ‘minfi’ ... ** this is package ‘minfi’ version ‘1.54.1’ ** 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 (minfi) begin installing package ‘methylumi’ * installing *source* package ‘oligo’ ... ** this is package ‘oligo’ version ‘1.72.0’ ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... gcc-14 -std=gnu23 -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-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHGNGNy/R.INSTALL63c5a50665047/oligo/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -shared -L/home/hornik/tmp/R/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/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHGNGNy/R.INSTALL63c5a50665047/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 ‘methylumi’ ... ** this is package ‘methylumi’ version ‘2.54.0’ ** 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 (methylumi) begin installing package ‘lumi’ * installing *source* package ‘pdInfoBuilder’ ... ** this is package ‘pdInfoBuilder’ version ‘1.72.0’ ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpzZaXPv/R.INSTALL63e181d4aa1c1/pdInfoBuilder/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o pdInfoBuilder.so pdInfoBuilder.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpzZaXPv/R.INSTALL63e181d4aa1c1/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) * installing *source* package ‘lumi’ ... ** this is package ‘lumi’ version ‘2.60.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** 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: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package can be loaded from final location No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘lumi’ ** testing if installed package keeps a record of temporary installation path * DONE (lumi) checking tkrplot_0.0-30.tar.gz ... checking biplotbootGUI_1.3.tar.gz ... checking ConvergenceConcepts_1.2.3.tar.gz ... checking cncaGUI_1.1.tar.gz ... checking idendr0_1.5.3.tar.gz ... checking forensim_4.3.3.tar.gz ... checking InterfaceqPCR_1.0.1.tar.gz ... checking leem_0.2.0.tar.gz ... checking multibiplotGUI_1.1.tar.gz ... checking plfMA_2.0.tar.gz ... checking uHMM_1.0.tar.gz ... checking RcmdrPlugin.PcaRobust_1.1.4.tar.gz ... checking rriskDistributions_2.1.2.tar.gz ... checking ade4TkGUI_0.3.4.tar.gz ... checking adehabitatHR_0.4.22.tar.gz ... checking adehabitatHS_0.3.18.tar.gz ... checking adehabitatLT_0.3.28.tar.gz ... checking adehabitatMA_0.3.17.tar.gz ... checking aplpack_1.3.5.tar.gz ... checking asbio_1.11.tar.gz ... checking baggingbwsel_1.1.tar.gz ... checking biotools_4.3.tar.gz ... checking dynBiplotGUI_1.1.6.tar.gz ... checking FFD_1.0-9.tar.gz ... checking fmri_1.9.12.1.tar.gz ... checking geoelectrics_0.2.2.tar.gz ... checking LogConcDEAD_1.6-12.tar.gz ... checking maGUI_4.0.tar.gz ... checking misc3d_0.9-1.tar.gz ... checking MareyMap_1.3.10.tar.gz ... checking RcmdrPlugin.RiskDemo_3.2.tar.gz ... checking TextMiningGUI_0.3.tar.gz ... checking midrangeMCP_3.1.1.tar.gz ... checking mritc_0.5-3.tar.gz ... checking RcmdrPlugin.TeachingDemos_1.2-0.tar.gz ... checking RHRV_5.0.0.tar.gz ... checking smovie_1.1.6.tar.gz ... checking sudoku_2.8.tar.gz ... checking MCPtests_1.0.1.tar.gz ... checking TeachingDemos_2.13.tar.gz ... checking sm_2.2-6.0.tar.gz ... checking relMix_1.4.1.tar.gz ... checking RSA_0.10.6.tar.gz ... checking RSAtools_0.1.1.tar.gz ... checking TVMM_3.2.1.tar.gz ... checking rpanel_1.1-5.2.tar.gz ... checking RcmdrPlugin.TeachStat_1.1.3.tar.gz ... Depends: Package: tkrplot Depends: R (>= 2.13), grDevices, tcltk Timings: user system elapsed tkrplot 25.144 4.091 31.073 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 7 39 Check results summary: tkrplot ... NOTE * checking CRAN incoming feasibility ... [7s/7s] NOTE * checking R code for possible problems ... [4s/4s] NOTE rdepends_ade4TkGUI ... OK rdepends_adehabitatHR ... OK rdepends_adehabitatHS ... OK rdepends_adehabitatLT ... OK rdepends_adehabitatMA ... OK rdepends_aplpack ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_asbio ... OK rdepends_baggingbwsel ... OK rdepends_biotools ... OK rdepends_biplotbootGUI ... OK rdepends_cncaGUI ... OK rdepends_ConvergenceConcepts ... OK rdepends_dynBiplotGUI ... OK rdepends_FFD ... OK rdepends_fmri ... OK rdepends_forensim ... OK rdepends_geoelectrics ... OK rdepends_idendr0 ... NOTE * checking for unstated dependencies in ‘demo’ ... NOTE rdepends_InterfaceqPCR ... OK rdepends_leem ... OK rdepends_LogConcDEAD ... OK rdepends_maGUI ... OK rdepends_MareyMap ... OK rdepends_MCPtests ... OK rdepends_midrangeMCP ... OK rdepends_misc3d ... NOTE * checking for unstated dependencies in ‘demo’ ... NOTE rdepends_mritc ... OK rdepends_multibiplotGUI ... OK rdepends_plfMA ... OK rdepends_RcmdrPlugin.PcaRobust ... OK rdepends_RcmdrPlugin.RiskDemo ... OK rdepends_RcmdrPlugin.TeachingDemos ... OK rdepends_RcmdrPlugin.TeachStat ... NOTE * checking Rd cross-references ... NOTE rdepends_relMix ... OK rdepends_RHRV ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_rpanel ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_rriskDistributions ... OK rdepends_RSA ... NOTE * checking Rd cross-references ... NOTE rdepends_RSAtools ... OK rdepends_sm ... OK rdepends_smovie ... OK rdepends_sudoku ... OK rdepends_TeachingDemos ... OK rdepends_TextMiningGUI ... OK rdepends_TVMM ... OK rdepends_uHMM ... OK Check results changes: Package: aplpack Check: CRAN incoming feasibility Old result: NOTE Package: biplotbootGUI Check: CRAN incoming feasibility Old result: NOTE Package: cncaGUI Check: CRAN incoming feasibility Old result: NOTE Package: ConvergenceConcepts Check: CRAN incoming feasibility Old result: NOTE Package: FFD Check: CRAN incoming feasibility Old result: NOTE Package: geoelectrics Check: CRAN incoming feasibility Old result: NOTE Package: idendr0 Check: CRAN incoming feasibility Old result: NOTE Package: InterfaceqPCR Check: CRAN incoming feasibility Old result: NOTE Package: misc3d Check: CRAN incoming feasibility Old result: NOTE Package: mritc Check: CRAN incoming feasibility Old result: NOTE Package: multibiplotGUI Check: CRAN incoming feasibility Old result: NOTE Package: plfMA Check: CRAN incoming feasibility Old result: NOTE Package: RcmdrPlugin.PcaRobust Check: CRAN incoming feasibility Old result: NOTE Package: RcmdrPlugin.RiskDemo Check: CRAN incoming feasibility Old result: NOTE Package: RcmdrPlugin.TeachingDemos Check: CRAN incoming feasibility Old result: NOTE Package: rpanel Check: CRAN incoming feasibility Old result: NOTE Package: rriskDistributions Check: CRAN incoming feasibility Old result: NOTE Package: RSA Check: CRAN incoming feasibility Old result: NOTE Package: sm Check: CRAN incoming feasibility Old result: NOTE Package: sudoku Check: CRAN incoming feasibility Old result: NOTE Package: TeachingDemos Check: CRAN incoming feasibility Old result: NOTE Package: uHMM Check: CRAN incoming feasibility Old result: NOTE