downloading reverse dependencies ‘crmPack’, ‘cytominer’, ‘doremi’, ‘EpiNow2’, ‘evoper’, ‘ExpGenetic’, ‘genBaRcode’, ‘GWASinspector’, ‘ISOpureR’, ‘MazamaCoreUtils’, ‘md.log’, ‘metadeconfoundR’, ‘pkgnet’, ‘previsionio’, ‘psborrow’, ‘psidR’, ‘QFASA’, ‘ragtop’, ‘rly’, ‘SlideCNA’, ‘SmartMeterAnalytics’, ‘SNPannotator’, ‘spect’, ‘sRNAGenetic’, ‘TCA’, ‘Unico’, ‘uptasticsearch’, ‘VennDiagram’, ‘wearables’, ‘compareDF’, ‘genekitr’, ‘log4r’, ‘revert’, ‘tryCatchLog’, ‘varitas’ trying URL 'file:///data/Repositories/CRAN/src/contrib/crmPack_2.0.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/cytominer_0.2.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/doremi_1.0.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/EpiNow2_1.7.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/evoper_0.5.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ExpGenetic_0.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/genBaRcode_1.2.8.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/GWASinspector_1.7.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ISOpureR_1.1.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/MazamaCoreUtils_0.5.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/md.log_0.2.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/metadeconfoundR_1.0.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/pkgnet_0.5.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/previsionio_11.7.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/psborrow_0.2.4.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/psidR_2.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/QFASA_1.2.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ragtop_1.2.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/rly_1.7.7.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/SlideCNA_0.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/SmartMeterAnalytics_1.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/SNPannotator_1.4.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/spect_1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/sRNAGenetic_0.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/TCA_1.2.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/Unico_0.1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/uptasticsearch_1.0.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/VennDiagram_1.7.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/wearables_0.8.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/compareDF_2.3.5.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/genekitr_1.2.8.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/log4r_0.4.4.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/revert_1.0.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/tryCatchLog_1.3.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/varitas_0.0.2.tar.gz' installing dependencies ‘BondValuation’, ‘BSgenome.Hsapiens.UCSC.hg19’, ‘BSgenome.Hsapiens.UCSC.hg38’, ‘caretEnsemble’, ‘cmdstanr’, ‘ComplexUpset’, ‘Compositional’, ‘detectseparation’, ‘enrichR’, ‘EnsDb.Hsapiens.v75’, ‘EnsDb.Hsapiens.v86’, ‘ensembldb’, ‘europepmc’, ‘futile.logger’, ‘geneset’, ‘geohashTools’, ‘ggvenn’, ‘GOplot’, ‘loggit’, ‘mltools’, ‘precommit’, ‘RHRV’, ‘rlog’, ‘RNetLogo’, ‘rrepast’, ‘rrvgo’, ‘rsyslog’, ‘runner’, ‘SAScii’, ‘ShortRead’, ‘treasury’, ‘treemap’, ‘varian’ Warning: package ‘cmdstanr’ is not available for this version of R A version of this package 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 ‘hwriter’, ‘ROI.plugin.lpsolve’, ‘lomb’, ‘AnnotationFilter’, ‘ProtGenerics’ begin installing package ‘hwriter’ begin installing package ‘ROI.plugin.lpsolve’ begin installing package ‘lomb’ begin installing package ‘AnnotationFilter’ begin installing package ‘ProtGenerics’ begin installing package ‘runner’ begin installing package ‘rsyslog’ begin installing package ‘precommit’ begin installing package ‘rrepast’ begin installing package ‘RNetLogo’ begin installing package ‘geohashTools’ begin installing package ‘SAScii’ begin installing package ‘Compositional’ begin installing package ‘BondValuation’ begin installing package ‘treasury’ begin installing package ‘mltools’ begin installing package ‘enrichR’ begin installing package ‘caretEnsemble’ begin installing package ‘varian’ begin installing package ‘europepmc’ begin installing package ‘geneset’ begin installing package ‘ggvenn’ begin installing package ‘ComplexUpset’ begin installing package ‘GOplot’ begin installing package ‘treemap’ begin installing package ‘loggit’ begin installing package ‘rlog’ begin installing package ‘futile.logger’ * installing *source* package ‘loggit’ ... ** this is package ‘loggit’ version ‘2.1.1’ ** package ‘loggit’ 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 (loggit) * installing *source* package ‘rlog’ ... ** this is package ‘rlog’ version ‘0.1.0’ ** package ‘rlog’ 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 (rlog) * installing *source* package ‘rsyslog’ ... ** this is package ‘rsyslog’ version ‘1.0.3’ ** package ‘rsyslog’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpboE7gn/R.INSTALL31c122276f7f8c/rsyslog/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rsyslog.c -o rsyslog.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o rsyslog.so rsyslog.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpboE7gn/R.INSTALL31c122276f7f8c/rsyslog/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-rsyslog/00new/rsyslog/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 (rsyslog) * installing *source* package ‘SAScii’ ... ** this is package ‘SAScii’ version ‘1.0.2’ ** package ‘SAScii’ 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 (SAScii) * installing *source* package ‘hwriter’ ... ** this is package ‘hwriter’ version ‘1.3.2.1’ ** package ‘hwriter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hwriter) * installing *source* package ‘geohashTools’ ... ** this is package ‘geohashTools’ version ‘0.3.3’ ** package ‘geohashTools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpwuPSwl/R.INSTALL31c11d2b7bc5c/geohashTools/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c decode.c -o decode.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c encode.c -o encode.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c neighbors.c -o neighbors.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils.c -o utils.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o geohashTools.so decode.o encode.o init.o neighbors.o utils.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpwuPSwl/R.INSTALL31c11d2b7bc5c/geohashTools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-geohashTools/00new/geohashTools/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 (geohashTools) * installing *source* package ‘ROI.plugin.lpsolve’ ... ** this is package ‘ROI.plugin.lpsolve’ version ‘1.0-2’ ** package ‘ROI.plugin.lpsolve’ 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 (ROI.plugin.lpsolve) begin installing package ‘detectseparation’ * installing *source* package ‘futile.logger’ ... ** this is package ‘futile.logger’ version ‘1.4.9’ ** 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 (futile.logger) begin installing package ‘BSgenome.Hsapiens.UCSC.hg19’ begin installing package ‘BSgenome.Hsapiens.UCSC.hg38’ begin installing package ‘ShortRead’ * installing *source* package ‘treasury’ ... ** this is package ‘treasury’ version ‘0.4.0’ ** package ‘treasury’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (treasury) * installing *source* package ‘ProtGenerics’ ... ** this is package ‘ProtGenerics’ version ‘1.42.0’ ** package ‘ProtGenerics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘smooth’ in package ‘ProtGenerics’ ** 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 (ProtGenerics) * installing *source* package ‘precommit’ ... ** this is package ‘precommit’ version ‘0.4.3’ ** package ‘precommit’ 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 (precommit) * installing *source* package ‘RNetLogo’ ... ** this is package ‘RNetLogo’ version ‘1.0-4’ ** package ‘RNetLogo’ 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 (RNetLogo) * installing *source* package ‘geneset’ ... ** this is package ‘geneset’ version ‘0.2.7’ ** package ‘geneset’ 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 (geneset) * installing *source* package ‘europepmc’ ... ** this is package ‘europepmc’ version ‘0.4.3’ ** package ‘europepmc’ 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 (europepmc) * installing *source* package ‘detectseparation’ ... ** this is package ‘detectseparation’ version ‘0.3’ ** package ‘detectseparation’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (detectseparation) * installing *source* package ‘mltools’ ... ** this is package ‘mltools’ version ‘0.3.5’ ** package ‘mltools’ 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 (mltools) * installing *source* package ‘GOplot’ ... ** this is package ‘GOplot’ version ‘1.0.2’ ** package ‘GOplot’ 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 (GOplot) * installing *source* package ‘ggvenn’ ... ** this is package ‘ggvenn’ version ‘0.1.19’ ** package ‘ggvenn’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggvenn) * installing *source* package ‘enrichR’ ... ** this is package ‘enrichR’ version ‘3.4’ ** package ‘enrichR’ 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 (enrichR) * installing *source* package ‘treemap’ ... ** this is package ‘treemap’ version ‘2.4-4’ ** package ‘treemap’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (treemap) begin installing package ‘rrvgo’ * 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) begin installing package ‘RHRV’ * installing *source* package ‘AnnotationFilter’ ... ** this is package ‘AnnotationFilter’ version ‘1.34.0’ ** package ‘AnnotationFilter’ 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 (AnnotationFilter) begin installing package ‘ensembldb’ * installing *source* package ‘rrepast’ ... ** this is package ‘rrepast’ version ‘0.8.0’ ** package ‘rrepast’ 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 (rrepast) * installing *source* package ‘ComplexUpset’ ... ** this is package ‘ComplexUpset’ version ‘1.3.3’ ** package ‘ComplexUpset’ 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 (ComplexUpset) * installing *source* package ‘BondValuation’ ... ** this is package ‘BondValuation’ version ‘0.1.1’ ** package ‘BondValuation’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0FuCy9/R.INSTALL31c12a47fb33d9/BondValuation/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BondValuation_init.c -o BondValuation_init.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MyRcppFunctions.cpp -o MyRcppFunctions.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/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++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o BondValuation.so BondValuation_init.o MyRcppFunctions.o RcppExports.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0FuCy9/R.INSTALL31c12a47fb33d9/BondValuation/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BondValuation/00new/BondValuation/libs ** 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 ** 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 (BondValuation) * installing *source* package ‘varian’ ... ** this is package ‘varian’ version ‘0.2.2’ ** package ‘varian’ 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 (varian) * installing *source* package ‘caretEnsemble’ ... ** this is package ‘caretEnsemble’ version ‘4.0.1’ ** package ‘caretEnsemble’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (caretEnsemble) * installing *source* package ‘Compositional’ ... ** this is package ‘Compositional’ version ‘8.0’ ** package ‘Compositional’ 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 (Compositional) * installing *source* package ‘RHRV’ ... ** this is package ‘RHRV’ version ‘5.0.0’ ** package ‘RHRV’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZpX0O8/R.INSTALL31ca066af4ee06/RHRV/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c filterhr.c -o filterhr.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pmodwpt.c -o pmodwpt.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rhrv_init.c -o rhrv_init.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RHRV.so filterhr.o pmodwpt.o rhrv_init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZpX0O8/R.INSTALL31ca066af4ee06/RHRV/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RHRV/00new/RHRV/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RHRV) * installing *source* package ‘rrvgo’ ... ** this is package ‘rrvgo’ version ‘1.22.0’ ** package ‘rrvgo’ 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 (rrvgo) * installing *source* package ‘runner’ ... ** this is package ‘runner’ version ‘0.4.5’ ** package ‘runner’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpk2CydD/R.INSTALL31c1245348138e/runner/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/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++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fill_run.cpp -o fill_run.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c lag_run.cpp -o lag_run.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c length_run.cpp -o length_run.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c minmax_run.cpp -o minmax_run.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c runner.cpp -o runner.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o runner.so RcppExports.o fill_run.o lag_run.o length_run.o minmax_run.o runner.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpk2CydD/R.INSTALL31c1245348138e/runner/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-runner/00new/runner/libs ** 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 ** 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 (runner) * installing *source* package ‘BSgenome.Hsapiens.UCSC.hg19’ ... ** this is package ‘BSgenome.Hsapiens.UCSC.hg19’ version ‘1.4.3’ ** 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 (BSgenome.Hsapiens.UCSC.hg19) * installing *source* package ‘BSgenome.Hsapiens.UCSC.hg38’ ... ** this is package ‘BSgenome.Hsapiens.UCSC.hg38’ version ‘1.4.5’ ** 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 (BSgenome.Hsapiens.UCSC.hg38) * installing *source* package ‘ShortRead’ ... ** this is package ‘ShortRead’ version ‘1.68.0’ ** package ‘ShortRead’ successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc-15 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-15 accepts -g... yes checking for gcc-15 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc-15 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphHv34u/R.INSTALL31c4f3307afb77/ShortRead/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_ShortRead.c -o R_init_ShortRead.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alphabet.c -o alphabet.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c count.c -o count.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io.c -o io.o io.c: In function ‘read_prb_as_character’: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] 227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0))); | ~^ | | | double | %s io.c: In function ‘_read_solexa_export_file’: io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 658 | error("invalid 'strand' field '%s', %s:%d", | ~^ | | | char * | %d 659 | *elt[13], fname, lineno); | ~~~~~~~~ | | | int io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 676 | error("invalid 'filtering' field '%s', %s:%d", | ~^ | | | char * | %d 677 | *elt[21], fname, lineno); | ~~~~~~~~ | | | int gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_bowtie.c -o io_bowtie.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_soap.c -o io_soap.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_maq_map.cc -o read_maq_map.o In file included from read_maq_map.cc:13: maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sampler.c -o sampler.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trim.c -o trim.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xsnap.c -o xsnap.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphHv34u/R.INSTALL31c4f3307afb77/ShortRead/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ShortRead/00new/ShortRead/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ShortRead) * installing *source* package ‘ensembldb’ ... ** this is package ‘ensembldb’ version ‘2.34.0’ ** package ‘ensembldb’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘.cds_for_id2’ in package ‘ensembldb’ ** 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 (ensembldb) begin installing package ‘EnsDb.Hsapiens.v75’ begin installing package ‘EnsDb.Hsapiens.v86’ * installing *source* package ‘EnsDb.Hsapiens.v75’ ... ** this is package ‘EnsDb.Hsapiens.v75’ version ‘2.99.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EnsDb.Hsapiens.v75) * installing *source* package ‘EnsDb.Hsapiens.v86’ ... ** this is package ‘EnsDb.Hsapiens.v86’ version ‘2.99.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EnsDb.Hsapiens.v86) checking futile.logger_1.4.9.tar.gz ... checking crmPack_2.0.1.tar.gz ... checking cytominer_0.2.2.tar.gz ... checking doremi_1.0.0.tar.gz ... checking EpiNow2_1.7.1.tar.gz ... checking evoper_0.5.0.tar.gz ... checking ExpGenetic_0.1.0.tar.gz ... checking genBaRcode_1.2.8.tar.gz ... checking GWASinspector_1.7.3.tar.gz ... checking ISOpureR_1.1.3.tar.gz ... checking MazamaCoreUtils_0.5.3.tar.gz ... checking md.log_0.2.0.tar.gz ... checking metadeconfoundR_1.0.2.tar.gz ... checking pkgnet_0.5.0.tar.gz ... checking previsionio_11.7.0.tar.gz ... checking psborrow_0.2.4.tar.gz ... checking psidR_2.3.tar.gz ... checking QFASA_1.2.1.tar.gz ... checking ragtop_1.2.0.tar.gz ... checking rly_1.7.7.tar.gz ... checking SlideCNA_0.1.0.tar.gz ... checking SmartMeterAnalytics_1.1.1.tar.gz ... checking SNPannotator_1.4.3.tar.gz ... checking spect_1.0.tar.gz ... checking sRNAGenetic_0.1.0.tar.gz ... checking TCA_1.2.1.tar.gz ... checking Unico_0.1.0.tar.gz ... checking uptasticsearch_1.0.0.tar.gz ... checking VennDiagram_1.7.3.tar.gz ... checking tryCatchLog_1.3.3.tar.gz ... checking compareDF_2.3.5.tar.gz ... checking genekitr_1.2.8.tar.gz ... checking revert_1.0.0.tar.gz ... checking varitas_0.0.2.tar.gz ... checking wearables_0.8.1.tar.gz ... checking log4r_0.4.4.tar.gz ... Depends: Package: futile.logger Depends: R (>= 3.0.0) Imports: utils, lambda.r (>= 1.1.0), futile.options Timings: user system elapsed futile.logger 25.754 3.668 30.186 Results: Check status summary: ERROR NOTE OK Source packages 0 0 1 Reverse depends 6 5 24 Check results summary: futile.logger ... OK rdepends_compareDF ... OK rdepends_crmPack ... ERROR * checking tests ... [53s/53s] ERROR rdepends_cytominer ... OK rdepends_doremi ... ERROR * checking package subdirectories ... NOTE * checking Rd files ... [0s/0s] NOTE * checking examples ... [2s/2s] ERROR * checking re-building of vignette outputs ... [12s/12s] ERROR rdepends_EpiNow2 ... OK rdepends_evoper ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_ExpGenetic ... OK rdepends_genBaRcode ... OK rdepends_genekitr ... OK rdepends_GWASinspector ... OK rdepends_ISOpureR ... NOTE * checking Rd files ... [1s/1s] NOTE rdepends_log4r ... OK rdepends_MazamaCoreUtils ... OK rdepends_md.log ... OK rdepends_metadeconfoundR ... OK rdepends_pkgnet ... OK rdepends_previsionio ... OK rdepends_psborrow ... OK rdepends_psidR ... ERROR * checking examples ... [1s/1s] ERROR * checking tests ... [3s/3s] ERROR rdepends_QFASA ... OK rdepends_ragtop ... OK rdepends_revert ... OK rdepends_rly ... ERROR * checking tests ... [9s/9s] ERROR rdepends_SlideCNA ... OK rdepends_SmartMeterAnalytics ... OK rdepends_SNPannotator ... OK rdepends_spect ... ERROR * checking tests ... [17s/17s] ERROR * checking re-building of vignette outputs ... [40s/40s] ERROR rdepends_sRNAGenetic ... OK rdepends_TCA ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_tryCatchLog ... OK rdepends_Unico ... OK rdepends_uptasticsearch ... OK rdepends_varitas ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_VennDiagram ... ERROR * checking tests ... [4s/4s] ERROR rdepends_wearables ... NOTE * checking package subdirectories ... NOTE Check results changes: Package: crmPack Check: tests New result: ERROR Package: md.log Check: CRAN incoming feasibility Old result: NOTE Package: rly Check: tests New result: ERROR Package: TCA Check: CRAN incoming feasibility Old result: NOTE Package: VennDiagram Check: CRAN incoming feasibility Old result: NOTE Package: VennDiagram Check: tests New result: ERROR