downloading reverse dependencies ‘arenar’, ‘microCRAN’, ‘plumbertableau’, ‘ReliaGrowR’, ‘starsTileServer’, ‘AzureContainers’, ‘gaawr2’, ‘gqlr’, ‘log’, ‘MicroMoB’, ‘occupationMeasurement’, ‘openmetrics’, ‘polished’, ‘rapidoc’, ‘redoc’, ‘rsconnect’, ‘shiny.telemetry’, ‘swagger’, ‘vetiver’ trying URL 'file:///data/Repositories/CRAN/src/contrib/arenar_0.2.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/microCRAN_0.9.0-1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/plumbertableau_0.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ReliaGrowR_0.3.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/starsTileServer_0.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/AzureContainers_1.3.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/gaawr2_0.0.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/gqlr_0.0.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/log_1.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/MicroMoB_0.1.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/occupationMeasurement_0.3.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/openmetrics_0.3.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/polished_0.8.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/rapidoc_9.3.4.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/redoc_2.0.0.75.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/rsconnect_1.7.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/shiny.telemetry_0.3.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/swagger_5.17.14.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/vetiver_0.2.7.tar.gz' installing dependencies ‘auditor’, ‘automagic’, ‘AzureKeyVault’, ‘bcrypt’, ‘BLR’, ‘bundle’, ‘cereal’, ‘EnsDb.Hsapiens.v75’, ‘ensembldb’, ‘fairmodels’, ‘gistr’, ‘GMMAT’, ‘graphql’, ‘HardyWeinberg’, ‘luz’, ‘miniCRAN’, ‘mlr3data’, ‘otp’, ‘paws.machine.learning’, ‘plumber’, ‘powerEQTL’, ‘probably’, ‘rapidoc’, ‘redoc’, ‘regress’, ‘RestRserve’, ‘semantic.dashboard’, ‘seqminer’, ‘shiny.semantic’, ‘smdocker’, ‘SNPassoc’, ‘stacks’, ‘timevis’ also installing the dependencies ‘hnp’, ‘Rserve’, ‘AnnotationFilter’, ‘ProtGenerics’, ‘poisbinom’, ‘semantic.assets’, ‘paws.compute’, ‘paws.developer.tools’, ‘paws.management’, ‘paws.security.identity’ begin installing package ‘hnp’ begin installing package ‘Rserve’ begin installing package ‘AnnotationFilter’ begin installing package ‘ProtGenerics’ begin installing package ‘poisbinom’ begin installing package ‘paws.compute’ begin installing package ‘semantic.assets’ begin installing package ‘paws.developer.tools’ begin installing package ‘paws.management’ begin installing package ‘paws.security.identity’ begin installing package ‘rapidoc’ begin installing package ‘redoc’ begin installing package ‘gistr’ begin installing package ‘fairmodels’ begin installing package ‘miniCRAN’ begin installing package ‘bcrypt’ begin installing package ‘AzureKeyVault’ begin installing package ‘BLR’ begin installing package ‘GMMAT’ begin installing package ‘HardyWeinberg’ begin installing package ‘powerEQTL’ begin installing package ‘regress’ begin installing package ‘seqminer’ begin installing package ‘graphql’ begin installing package ‘automagic’ begin installing package ‘otp’ begin installing package ‘timevis’ begin installing package ‘bundle’ * installing *source* package ‘redoc’ ... ** this is package ‘redoc’ version ‘2.0.0.75’ ** package ‘redoc’ 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 (redoc) begin installing package ‘cereal’ * installing *source* package ‘rapidoc’ ... ** this is package ‘rapidoc’ version ‘9.3.4’ ** package ‘rapidoc’ 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 (rapidoc) begin installing package ‘luz’ * installing *source* package ‘automagic’ ... ** this is package ‘automagic’ version ‘0.5.1’ ** package ‘automagic’ 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 (automagic) begin installing package ‘mlr3data’ * installing *source* package ‘bcrypt’ ... ** this is package ‘bcrypt’ version ‘1.2.0’ ** package ‘bcrypt’ 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/RtmpZXhaNf/R.INSTALL30c2fd278df7e8/bcrypt/src' rm -f bcrypt.so bcrypt_r.o register.o bcrypt/libstatbcrypt.a bcrypt/bcrypt.o bcrypt/blowfish.o bcrypt/bcrypt_pbkdf.o bcrypt/sha2.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ibcrypt -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcrypt_r.c -o bcrypt_r.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ibcrypt -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c register.c -o register.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ibcrypt -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcrypt/bcrypt.c -o bcrypt/bcrypt.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ibcrypt -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcrypt/blowfish.c -o bcrypt/blowfish.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ibcrypt -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcrypt/bcrypt_pbkdf.c -o bcrypt/bcrypt_pbkdf.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ibcrypt -DSTRICT_R_HEADERS -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcrypt/sha2.c -o bcrypt/sha2.o ar rcs bcrypt/libstatbcrypt.a bcrypt/bcrypt.o bcrypt/blowfish.o bcrypt/bcrypt_pbkdf.o bcrypt/sha2.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o bcrypt.so bcrypt_r.o register.o -Lbcrypt -lstatbcrypt -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZXhaNf/R.INSTALL30c2fd278df7e8/bcrypt/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-bcrypt/00new/bcrypt/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 (bcrypt) begin installing package ‘paws.machine.learning’ * installing *source* package ‘regress’ ... ** this is package ‘regress’ version ‘1.3-22’ ** package ‘regress’ 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 (regress) begin installing package ‘probably’ * installing *source* package ‘bundle’ ... ** this is package ‘bundle’ version ‘0.1.3’ ** package ‘bundle’ 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 (bundle) begin installing package ‘stacks’ * installing *source* package ‘BLR’ ... ** this is package ‘BLR’ version ‘1.6’ ** package ‘BLR’ 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/RtmpsLFee0/R.INSTALL30c2fb3f3127f2/BLR/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 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 sample_betas.c -o sample_betas.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o BLR.so init.o sample_betas.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpsLFee0/R.INSTALL30c2fb3f3127f2/BLR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BLR/00new/BLR/libs ** 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 ** 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 (BLR) begin installing package ‘plumber’ * installing *source* package ‘powerEQTL’ ... ** this is package ‘powerEQTL’ version ‘0.3.6’ ** package ‘powerEQTL’ 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 (powerEQTL) * installing *source* package ‘semantic.assets’ ... ** this is package ‘semantic.assets’ version ‘1.1.0’ ** package ‘semantic.assets’ 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 (semantic.assets) begin installing package ‘shiny.semantic’ * installing *source* package ‘timevis’ ... ** this is package ‘timevis’ version ‘2.1.0’ ** package ‘timevis’ 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 ** 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 (timevis) * 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 ‘miniCRAN’ ... ** this is package ‘miniCRAN’ version ‘0.3.1’ ** package ‘miniCRAN’ 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 (miniCRAN) * installing *source* package ‘otp’ ... ** this is package ‘otp’ version ‘0.1.1’ ** package ‘otp’ 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 (otp) * installing *source* package ‘cereal’ ... ** this is package ‘cereal’ version ‘0.1.0’ ** package ‘cereal’ 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 (cereal) * installing *source* package ‘hnp’ ... ** this is package ‘hnp’ version ‘1.2-7’ ** package ‘hnp’ 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 (hnp) begin installing package ‘auditor’ * installing *source* package ‘gistr’ ... ** this is package ‘gistr’ version ‘0.9.0’ ** package ‘gistr’ 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 (gistr) * installing *source* package ‘AzureKeyVault’ ... ** this is package ‘AzureKeyVault’ version ‘1.0.6’ ** package ‘AzureKeyVault’ 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 (AzureKeyVault) * installing *source* package ‘fairmodels’ ... ** this is package ‘fairmodels’ version ‘1.2.2’ ** package ‘fairmodels’ 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 (fairmodels) * installing *source* package ‘shiny.semantic’ ... ** this is package ‘shiny.semantic’ version ‘0.5.1’ ** package ‘shiny.semantic’ 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 (shiny.semantic) begin installing package ‘semantic.dashboard’ * installing *source* package ‘poisbinom’ ... ** this is package ‘poisbinom’ version ‘1.0.2’ ** package ‘poisbinom’ 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/RtmpDymtMC/R.INSTALL30c2bd27067889/poisbinom/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 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 init.c -o 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 poisbinom.cpp -o poisbinom.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDymtMC/R.INSTALL30c2bd27067889/poisbinom/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poisbinom/00new/poisbinom/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 (poisbinom) begin installing package ‘SNPassoc’ * installing *source* package ‘semantic.dashboard’ ... ** this is package ‘semantic.dashboard’ version ‘0.2.1’ ** package ‘semantic.dashboard’ 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 (semantic.dashboard) * installing *source* package ‘plumber’ ... ** this is package ‘plumber’ version ‘1.3.2’ ** 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 (plumber) * installing *source* package ‘auditor’ ... ** this is package ‘auditor’ version ‘1.3.5’ ** package ‘auditor’ 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 (auditor) * installing *source* package ‘stacks’ ... ** this is package ‘stacks’ version ‘1.1.1’ ** package ‘stacks’ 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 (stacks) * 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 ‘mlr3data’ ... ** this is package ‘mlr3data’ version ‘0.9.0’ ** package ‘mlr3data’ 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 ** 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 (mlr3data) * installing *source* package ‘luz’ ... ** this is package ‘luz’ version ‘0.5.1’ ** package ‘luz’ 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 (luz) * installing *source* package ‘probably’ ... ** this is package ‘probably’ version ‘1.2.0’ ** package ‘probably’ 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 (probably) * installing *source* package ‘SNPassoc’ ... ** this is package ‘SNPassoc’ version ‘2.1-2’ ** package ‘SNPassoc’ 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 (SNPassoc) * installing *source* package ‘HardyWeinberg’ ... ** this is package ‘HardyWeinberg’ version ‘1.7.9’ ** package ‘HardyWeinberg’ 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/Rtmp4SHgnG/R.INSTALL30c3067633fcba/HardyWeinberg/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 HWxChromosomal.cpp -o HWxChromosomal.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 -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 SNPHWEX.cpp -o SNPHWEX.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 support.cpp -o support.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp4SHgnG/R.INSTALL30c3067633fcba/HardyWeinberg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-HardyWeinberg/00new/HardyWeinberg/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 (HardyWeinberg) * installing *source* package ‘Rserve’ ... ** this is package ‘Rserve’ version ‘1.8-16’ ** package ‘Rserve’ successfully unpacked and MD5 sums checked ** using staged installation checking whether to compile the server... yes checking whether to compile the client... no 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 the compiler supports GNU C... yes checking whether gcc-15 accepts -g... yes checking for gcc-15 option to enable C11 features... none needed checking for sys/wait.h that is POSIX.1 compatible... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for vfork.h... no checking for limits.h... yes checking for string.h... (cached) yes checking for memory.h... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for sys/socket.h... yes checking for sys/un.h... yes checking for netinet/in.h... yes checking for netinet/tcp.h... yes checking for an ANSI C-conforming const... yes checking whether byte ordering is bigendian... no checking size of size_t... 8 checking for pid_t... yes checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking return type of signal handlers... void checking for memset... yes checking for mkdir... yes checking for rmdir... yes checking for select... yes checking for socket... yes checking for srandomdev... no checking for library containing crypt... -lcrypt checking for crypt.h... yes checking for socklen_t... yes checking for connect... yes checking whether to enable IPv6... no checking for dlopen in -ldl... yes checking for openssl/rsa.h... yes checking for library containing RSA_generate_key... -lcrypto checking for openssl/ssl.h... yes checking for library containing SSL_CTX_load_verify_locations... -lssl checking whether threads are desired... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for working threads support... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/client/cxx/Makefile config.status: creating src/config.h ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-11) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDhHIc1/R.INSTALL30c2b365e925f/Rserve/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RSserver.c -o RSserver.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rserv.c -o Rserv.o Rserv.c: In function ‘auth_user’: Rserv.c:2447:21: warning: variable ‘ctrl_flag’ set but not used [-Wunused-but-set-variable] 2447 | int ctrl_flag = 0, u_uid = 0, u_gid = 0; | ^~~~~~~~~ Rserv.c: In function ‘Rserve_fork_compute’: Rserv.c:3312:25: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3312 | int rn, cmd; | ^~~ Rserv.c: In function ‘OCAP_iteration’: Rserv.c:3468:29: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3468 | int cmd; | ^~~ Rserv.c: In function ‘Rserve_QAP1_connected’: Rserv.c:3915:9: warning: variable ‘unaligned’ set but not used [-Wunused-but-set-variable] 3915 | int unaligned=0; | ^~~~~~~~~ Rserv.c: In function ‘handle_server_event’: Rserv.c:5030:13: warning: unused variable ‘succ’ [-Wunused-variable] 5030 | int succ = 0; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c base64.c -o base64.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c date.c -o date.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c http.c -o http.o In file included from http.c:10: bsdcmpt.h:17:20: warning: ‘strnstr’ defined but not used [-Wunused-function] 17 | static const char *strnstr(const char *haystack, const char *needle, size_t len) { | ^~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ioc.c -o ioc.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c md5.c -o md5.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c oc.c -o oc.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qap_decode.c -o qap_decode.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c qap_encode.c -o qap_encode.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c session.c -o session.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sha1.c -o sha1.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c standalone.c -o standalone.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tls.c -o tls.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ulog.c -o ulog.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils.c -o utils.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c websockets.c -o websockets.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c winembed.c -o winembed.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Rserve.so RSserver.o Rserv.o base64.o date.o http.o ioc.o md5.o oc.o qap_decode.o qap_encode.o session.o sha1.o standalone.o tls.o ulog.o utils.o websockets.o winembed.o -lssl -lcrypto -ldl -lcrypt -L/home/hornik/tmp/R-d-gcc-15/lib -lR gcc-15 -DSTANDALONE_RSERVE -DDAEMON -I. -Iinclude -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I/usr/local/include -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/home/hornik/tmp/R-d-gcc-15/include -o Rserve standalone.c md5.c session.c qap_decode.c qap_encode.c sha1.c base64.c websockets.c RSserver.c tls.c http.c oc.c ulog.c ioc.c utils.c date.c -Wl,-O1 -lssl -lcrypto -ldl -lcrypt -L"/home/hornik/tmp/R-d-gcc-15/lib" -lR -lssl -lcrypto -ldl -lcrypt In file included from standalone.c:6: Rserv.c: In function ‘auth_user’: Rserv.c:2447:21: warning: variable ‘ctrl_flag’ set but not used [-Wunused-but-set-variable] 2447 | int ctrl_flag = 0, u_uid = 0, u_gid = 0; | ^~~~~~~~~ Rserv.c: In function ‘Rserve_fork_compute’: Rserv.c:3312:25: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3312 | int rn, cmd; | ^~~ Rserv.c: In function ‘OCAP_iteration’: Rserv.c:3468:29: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3468 | int cmd; | ^~~ Rserv.c: In function ‘Rserve_QAP1_connected’: Rserv.c:3915:9: warning: variable ‘unaligned’ set but not used [-Wunused-but-set-variable] 3915 | int unaligned=0; | ^~~~~~~~~ Rserv.c: In function ‘handle_server_event’: Rserv.c:5030:13: warning: unused variable ‘succ’ [-Wunused-variable] 5030 | int succ = 0; | ^~~~ In file included from http.c:10: bsdcmpt.h:17:20: warning: ‘strnstr’ defined but not used [-Wunused-function] 17 | static const char *strnstr(const char *haystack, const char *needle, size_t len) { | ^~~~~~~ gcc-15 -DSTANDALONE_RSERVE -DRSERV_DEBUG -DNODAEMON -I. -Iinclude -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -I/home/hornik/tmp/R-d-gcc-15/include -o Rserve.dbg standalone.c md5.c session.c qap_decode.c qap_encode.c sha1.c base64.c websockets.c RSserver.c tls.c http.c oc.c ulog.c ioc.c utils.c date.c -Wl,-O1 -lssl -lcrypto -ldl -lcrypt -L"/home/hornik/tmp/R-d-gcc-15/lib" -lR -lssl -lcrypto -ldl -lcrypt In file included from standalone.c:6: Rserv.c: In function ‘auth_user’: Rserv.c:2447:21: warning: variable ‘ctrl_flag’ set but not used [-Wunused-but-set-variable] 2447 | int ctrl_flag = 0, u_uid = 0, u_gid = 0; | ^~~~~~~~~ Rserv.c: In function ‘Rserve_fork_compute’: Rserv.c:3312:25: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3312 | int rn, cmd; | ^~~ Rserv.c: In function ‘OCAP_iteration’: Rserv.c:3468:29: warning: variable ‘cmd’ set but not used [-Wunused-but-set-variable] 3468 | int cmd; | ^~~ Rserv.c: In function ‘Rserve_QAP1_connected’: Rserv.c:3915:9: warning: variable ‘unaligned’ set but not used [-Wunused-but-set-variable] 3915 | int unaligned=0; | ^~~~~~~~~ Rserv.c: In function ‘handle_server_event’: Rserv.c:5030:13: warning: unused variable ‘succ’ [-Wunused-variable] 5030 | int succ = 0; | ^~~~ standalone.c: In function ‘main’: standalone.c:38:16: warning: variable ‘rs_silent’ set but not used [-Wunused-but-set-variable] 38 | int rs_silent = 0; | ^~~~~~~~~ In file included from http.c:10: bsdcmpt.h:17:20: warning: ‘strnstr’ defined but not used [-Wunused-function] 17 | static const char *strnstr(const char *haystack, const char *needle, size_t len) { | ^~~~~~~ ./mergefat Rserve "/home/hornik/tmp/R-d-gcc-15/bin/Rserve" ./mergefat Rserve.dbg "/home/hornik/tmp/R-d-gcc-15/bin/Rserve.dbg" make -C proxy 'CC=gcc-15' 'CPPFLAGS=-I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include ' CFLAGS='-g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native ' 'LDFLAGS=-Wl,-O1' 'LIBS=-lssl -lcrypto -ldl -lcrypt ' && cp -p proxy/forward . make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpDhHIc1/R.INSTALL30c2b365e925f/Rserve/src/proxy' ln -sfn ../ulog.h ulog.h gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o forward.o forward.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o http.o http.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o http_tools.o http_tools.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o server.o server.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o tls.o tls.c ln -sfn ../md5.h md5.h ln -sfn ../sha1.h sha1.h ln -sfn ../base64.c base64.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o websockets.o websockets.c websockets.c: In function ‘WS_connected’: websockets.c:343:47: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 343 | ws_connected_fn_t connected = (ws_connected_fn_t) arg->srv->aux; | ^ websockets.c: In function ‘WS13_upgrade’: websockets.c:378:34: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 378 | srv->aux = (void*) connected; | ^ websockets.c:411:47: warning: ISO C forbids conversion of object pointer to function pointer type [-Wpedantic] 411 | ws_connected_fn_t connected = (ws_connected_fn_t) srv->aux; | ^ websockets.c: In function ‘create_WS_server’: websockets.c:868:34: warning: ISO C forbids conversion of function pointer to object pointer type [-Wpedantic] 868 | srv->aux = (void*) connected; | ^ ln -sfn ../md5.c md5.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o md5.o md5.c ln -sfn ../sha1.c sha1.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o sha1.o sha1.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o base64.o base64.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o date.o date.c ln -sfn ../ulog.c ulog.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o ulog.o ulog.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o chandler.o chandler.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -I.. -DFORKED -I/usr/local/include -DRSERVE_PKG -I. -Iinclude -I/usr/local/include -I/usr/local/include -c -o rscript.o rscript.c gcc-15 -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -Wl,-O1 -o forward forward.o http.o http_tools.o server.o tls.o websockets.o md5.o sha1.o base64.o date.o ulog.o chandler.o rscript.o -lssl -lcrypto -ldl -lcrypt make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpDhHIc1/R.INSTALL30c2b365e925f/Rserve/src/proxy' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDhHIc1/R.INSTALL30c2b365e925f/Rserve/src' installing via 'install.libs.R' to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rserve/00new/Rserve ** 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 (Rserve) begin installing package ‘RestRserve’ * installing *source* package ‘graphql’ ... ** this is package ‘graphql’ version ‘1.5.3’ ** package ‘graphql’ 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/Rtmpmw4U6E/R.INSTALL30c30d6f8c4bfb/graphql/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -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 -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c dump_json_ast.cpp -o dump_json_ast.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/Ast.cpp -o libgraphqlparser/Ast.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/GraphQLParser.cpp -o libgraphqlparser/GraphQLParser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/JsonVisitor.cpp -o libgraphqlparser/JsonVisitor.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/lexer.cpp -o libgraphqlparser/lexer.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/parser.tab.cpp -o libgraphqlparser/parser.tab.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/c/GraphQLParser.cpp -o libgraphqlparser/c/GraphQLParser.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/c/GraphQLAst.cpp -o libgraphqlparser/c/GraphQLAst.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/c/GraphQLAstNode.cpp -o libgraphqlparser/c/GraphQLAstNode.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/c/GraphQLAstToJSON.cpp -o libgraphqlparser/c/GraphQLAstToJSON.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Ilibgraphqlparser -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 -fvisibility=hidden -fpic -g -O2 -Wall -pedantic -mtune=native -c libgraphqlparser/c/GraphQLAstVisitor.cpp -o libgraphqlparser/c/GraphQLAstVisitor.o ar rcs libgraphqlparser/libstatgraphparser.a libgraphqlparser/Ast.o libgraphqlparser/GraphQLParser.o libgraphqlparser/JsonVisitor.o libgraphqlparser/lexer.o libgraphqlparser/parser.tab.o libgraphqlparser/c/GraphQLParser.o libgraphqlparser/c/GraphQLAst.o libgraphqlparser/c/GraphQLAstNode.o libgraphqlparser/c/GraphQLAstToJSON.o libgraphqlparser/c/GraphQLAstVisitor.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o graphql.so RcppExports.o dump_json_ast.o -Llibgraphqlparser -lstatgraphparser -L/home/hornik/tmp/R-d-gcc-15/lib -lR rm -f libgraphqlparser/Ast.o libgraphqlparser/GraphQLParser.o libgraphqlparser/JsonVisitor.o libgraphqlparser/lexer.o libgraphqlparser/parser.tab.o libgraphqlparser/c/GraphQLParser.o libgraphqlparser/c/GraphQLAst.o libgraphqlparser/c/GraphQLAstNode.o libgraphqlparser/c/GraphQLAstToJSON.o libgraphqlparser/c/GraphQLAstVisitor.o libgraphqlparser/libstatgraphparser.a make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpmw4U6E/R.INSTALL30c30d6f8c4bfb/graphql/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-graphql/00new/graphql/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 (graphql) * installing *source* package ‘GMMAT’ ... ** this is package ‘GMMAT’ version ‘1.5.0’ ** package ‘GMMAT’ successfully unpacked and MD5 sums checked ** using staged installation 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 g++-15 -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... g++-15 -std=gnu++17 -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 ZSTD_decompress in -lzstd... yes checking zstd.h usability... yes checking zstd.h presence... yes checking for zstd.h... yes configure: Will use system-wide zstd library checking for libdeflate_zlib_decompress in -ldeflate... yes checking libdeflate.h usability... yes checking libdeflate.h presence... yes checking for libdeflate.h... yes configure: Will use system-wide libdeflate library 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/RtmpmBxCFy/R.INSTALL30c3008f3e59a/GMMAT/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -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 -DARMA_64BIT_WORD -fpic -g -O2 -Wall -pedantic -mtune=native -c fitglmm.cpp -o fitglmm.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -Izstd/lib -Izstd/lib/common -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 -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o GMMAT.so fitglmm.o registerDynamicSymbol.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -lz -lbz2 -lzstd -ldeflate -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmBxCFy/R.INSTALL30c3008f3e59a/GMMAT/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GMMAT/00new/GMMAT/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 (GMMAT) * installing *source* package ‘paws.developer.tools’ ... ** this is package ‘paws.developer.tools’ version ‘0.9.0’ ** package ‘paws.developer.tools’ 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 (paws.developer.tools) * 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’ * installing *source* package ‘RestRserve’ ... ** this is package ‘RestRserve’ version ‘1.2.4’ ** package ‘RestRserve’ 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/RtmphRSxM2/R.INSTALL30d76673ce4ef2/RestRserve/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 -DRCPP_NO_MODULES -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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c format_cookies.cpp -o format_cookies.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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c format_headers.cpp -o format_headers.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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c parse_cookies.cpp -o parse_cookies.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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c parse_headers.cpp -o parse_headers.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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c parse_multipart.cpp -o parse_multipart.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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c url_decode.cpp -o url_decode.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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c url_encode.cpp -o url_encode.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 -DRCPP_NO_MODULES -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RestRserve.so RcppExports.o format_cookies.o format_headers.o parse_cookies.o parse_headers.o parse_multipart.o url_decode.o url_encode.o utils.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphRSxM2/R.INSTALL30d76673ce4ef2/RestRserve/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RestRserve/00new/RestRserve/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 (RestRserve) * installing *source* package ‘seqminer’ ... ** this is package ‘seqminer’ version ‘9.7’ ** package ‘seqminer’ successfully unpacked and MD5 sums checked ** using staged installation configure: CC = gcc-15 configure: CFLAGS = -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native configure: CXX = g++-15 -std=gnu++17 configure: CXXFLAGS = -g -O2 -Wall -pedantic -mtune=native 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 g++-15 -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... g++-15 -std=gnu++17 -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 BZ2_bzDecompressInit in -lbz2... yes checking bzlib.h usability... yes checking bzlib.h presence... yes checking for bzlib.h... yes configure: Will use system-wide bzip2 library checking for ZSTD_compress in -lzstd... yes checking zstd.h usability... yes checking zstd.h presence... yes checking for zstd.h... yes configure: Will use system-wide zstd library checking for sqlite3_open in -lsqlite3... yes checking sqlite3.h usability... yes checking sqlite3.h presence... yes checking for sqlite3.h... yes configure: Will use system-wide sqlite library checking for regcomp in -lc... yes checking regex.h usability... yes checking regex.h presence... yes checking for regex.h... yes checking for working REG_STARTEND... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/config.h ** 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’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpqDGMWL/R.INSTALL30c30b6d75d7b5/seqminer/src' have SQLite have bzip2 g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BCFReader.cpp -o BCFReader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenFile.cpp -o BGenFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenIndex.cpp -o BGenIndex.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BGenVariant.cpp -o BGenVariant.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Exception.cpp -o Exception.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c FileIO.cpp -o FileIO.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c GeneLoader.cpp -o GeneLoader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MmapFile.cpp -o MmapFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PatternMatch.cpp -o PatternMatch.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PeopleSet.cpp -o PeopleSet.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlinkInputFile.cpp -o PlinkInputFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PlinkOutputFile.cpp -o PlinkOutputFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Profiler.cpp -o Profiler.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c R_CPP_interface.cpp -o R_CPP_interface.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RangeList.cpp -o RangeList.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rannotation.cpp -o Rannotation.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SimpleMatrix.cpp -o SimpleMatrix.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SingleChromosomeBCFIndex.cpp -o SingleChromosomeBCFIndex.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c SingleChromosomeVCFIndex.cpp -o SingleChromosomeVCFIndex.o SingleChromosomeVCFIndex.cpp: In member function ‘int SingleChromosomeVCFIndex::createIndex()’: SingleChromosomeVCFIndex.cpp:69:15: warning: unused variable ‘fn’ [-Wunused-variable] 69 | const char* fn = vcfFile_.c_str(); | ^~ SingleChromosomeVCFIndex.cpp: In member function ‘int SingleChromosomeVCFIndex::mapIndex()’: SingleChromosomeVCFIndex.cpp:201:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 201 | if (Nrecord != d[1]) { | ~~~~~~~~^~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TypeConversion.cpp -o TypeConversion.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -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++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFHeader.cpp -o VCFHeader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFIndividual.cpp -o VCFIndividual.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFInfo.cpp -o VCFInfo.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFInputFile.cpp -o VCFInputFile.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c VCFUtil.cpp -o VCFUtil.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcf.c -o bcf.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcf_index.c -o bcf_index.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bcfutils.c -o bcfutils.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bedidx.c -o bedidx.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bgen2genoLoader.cpp -o bgen2genoLoader.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bgzf.c -o bgzf.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c knetfile.c -o knetfile.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c kstring.c -o kstring.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c plink2genoLoader.cpp -o plink2genoLoader.o plink2genoLoader.cpp: In function ‘int readBedToMatrixByIndex(const std::string&, int, int, const std::vector&, const std::vector&, SEXP)’: plink2genoLoader.cpp:126:3: warning: ‘snpMajorMode’ may be used uninitialized [-Wmaybe-uninitialized] 126 | if (snpMajorMode) { | ^~ plink2genoLoader.cpp:78:8: note: ‘snpMajorMode’ was declared here 78 | bool snpMajorMode; | ^~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rvMetaLoader.cpp -o rvMetaLoader.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scbcf2genoLoader.cpp -o scbcf2genoLoader.o scbcf2genoLoader.cpp: In function ‘int parseBCFVariant(const BCFHeader&, uint32_t, uint32_t, std::vector, std::vector*, std::vector >*)’: scbcf2genoLoader.cpp:287:10: warning: unused variable ‘format_type’ [-Wunused-variable] 287 | int8_t format_type = *pIndv; | ^~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c scvcf2genoLoader.cpp -o scvcf2genoLoader.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqForStat.c -o seqForStat.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqminer.c -o seqminer.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c seqminer_init.c -o seqminer_init.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tabixLoader.cpp -o tabixLoader.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tabix_index.c -o tabix_index.o tabix_index.c:19:14: warning: ‘currentTime’ defined but not used [-Wunused-function] 19 | static char* currentTime(void) { | ^~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -D_USE_KNETFILE -I. -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c vcf.c -o vcf.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -D_USE_KNETFILE -I. -g -O2 -Wall -pedantic -mtune=native -DHAVE_SQLITE -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -Izstd/lib -Izstd/lib/common -DXXH_NAMESPACE=ZSTD_ -Izstd/lib/legacy -DZSTD_LEGACY_SUPPORT=5 -DR_NO_REMAP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c vcf2genoLoader.cpp -o vcf2genoLoader.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o seqminer.so BCFReader.o BGenFile.o BGenIndex.o BGenVariant.o Exception.o FileIO.o GeneLoader.o MmapFile.o PatternMatch.o PeopleSet.o PlinkInputFile.o PlinkOutputFile.o Profiler.o R_CPP_interface.o RangeList.o Rannotation.o SimpleMatrix.o SingleChromosomeBCFIndex.o SingleChromosomeVCFIndex.o TypeConversion.o Utils.o VCFHeader.o VCFIndividual.o VCFInfo.o VCFInputFile.o VCFUtil.o bcf.o bcf_index.o bcfutils.o bedidx.o bgen2genoLoader.o bgzf.o knetfile.o kstring.o plink2genoLoader.o rvMetaLoader.o scbcf2genoLoader.o scvcf2genoLoader.o seqForStat.o seqminer.o seqminer_init.o tabixLoader.o tabix_index.o vcf.o vcf2genoLoader.o -lz -lm -lbz2 -lzstd -lsqlite3 -lzstd -lsqlite3 -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqDGMWL/R.INSTALL30c30b6d75d7b5/seqminer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-seqminer/00new/seqminer/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 (seqminer) * installing *source* package ‘paws.management’ ... ** this is package ‘paws.management’ version ‘0.9.0’ ** package ‘paws.management’ 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 (paws.management) * 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 ‘paws.compute’ ... ** this is package ‘paws.compute’ version ‘0.9.0’ ** package ‘paws.compute’ 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 (paws.compute) * installing *source* package ‘paws.security.identity’ ... ** this is package ‘paws.security.identity’ version ‘0.9.0’ ** package ‘paws.security.identity’ 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 (paws.security.identity) * installing *source* package ‘paws.machine.learning’ ... ** this is package ‘paws.machine.learning’ version ‘0.9.0’ ** package ‘paws.machine.learning’ 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 (paws.machine.learning) begin installing package ‘smdocker’ * installing *source* package ‘smdocker’ ... ** this is package ‘smdocker’ version ‘0.1.4’ ** package ‘smdocker’ 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 (smdocker) checking plumber_1.3.2.tar.gz ... checking arenar_0.2.0.tar.gz ... checking microCRAN_0.9.0-1.tar.gz ... checking plumbertableau_0.1.1.tar.gz ... checking ReliaGrowR_0.3.2.tar.gz ... checking starsTileServer_0.1.1.tar.gz ... checking AzureContainers_1.3.3.tar.gz ... checking gaawr2_0.0.3.tar.gz ... checking gqlr_0.0.2.tar.gz ... checking log_1.1.1.tar.gz ... checking MicroMoB_0.1.2.tar.gz ... checking occupationMeasurement_0.3.2.tar.gz ... checking openmetrics_0.3.0.tar.gz ... checking polished_0.8.1.tar.gz ... checking rapidoc_9.3.4.tar.gz ... checking redoc_2.0.0.75.tar.gz ... checking rsconnect_1.7.0.tar.gz ... checking shiny.telemetry_0.3.2.tar.gz ... checking swagger_5.17.14.1.tar.gz ... checking vetiver_0.2.7.tar.gz ... Depends: Package: plumber Depends: R (>= 3.0.0) Imports: crayon, httpuv (>= 1.5.5), jsonlite (>= 0.9.16), lifecycle (>= 1.0.0), magrittr, mime, promises (>= 1.1.0), R6 (>= 2.0.0), rlang (>= 1.0.0), sodium, stringi (>= 0.3.0), swagger (>= 3.33.0), webutils (>= 1.1) Timings: user system elapsed plumber 60.927 5.068 68.373 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 3 16 Check results summary: plumber ... OK rdepends_arenar ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_AzureContainers ... OK rdepends_gaawr2 ... OK rdepends_gqlr ... OK rdepends_log ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_microCRAN ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_MicroMoB ... OK rdepends_occupationMeasurement ... OK rdepends_openmetrics ... OK rdepends_plumbertableau ... OK rdepends_polished ... OK rdepends_rapidoc ... OK rdepends_redoc ... OK rdepends_ReliaGrowR ... OK rdepends_rsconnect ... OK rdepends_shiny.telemetry ... OK rdepends_starsTileServer ... OK rdepends_swagger ... OK rdepends_vetiver ... OK