downloading reverse dependencies ... downloading ambiorix_2.2.0.tar.gz ... ok downloading animate_0.3.9.4.tar.gz ... ok downloading bea.R_1.0.6.tar.gz ... ok downloading beakr_0.4.3.tar.gz ... ok downloading blogdown_1.21.tar.gz ... ok downloading BrownDog_0.2.1.tar.gz ... ok downloading bs4Dash_2.3.4.tar.gz ... ok downloading cookies_0.2.3.tar.gz ... ok downloading DT_0.33.tar.gz ... ok downloading emuR_2.5.0.tar.gz ... ok downloading fiery_1.2.1.tar.gz ... ok downloading ggfigdone_0.1.2.tar.gz ... ok downloading JBrowseR_0.10.2.tar.gz ... ok downloading jrc_0.6.0.tar.gz ... ok downloading mlflow_2.21.3.tar.gz ... ok downloading opencpu_2.2.14.tar.gz ... ok downloading pagedown_0.22.tar.gz ... ok downloading plotscaper_0.2.8.tar.gz ... ok downloading plumber_1.3.0.tar.gz ... ok downloading plumbertableau_0.1.1.tar.gz ... ok downloading Rfacebook_0.6.15.tar.gz ... ok downloading rfigshare_0.3.8.tar.gz ... ok downloading Rlinkedin_0.2.tar.gz ... ok downloading servr_0.32.tar.gz ... ok downloading shiny_1.10.0.tar.gz ... ok downloading shinylight_1.2.tar.gz ... ok downloading shinyloadtest_1.2.0.tar.gz ... ok downloading shinytest_1.6.1.tar.gz ... ok downloading sleepwalk_0.3.2.tar.gz ... ok downloading telegram.bot_3.0.0.tar.gz ... ok downloading tfdeploy_0.6.1.tar.gz ... ok downloading VOSONDash_0.5.7.tar.gz ... ok downloading webdav_0.1.4.tar.gz ... ok downloading webdeveloper_1.0.5.tar.gz ... ok downloading webglobe_1.0.3.tar.gz ... ok downloading workflowr_1.7.1.tar.gz ... ok downloading AzureAuth_1.3.3.tar.gz ... ok downloading AzureRMR_2.4.4.tar.gz ... ok downloading curl_6.2.2.tar.gz ... ok downloading gaawr2_0.0.3.tar.gz ... ok downloading gargle_1.5.2.tar.gz ... ok downloading golem_0.5.1.tar.gz ... ok downloading googleVis_0.7.3.tar.gz ... ok downloading httr_1.4.7.tar.gz ... ok downloading httr2_1.1.2.tar.gz ... ok downloading learnr_0.11.5.tar.gz ... ok downloading osmapiR_0.2.3.tar.gz ... ok downloading rlc_0.5.0.tar.gz ... ok downloading rorcid_0.7.0.tar.gz ... ok downloading shinylive_0.3.0.tar.gz ... ok downloading sship_0.9.0.tar.gz ... ok downloading tidyllm_0.3.4.tar.gz ... ok downloading tricolore_1.2.4.tar.gz ... ok downloading urlshorteneR_2.0.0.tar.gz ... ok downloading vetiver_0.2.5.tar.gz ... ok downloading vkR_0.2.tar.gz ... ok downloading vosonSML_0.32.7.tar.gz ... ok downloading webfakes_1.3.2.tar.gz ... ok downloading webshot_0.5.5.tar.gz ... ok downloading webshot2_0.1.1.tar.gz ... ok downloading websocket_1.4.4.tar.gz ... ok downloading webutils_1.2.2.tar.gz ... ok installing dependencies ‘attachment’, ‘aws.ec2metadata’, ‘AzureStor’, ‘BGLR’, ‘BLR’, ‘brotli’, ‘bundle’, ‘carrier’, ‘cereal’, ‘cloudml’, ‘compare’, ‘dockerfiler’, ‘dotenv’, ‘ellmer’, ‘EnsDb.Hsapiens.v75’, ‘ensembldb’, ‘forge’, ‘fortunes’, ‘ggtern’, ‘globals’, ‘GMMAT’, ‘handlr’, ‘HardyWeinberg’, ‘html5’, ‘httpuv’, ‘hwriter’, ‘jrc’, ‘LiblineaR’, ‘log’, ‘luz’, ‘mlr3data’, ‘paws.machine.learning’, ‘pins’, ‘pixels’, ‘pkgcache’, ‘pkgdepends’, ‘powerEQTL’, ‘rapidoc’, ‘rcrossref’, ‘reactlog’, ‘redoc’, ‘regress’, ‘reqres’, ‘revealjs’, ‘rgexf’, ‘robotstxt’, ‘rtweet’, ‘seqminer’, ‘smdocker’, ‘SNPassoc’, ‘stacks’, ‘thematic’, ‘unix’, ‘vosonSML’, ‘wrassp’, ‘yyjsonr’ Warning: package ‘rtweet’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘AnnotationFilter’, ‘ProtGenerics’, ‘poisbinom’, ‘paws.compute’, ‘paws.developer.tools’, ‘paws.management’, ‘paws.security.identity’, ‘spiderbar’ begin installing package ‘AnnotationFilter’ begin installing package ‘poisbinom’ begin installing package ‘ProtGenerics’ begin installing package ‘paws.compute’ begin installing package ‘paws.developer.tools’ begin installing package ‘paws.management’ begin installing package ‘paws.security.identity’ begin installing package ‘spiderbar’ begin installing package ‘log’ begin installing package ‘yyjsonr’ begin installing package ‘thematic’ begin installing package ‘wrassp’ begin installing package ‘compare’ begin installing package ‘forge’ begin installing package ‘carrier’ begin installing package ‘unix’ begin installing package ‘revealjs’ begin installing package ‘redoc’ begin installing package ‘rapidoc’ begin installing package ‘reactlog’ begin installing package ‘cloudml’ begin installing package ‘httpuv’ begin installing package ‘vosonSML’ begin installing package ‘fortunes’ begin installing package ‘html5’ begin installing package ‘AzureStor’ begin installing package ‘BLR’ begin installing package ‘BGLR’ * 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 ‘GMMAT’ * 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 ‘HardyWeinberg’ * installing *source* package ‘fortunes’ ... ** this is package ‘fortunes’ version ‘1.5-4’ ** package ‘fortunes’ 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 (fortunes) begin installing package ‘powerEQTL’ * installing *source* package ‘reactlog’ ... ** this is package ‘reactlog’ version ‘1.1.1’ ** package ‘reactlog’ 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 (reactlog) begin installing package ‘regress’ * installing *source* package ‘carrier’ ... ** this is package ‘carrier’ version ‘0.1.1’ ** package ‘carrier’ 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 (carrier) begin installing package ‘seqminer’ * installing *source* package ‘forge’ ... ** this is package ‘forge’ version ‘0.2.0’ ** package ‘forge’ 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 (forge) begin installing package ‘aws.ec2metadata’ * 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-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp7Sc6R5/R.INSTALL1683a845bcb0b9/BLR/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o BLR.so init.o sample_betas.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7Sc6R5/R.INSTALL1683a845bcb0b9/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 ‘attachment’ * installing *source* package ‘compare’ ... ** this is package ‘compare’ version ‘0.2-6’ ** package ‘compare’ 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 (compare) begin installing package ‘dockerfiler’ * installing *source* package ‘html5’ ... ** this is package ‘html5’ version ‘1.0.2’ ** package ‘html5’ 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 (html5) begin installing package ‘hwriter’ * installing *source* package ‘log’ ... ** this is package ‘log’ version ‘1.1.1’ ** package ‘log’ 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 (log) * installing *source* package ‘revealjs’ ... ** this is package ‘revealjs’ version ‘0.10.0’ ** package ‘revealjs’ 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 (revealjs) begin installing package ‘handlr’ begin installing package ‘pkgcache’ * installing *source* package ‘unix’ ... ** this is package ‘unix’ version ‘1.5.9’ ** package ‘unix’ successfully unpacked and MD5 sums checked ** using staged installation Checking for AppArmor... (Linux) Found pkg-config cflags/libs! Using PKG_CFLAGS= Using PKG_LIBS=-lapparmor ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1xG5V3/R.INSTALL16838d18016322/unix/src' rm -f unix.so chroot.o fork.o process.o register.o rlimit.o userinfo.o util.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DHAVE_APPARMOR -DSYS_BUILD_SAFE -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c chroot.c -o chroot.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DHAVE_APPARMOR -DSYS_BUILD_SAFE -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fork.c -o fork.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DHAVE_APPARMOR -DSYS_BUILD_SAFE -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c process.c -o process.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DHAVE_APPARMOR -DSYS_BUILD_SAFE -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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DHAVE_APPARMOR -DSYS_BUILD_SAFE -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rlimit.c -o rlimit.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DHAVE_APPARMOR -DSYS_BUILD_SAFE -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c userinfo.c -o userinfo.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DHAVE_APPARMOR -DSYS_BUILD_SAFE -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o unix.so chroot.o fork.o process.o register.o rlimit.o userinfo.o util.o -lapparmor -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1xG5V3/R.INSTALL16838d18016322/unix/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-unix/00new/unix/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 (unix) begin installing package ‘ellmer’ * installing *source* package ‘cloudml’ ... ** this is package ‘cloudml’ version ‘0.6.1’ ** package ‘cloudml’ 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 (cloudml) begin installing package ‘ggtern’ * installing *source* package ‘ProtGenerics’ ... ** this is package ‘ProtGenerics’ version ‘1.39.2’ ** 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) begin installing package ‘dotenv’ * installing *source* package ‘powerEQTL’ ... ** this is package ‘powerEQTL’ version ‘0.3.4’ ** 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) begin installing package ‘bundle’ * installing *source* package ‘regress’ ... ** this is package ‘regress’ version ‘1.3-21’ ** 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 ‘cereal’ * installing *source* package ‘thematic’ ... ** this is package ‘thematic’ version ‘0.1.6’ ** package ‘thematic’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (thematic) begin installing package ‘pins’ * installing *source* package ‘aws.ec2metadata’ ... ** this is package ‘aws.ec2metadata’ version ‘0.2.0’ ** package ‘aws.ec2metadata’ 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 (aws.ec2metadata) begin installing package ‘LiblineaR’ * installing *source* package ‘hwriter’ ... ** this is package ‘hwriter’ version ‘1.3.2.1’ ** package ‘hwriter’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hwriter) begin installing package ‘luz’ * installing *source* package ‘dotenv’ ... ** this is package ‘dotenv’ version ‘1.0.3’ ** package ‘dotenv’ 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 (dotenv) begin installing package ‘mlr3data’ * installing *source* package ‘AzureStor’ ... ** this is package ‘AzureStor’ version ‘3.7.0’ ** package ‘AzureStor’ 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 (AzureStor) begin installing package ‘paws.machine.learning’ * 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) begin installing package ‘globals’ * installing *source* package ‘dockerfiler’ ... ** this is package ‘dockerfiler’ version ‘0.2.4’ ** package ‘dockerfiler’ 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 (dockerfiler) begin installing package ‘brotli’ * installing *source* package ‘bundle’ ... ** this is package ‘bundle’ version ‘0.1.2’ ** 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) * installing *source* package ‘attachment’ ... ** this is package ‘attachment’ version ‘0.4.5’ ** package ‘attachment’ 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 (attachment) * installing *source* package ‘vosonSML’ ... ** this is package ‘vosonSML’ version ‘0.32.7’ ** package ‘vosonSML’ 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 (vosonSML) * installing *source* package ‘handlr’ ... ** this is package ‘handlr’ version ‘0.3.1’ ** package ‘handlr’ 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 (handlr) * installing *source* package ‘globals’ ... ** this is package ‘globals’ version ‘0.17.0’ ** package ‘globals’ 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 (globals) begin installing package ‘stacks’ * installing *source* package ‘LiblineaR’ ... ** this is package ‘LiblineaR’ version ‘2.10-24’ ** package ‘LiblineaR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMMaI8b/R.INSTALL1690365ca7bc5c/LiblineaR/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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 g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c linear.cpp -o linear.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c predictLinear.c -o predictLinear.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trainLinear.c -o trainLinear.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tron.cpp -o tron.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o LiblineaR.so init.o linear.o predictLinear.o trainLinear.o tron.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMMaI8b/R.INSTALL1690365ca7bc5c/LiblineaR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-LiblineaR/00new/LiblineaR/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 (LiblineaR) * installing *source* package ‘ellmer’ ... ** this is package ‘ellmer’ version ‘0.1.1’ ** package ‘ellmer’ 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 (ellmer) * installing *source* package ‘poisbinom’ ... ** this is package ‘poisbinom’ version ‘1.0.1’ ** package ‘poisbinom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHDfARN/R.INSTALL16835589ebc82/poisbinom/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o poisbinom.so RcppExports.o init.o poisbinom.o -lfftw3 -lm -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHDfARN/R.INSTALL16835589ebc82/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 ‘BGLR’ ... ** this is package ‘BGLR’ version ‘1.1.4’ ** package ‘BGLR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZOc3b7/R.INSTALL1683aa134a735/BGLR/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util_sample.c -o util_sample.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util_plink.c -o util_plink.o util_plink.c: In function ‘read_string’: util_plink.c:39:25: warning: pointer ‘buffer’ may be used after ‘realloc’ [-Wuse-after-free] 39 | free(buffer); | ^~~~~~~~~~~~ util_plink.c:36:43: note: call to ‘realloc’ here 36 | char *tmp = (char *) realloc(buffer, buf_size); | ^~~~~~~~~~~~~~~~~~~~~~~~~ util_plink.c: In function ‘read_ped_’: util_plink.c:190:23: warning: ‘Line_copy’ may be used uninitialized [-Wmaybe-uninitialized] 190 | token=strtok(Line_copy,"\t "); | ^~~~~~~~~~~~~~~~~~~~~~~ util_plink.c:105:15: note: ‘Line_copy’ was declared here 105 | char *Line_copy; | ^~~~~~~~~ util_plink.c:263:17: warning: ‘Line’ may be used uninitialized [-Wmaybe-uninitialized] 263 | free(Line); | ^~~~~~~~~~ util_plink.c:104:15: note: ‘Line’ was declared here 104 | char *Line; | ^~~~ util_plink.c:229:51: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 229 | if(tmp=='0' && token[0]=='0') | ^ util_plink.c:114:14: note: ‘tmp’ was declared here 114 | char tmp; | ^~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util_sample_cross.c -o util_sample_cross.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sampler_multitrait.c -o sampler_multitrait.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -I. -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o BGLR.so util_sample.o util_plink.o util_sample_cross.o sampler_multitrait.o init.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZOc3b7/R.INSTALL1683aa134a735/BGLR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BGLR/00new/BGLR/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BGLR) * installing *source* package ‘pins’ ... ** this is package ‘pins’ version ‘1.4.0’ ** package ‘pins’ 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 (pins) * installing *source* package ‘AnnotationFilter’ ... ** this is package ‘AnnotationFilter’ version ‘1.31.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (AnnotationFilter) begin installing package ‘ensembldb’ * installing *source* package ‘ggtern’ ... ** this is package ‘ggtern’ version ‘3.5.0’ ** package ‘ggtern’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ggtern) * 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 ‘wrassp’ ... ** this is package ‘wrassp’ version ‘1.0.5’ ** package ‘wrassp’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpLI7V6v/R.INSTALL16837e4c2f0ac9/wrassp/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/acf.c -o assp/acf.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/dataobj.c -o assp/dataobj.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/freqconv.c -o assp/freqconv.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/mhs.c -o assp/mhs.o assp/mhs.c: In function ‘computeMHS’: assp/mhs.c:448:12: warning: variable ‘FILE_IN’ set but not used [-Wunused-but-set-variable] 448 | int FILE_IN, FILE_OUT, CREATED, VOICED; | ^~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/smp2dur.c -o assp/smp2dur.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/asspana.c -o assp/asspana.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/diff.c -o assp/diff.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/headers.c -o assp/headers.o assp/headers.c: In function ‘getAIFhdr’: assp/headers.c:882:12: warning: variable ‘blockSize’ set but not used [-Wunused-but-set-variable] 882 | uint32_t blockSize; | ^~~~~~~~~ assp/headers.c: In function ‘getCSLhdr’: assp/headers.c:1231:12: warning: variable ‘peakMag’ set but not used [-Wunused-but-set-variable] 1231 | int16_t peakMag; | ^~~~~~~ assp/headers.c: In function ‘getWAVhdr’: assp/headers.c:1828:22: warning: variable ‘lspPosMask’ set but not used [-Wunused-but-set-variable] 1828 | uint32_t byteRate, lspPosMask; | ^~~~~~~~~~ assp/headers.c:1828:12: warning: variable ‘byteRate’ set but not used [-Wunused-but-set-variable] 1828 | uint32_t byteRate, lspPosMask; | ^~~~~~~~ assp/headers.c: In function ‘putSSFFhdr’: assp/headers.c:2824:7: warning: unused variable ‘prev_header_length’ [-Wunused-variable] 2824 | int prev_header_length = strlen(header); | ^~~~~~~~~~~~~~~~~~ assp/headers.c: At top level: assp/headers.c:875:11: warning: ‘getAIFhdr’ defined but not used [-Wunused-function] 875 | LOCAL int getAIFhdr(DOBJ *dop) | ^~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/miscstring.c -o assp/miscstring.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/spectra.c -o assp/spectra.o assp/spectra.c: In function ‘freeSPECT_GD’: assp/spectra.c:734:13: warning: unused variable ‘gd’ [-Wunused-variable] 734 | SPECT_GD *gd; | ^~ assp/spectra.c: In function ‘getCepstrum’: assp/spectra.c:932:23: warning: unused variable ‘M’ [-Wunused-variable] 932 | register long n, N, M, L; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/asspfio.c -o assp/asspfio.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/dsputils.c -o assp/dsputils.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/isgerman.c -o assp/isgerman.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/myrand.c -o assp/myrand.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/statistics.c -o assp/statistics.o assp/statistics.c: In function ‘statPrintHist’: assp/statistics.c:478:10: warning: unused variable ‘centre’ [-Wunused-variable] 478 | double centre; | ^~~~~~ assp/statistics.c:477:10: warning: unused variable ‘i’ [-Wunused-variable] 477 | size_t i; | ^ assp/statistics.c:476:14: warning: unused variable ‘nd1’ [-Wunused-variable] 476 | int nd, nd1; | ^~~ assp/statistics.c:476:10: warning: unused variable ‘nd’ [-Wunused-variable] 476 | int nd, nd1; | ^~ assp/statistics.c:475:10: warning: unused variable ‘format’ [-Wunused-variable] 475 | char format[32]; | ^~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/asspmess.c -o assp/asspmess.o assp/asspmess.c: In function ‘prtAsspMsg’: assp/asspmess.c:169:9: warning: unused variable ‘funcVal’ [-Wunused-variable] 169 | int funcVal; | ^~~~~~~ assp/asspmess.c:168:20: warning: unused variable ‘indent’ [-Wunused-variable] 168 | char *msg, *bug, indent[16]; | ^~~~~~ assp/asspmess.c:168:15: warning: unused variable ‘bug’ [-Wunused-variable] 168 | char *msg, *bug, indent[16]; | ^~~ assp/asspmess.c:168:9: warning: unused variable ‘msg’ [-Wunused-variable] 168 | char *msg, *bug, indent[16]; | ^~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/fft.c -o assp/fft.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/ksv.c -o assp/ksv.o assp/ksv.c: In function ‘computeKSV’: assp/ksv.c:503:20: warning: unused variable ‘n’ [-Wunused-variable] 503 | int err, nd, n, type; | ^ assp/ksv.c:503:16: warning: unused variable ‘nd’ [-Wunused-variable] 503 | int err, nd, n, type; | ^~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/myrint.c -o assp/myrint.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/trace.c -o assp/trace.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/aucheck.c -o assp/aucheck.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/fgetl.c -o assp/fgetl.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/labelobj.c -o assp/labelobj.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/numdecim.c -o assp/numdecim.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/winfuncs.c -o assp/winfuncs.o assp/winfuncs.c: In function ‘listWFs’: assp/winfuncs.c:1139:11: warning: unused variable ‘specs’ [-Wunused-variable] 1139 | WFDATA *specs; | ^~~~~ assp/winfuncs.c:1138:11: warning: unused variable ‘wPtr’ [-Wunused-variable] 1138 | WFLIST *wPtr; | ^~~~ assp/winfuncs.c:1137:14: warning: unused variable ‘m’ [-Wunused-variable] 1137 | int l, m; | ^ assp/winfuncs.c:1137:11: warning: unused variable ‘l’ [-Wunused-variable] 1137 | int l, m; | ^ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/auconv.c -o assp/auconv.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/filter.c -o assp/filter.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/lpc.c -o assp/lpc.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/parsepath.c -o assp/parsepath.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/zcr.c -o assp/zcr.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/bitarray.c -o assp/bitarray.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/filters.c -o assp/filters.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/math.c -o assp/math.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/rfc.c -o assp/rfc.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/chain.c -o assp/chain.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/fmt.c -o assp/fmt.o assp/fmt.c:1795:11: warning: ‘printRaw’ defined but not used [-Wunused-function] 1795 | LOCAL int printRaw(FMTDATA *fPtr, long frameNr, int numFMT, DOBJ *dop) | ^~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/memswab.c -o assp/memswab.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c assp/rms.c -o assp/rms.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dataobj.c -o dataobj.o dataobj.c: In function ‘dobj2AsspDataObj’: dataobj.c:170:21: warning: unused variable ‘genVar’ [-Wunused-variable] 170 | TSSFF_Generic *genVar = NULL; | ^~~~~~ dataobj.c: In function ‘getDObjTrackData’: dataobj.c:405:21: warning: variable ‘i8Ptr’ set but not used [-Wunused-but-set-variable] 405 | int8_t *i8Ptr; | ^~~~~ dataobj.c:397:21: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 397 | int i, | ^ dataobj.c: In function ‘sexp2dobj’: dataobj.c:608:21: warning: unused variable ‘varNames’ [-Wunused-variable] 608 | varNames; | ^~~~~~~~ dataobj.c:602:21: warning: unused variable ‘numFields’ [-Wunused-variable] 602 | size_t numFields = -1; | ^~~~~~~~~ dataobj.c: In function ‘addTrackData’: dataobj.c:894:21: warning: variable ‘i8Ptr’ set but not used [-Wunused-but-set-variable] 894 | int8_t *i8Ptr; | ^~~~~ dataobj.c:886:21: warning: variable ‘i’ set but not used [-Wunused-but-set-variable] 886 | int i, | ^ dataobj.c: At top level: dataobj.c:142:1: warning: ‘DObjFinalizer’ defined but not used [-Wunused-function] 142 | DObjFinalizer(SEXP dPtr) | ^~~~~~~~~~~~~ dataobj.c: In function ‘getDObjTrackData’: dataobj.c:413:21: warning: ‘Rans’ may be used uninitialized [-Wmaybe-uninitialized] 413 | double *Rans; | ^~~~ dataobj.c:414:21: warning: ‘Ians’ may be used uninitialized [-Wmaybe-uninitialized] 414 | int *Ians; | ^~~~ dataobj.c:404:21: warning: ‘u8Ptr’ may be used uninitialized [-Wmaybe-uninitialized] 404 | uint8_t *u8Ptr; | ^~~~~ dataobj.c: In function ‘addTrackData’: dataobj.c:933:30: warning: ‘u8Ptr’ may be used uninitialized [-Wmaybe-uninitialized] 933 | u8Ptr[n] = (int8_t) numPtr[m + n * dop->numRecords]; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dataobj.c:893:21: note: ‘u8Ptr’ was declared here 893 | uint8_t *u8Ptr; | ^~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c performAssp.c -o performAssp.o performAssp.c: In function ‘computeFilter’: performAssp.c:1231:21: warning: variable ‘FILE_IN’ set but not used [-Wunused-but-set-variable] 1231 | int FILE_IN, | ^~~~~~~ In file included from wrassp.h:5, from performAssp.c:1: performAssp.c: In function ‘performAssp’: /home/hornik/tmp/R-d-gcc-14/include/Rinternals.h:934:33: warning: ‘utilsPackage’ may be used uninitialized [-Wmaybe-uninitialized] 934 | #define eval Rf_eval performAssp.c:1188:13: note: in expansion of macro ‘eval’ 1188 | eval(R_fcall3, utilsPackage); | ^~~~ performAssp.c:490:9: note: ‘utilsPackage’ was declared here 490 | utilsPackage, /* to update the prograssbar */ | ^~~~~~~~~~~~ performAssp.c:1187:28: warning: ‘newVal’ may be used uninitialized [-Wmaybe-uninitialized] 1187 | INTEGER(newVal)[0] = i + 1; | ^ performAssp.c:491:9: note: ‘newVal’ was declared here 491 | newVal, | ^~~~~~ performAssp.c:1217:12: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 1217 | return res; | ^~~ performAssp.c:488:21: note: ‘res’ was declared here 488 | res, | ^~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c types.c -o types.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I assp -DWRASSP -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wrassp_init.c -o wrassp_init.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o wrassp.so assp/acf.o assp/dataobj.o assp/freqconv.o assp/mhs.o assp/smp2dur.o assp/asspana.o assp/diff.o assp/headers.o assp/miscstring.o assp/spectra.o assp/asspfio.o assp/dsputils.o assp/isgerman.o assp/myrand.o assp/statistics.o assp/asspmess.o assp/fft.o assp/ksv.o assp/myrint.o assp/trace.o assp/aucheck.o assp/fgetl.o assp/labelobj.o assp/numdecim.o assp/winfuncs.o assp/auconv.o assp/filter.o assp/lpc.o assp/parsepath.o assp/zcr.o assp/bitarray.o assp/filters.o assp/math.o assp/rfc.o assp/chain.o assp/fmt.o assp/memswab.o assp/rms.o dataobj.o performAssp.o types.o wrassp_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpLI7V6v/R.INSTALL16837e4c2f0ac9/wrassp/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-wrassp/00new/wrassp/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (wrassp) * installing *source* package ‘luz’ ... ** this is package ‘luz’ version ‘0.4.0’ ** package ‘luz’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading R6Class keep_best_model_callback: finalize() method is public, but it should be private as of R6 2.4.0. This code will continue to work, but in a future version of R6, finalize() will be required to be private. ** 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 ‘pkgcache’ ... ** this is package ‘pkgcache’ version ‘2.2.3’ ** package ‘pkgcache’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8OP834/R.INSTALL168acc404ecde9/pkgcache/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c errors.c -o errors.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lib.c -o lib.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c winfiles.c -o winfiles.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o pkgcache.so errors.o init.o lib.o winfiles.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8OP834/R.INSTALL168acc404ecde9/pkgcache/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pkgcache/00new/pkgcache/libs ** R ** inst ** byte-compile and prepare package for lazy loading R6Class : finalize() method is public, but it should be private as of R6 2.4.0. This code will continue to work, but in a future version of R6, finalize() will be required to be private. ** help *** installing help indices *** copying figures ** 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 (pkgcache) begin installing package ‘pkgdepends’ * installing *source* package ‘stacks’ ... ** this is package ‘stacks’ version ‘1.0.5’ ** 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 ‘spiderbar’ ... ** this is package ‘spiderbar’ version ‘0.2.5’ ** package ‘spiderbar’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpeSdPrO/R.INSTALL16835829ea3c7a/spiderbar/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 agent.cpp -o agent.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 directive.cpp -o directive.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 psl.cpp -o psl.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 punycode.cpp -o punycode.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 repmain.cpp -o repmain.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 robots.cpp -o robots.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 url.cpp -o url.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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 utf8.cpp -o utf8.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o spiderbar.so RcppExports.o agent.o directive.o psl.o punycode.o repmain.o robots.o url.o utf8.o -L. -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpeSdPrO/R.INSTALL16835829ea3c7a/spiderbar/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-spiderbar/00new/spiderbar/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 (spiderbar) begin installing package ‘robotstxt’ * installing *source* package ‘robotstxt’ ... ** this is package ‘robotstxt’ version ‘0.7.15’ ** package ‘robotstxt’ 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 (robotstxt) * 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 ‘yyjsonr’ ... ** this is package ‘yyjsonr’ version ‘0.1.20’ ** package ‘yyjsonr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp1TgI5I/R.INSTALL1683686d15a3ff/yyjsonr/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R-yyjson-parse.c -o R-yyjson-parse.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R-yyjson-serialize.c -o R-yyjson-serialize.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c geojson-parse.c -o geojson-parse.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c geojson-serialize.c -o geojson-serialize.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ndjson-parse.c -o ndjson-parse.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ndjson-serialize.c -o ndjson-serialize.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c utils.c -o utils.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c yyjson.c -o yyjson.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o yyjsonr.so R-yyjson-parse.o R-yyjson-serialize.o geojson-parse.o geojson-serialize.o init.o ndjson-parse.o ndjson-serialize.o utils.o yyjson.o -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp1TgI5I/R.INSTALL1683686d15a3ff/yyjsonr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-yyjsonr/00new/yyjsonr/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 (yyjsonr) * installing *source* package ‘HardyWeinberg’ ... ** this is package ‘HardyWeinberg’ version ‘1.7.8’ ** package ‘HardyWeinberg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjeofeV/R.INSTALL168755629c2406/HardyWeinberg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o HardyWeinberg.so HWxChromosomal.o RcppExports.o SNPHWEX.o support.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjeofeV/R.INSTALL168755629c2406/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 ‘brotli’ ... ** this is package ‘brotli’ version ‘1.3.2’ ** package ‘brotli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHtS4jL/R.INSTALL16930155c6e6d/brotli/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wrapper.c -o wrapper.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/backward_references.c -o enc/backward_references.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/bit_cost.c -o enc/bit_cost.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/block_splitter.c -o enc/block_splitter.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/brotli_bit_stream.c -o enc/brotli_bit_stream.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/cluster.c -o enc/cluster.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/compress_fragment_two_pass.c -o enc/compress_fragment_two_pass.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/compress_fragment.c -o enc/compress_fragment.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/encode.c -o enc/encode.o enc/encode.c:1473:20: warning: argument 5 of type ‘const uint8_t *’ {aka ‘const unsigned char *’} declared as a pointer [-Wvla-parameter] 1473 | const uint8_t* input_buffer, size_t* encoded_size, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from enc/encode.c:9: include/brotli/encode.h:314:19: note: previously declared as a variable length array ‘const uint8_t[input_size]’ {aka ‘const unsigned char[input_size]’} 314 | const uint8_t input_buffer[BROTLI_ARRAY_PARAM(input_size)], | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ enc/encode.c:1474:14: warning: argument 7 of type ‘uint8_t *’ {aka ‘unsigned char *’} declared as a pointer [-Wvla-parameter] 1474 | uint8_t* encoded_buffer) { | ~~~~~~~~~^~~~~~~~~~~~~~ include/brotli/encode.h:316:13: note: previously declared as a variable length array ‘uint8_t[*encoded_size]’ {aka ‘unsigned char[*encoded_size]’} 316 | uint8_t encoded_buffer[BROTLI_ARRAY_PARAM(*encoded_size)]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/entropy_encode.c -o enc/entropy_encode.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/histogram.c -o enc/histogram.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/literal_cost.c -o enc/literal_cost.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/memory.c -o enc/memory.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/metablock.c -o enc/metablock.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/static_dict.c -o enc/static_dict.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/utf8_util.c -o enc/utf8_util.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dec/bit_reader.c -o dec/bit_reader.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dec/huffman.c -o dec/huffman.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dec/state.c -o dec/state.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dec/decode.c -o dec/decode.o dec/decode.c:2036:41: warning: argument 2 of type ‘const uint8_t *’ {aka ‘const unsigned char *’} declared as a pointer [-Wvla-parameter] 2036 | size_t encoded_size, const uint8_t* encoded_buffer, size_t* decoded_size, | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from dec/decode.c:7: include/brotli/decode.h:204:19: note: previously declared as a variable length array ‘const uint8_t[encoded_size]’ {aka ‘const unsigned char[encoded_size]’} 204 | const uint8_t encoded_buffer[BROTLI_ARRAY_PARAM(encoded_size)], | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dec/decode.c:2037:14: warning: argument 4 of type ‘uint8_t *’ {aka ‘unsigned char *’} declared as a pointer [-Wvla-parameter] 2037 | uint8_t* decoded_buffer) { | ~~~~~~~~~^~~~~~~~~~~~~~ include/brotli/decode.h:206:13: note: previously declared as a variable length array ‘uint8_t[*decoded_size]’ {aka ‘unsigned char[*decoded_size]’} 206 | uint8_t decoded_buffer[BROTLI_ARRAY_PARAM(*decoded_size)]); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common/dictionary.c -o common/dictionary.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/backward_references_hq.c -o enc/backward_references_hq.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/dictionary_hash.c -o enc/dictionary_hash.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common/transform.c -o common/transform.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/encoder_dict.c -o enc/encoder_dict.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common/platform.c -o common/platform.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common/context.c -o common/context.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common/constants.c -o common/constants.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/command.c -o enc/command.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c enc/fast_log.c -o enc/fast_log.o ar rcs enc/libstatbrotli.a enc/backward_references.o enc/bit_cost.o enc/block_splitter.o enc/brotli_bit_stream.o enc/cluster.o enc/compress_fragment_two_pass.o enc/compress_fragment.o enc/encode.o enc/entropy_encode.o enc/histogram.o enc/literal_cost.o enc/memory.o enc/metablock.o enc/static_dict.o enc/utf8_util.o dec/bit_reader.o dec/huffman.o dec/state.o dec/decode.o common/dictionary.o enc/backward_references_hq.o enc/dictionary_hash.o common/transform.o enc/encoder_dict.o common/platform.o common/context.o common/constants.o enc/command.o enc/fast_log.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o brotli.so wrapper.o -Lenc -lstatbrotli -L/home/hornik/tmp/R-d-gcc-14/lib -lR gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DBROTLI_BUILD_PORTABLE -Iinclude -include config.h -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fvisibility=hidden -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tools/brotli.c -o tools/brotli.o mkdir -p ../inst/bin g++-14 -std=gnu++17 -o ../inst/bin/bro tools/brotli.o -Lenc -lstatbrotli -Wl,-O1 rm -f enc/backward_references.o enc/bit_cost.o enc/block_splitter.o enc/brotli_bit_stream.o enc/cluster.o enc/compress_fragment_two_pass.o enc/compress_fragment.o enc/encode.o enc/entropy_encode.o enc/histogram.o enc/literal_cost.o enc/memory.o enc/metablock.o enc/static_dict.o enc/utf8_util.o dec/bit_reader.o dec/huffman.o dec/state.o dec/decode.o common/dictionary.o enc/backward_references_hq.o enc/dictionary_hash.o common/transform.o enc/encoder_dict.o common/platform.o common/context.o common/constants.o enc/command.o enc/fast_log.o ../inst/bin/bro enc/libstatbrotli.a tools/brotli.o make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHtS4jL/R.INSTALL16930155c6e6d/brotli/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-brotli/00new/brotli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (brotli) begin installing package ‘reqres’ * installing *source* package ‘pkgdepends’ ... ** this is package ‘pkgdepends’ version ‘0.8.0’ ** package ‘pkgdepends’ successfully unpacked and MD5 sums checked ** using staged installation *** Running ./configure ** 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 (pkgdepends) * installing *source* package ‘reqres’ ... ** this is package ‘reqres’ version ‘0.2.5’ ** package ‘reqres’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (reqres) * installing *source* package ‘GMMAT’ ... ** this is package ‘GMMAT’ version ‘1.4.2’ ** 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++-14 -std=gnu++17 accepts -g... yes checking how to run the C++ preprocessor... g++-14 -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-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9wPWYW/R.INSTALL16872a1933adb2/GMMAT/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o GMMAT.so fitglmm.o registerDynamicSymbol.o -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -lz -lbz2 -lzstd -ldeflate -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9wPWYW/R.INSTALL16872a1933adb2/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 ‘2.31.0’ ** 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 ‘httpuv’ ... ** this is package ‘httpuv’ version ‘1.6.16’ ** using staged installation ** Using libuv found by pkg-config in /usr ** PKG_CFLAGS= ** PKG_LIBS=-luv -lpthread -ldl -lrt ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpbNSPbZ/R.INSTALL16839eea9dd94/httpuv/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c callback.cpp -o callback.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c callbackqueue.cpp -o callbackqueue.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c filedatasource-unix.cpp -o filedatasource-unix.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c filedatasource-win.cpp -o filedatasource-win.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c fs.cpp -o fs.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c gzipdatasource.cpp -o gzipdatasource.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c http.cpp -o http.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c httprequest.cpp -o httprequest.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c httpresponse.cpp -o httpresponse.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c httpuv.cpp -o httpuv.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c md5.c -o md5.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c mime.cpp -o mime.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c socket.cpp -o socket.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c staticpath.cpp -o staticpath.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c thread.cpp -o thread.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c timegm.cpp -o timegm.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c utils.cpp -o utils.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c uvutil.cpp -o uvutil.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c webapplication.cpp -o webapplication.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c websockets-base.cpp -o websockets-base.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c websockets-hixie76.cpp -o websockets-hixie76.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c websockets-hybi03.cpp -o websockets-hybi03.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c websockets-ietf.cpp -o websockets-ietf.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c websockets.cpp -o websockets.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c winutils.cpp -o winutils.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c http-parser/http_parser.c -o http-parser/http_parser.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sha1/sha1.c -o sha1/sha1.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -pthread -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/later/include' -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 -DSTRICT_R_HEADERS -fpic -g -O2 -Wall -pedantic -mtune=native -c base64/base64.cpp -o base64/base64.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o httpuv.so RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o fs.o gzipdatasource.o http.o httprequest.o httpresponse.o httpuv.o md5.o mime.o socket.o staticpath.o thread.o timegm.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o winutils.o -luv -lpthread -ldl -lrt ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpbNSPbZ/R.INSTALL16839eea9dd94/httpuv/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-httpuv/00new/httpuv/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 (httpuv) begin installing package ‘pixels’ begin installing package ‘rcrossref’ begin installing package ‘rgexf’ begin installing package ‘jrc’ * installing *source* package ‘pixels’ ... ** this is package ‘pixels’ version ‘0.1.1’ ** package ‘pixels’ 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 (pixels) * installing *source* package ‘jrc’ ... ** this is package ‘jrc’ version ‘0.6.0’ ** package ‘jrc’ 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 (jrc) * 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-14 -std=gnu23 configure: CFLAGS = -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native configure: CXX = g++-14 -std=gnu++11 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++-14 -std=gnu++11 accepts -g... yes checking how to run the C++ preprocessor... g++-14 -std=gnu++11 -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-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpjQmvd0/R.INSTALL1687c12df13262/seqminer/src' have SQLite have bzip2 g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/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++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/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-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpjQmvd0/R.INSTALL1687c12df13262/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 ‘rgexf’ ... ** this is package ‘rgexf’ version ‘0.16.3’ ** package ‘rgexf’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** demo ** 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 (rgexf) * 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 ‘rcrossref’ ... ** this is package ‘rcrossref’ version ‘1.2.0’ ** package ‘rcrossref’ 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 (rcrossref) * 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 ‘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.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 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checking telegram.bot_3.0.0.tar.gz ... checking gaawr2_0.0.3.tar.gz ... checking googleVis_0.7.3.tar.gz ... checking rlc_0.5.0.tar.gz ... checking learnr_0.11.5.tar.gz ... checking vetiver_0.2.5.tar.gz ... checking webutils_1.2.2.tar.gz ... checking tfdeploy_0.6.1.tar.gz ... checking shinylive_0.3.0.tar.gz ... checking webshot2_0.1.1.tar.gz ... checking vosonSML_0.32.7.tar.gz ... checking websocket_1.4.4.tar.gz ... checking webglobe_1.0.3.tar.gz ... checking curl_6.2.2.tar.gz ... checking osmapiR_0.2.3.tar.gz ... checking webfakes_1.3.2.tar.gz ... checking webshot_0.5.5.tar.gz ... checking shinytest_1.6.1.tar.gz ... checking tricolore_1.2.4.tar.gz ... checking vkR_0.2.tar.gz ... checking AzureRMR_2.4.4.tar.gz ... Depends: Package: httpuv Depends: R (>= 2.15.1) Imports: later (>= 0.8.0), promises, R6, Rcpp (>= 1.0.7), utils LinkingTo: later, Rcpp Timings: user system elapsed httpuv 111.221 7.759 121.49 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 13 49 Check results summary: httpuv ... OK rdepends_ambiorix ... OK rdepends_animate ... NOTE * checking DESCRIPTION meta-information ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_AzureAuth ... OK rdepends_AzureRMR ... NOTE * checking Rd cross-references ... NOTE rdepends_bea.R ... OK rdepends_beakr ... OK rdepends_blogdown ... OK rdepends_BrownDog ... OK rdepends_bs4Dash ... OK rdepends_cookies ... OK rdepends_curl ... NOTE * checking compiled code ... NOTE rdepends_DT ... NOTE * checking Rd cross-references ... NOTE rdepends_emuR ... NOTE * checking Rd cross-references ... NOTE rdepends_fiery ... OK rdepends_gaawr2 ... OK rdepends_gargle ... NOTE * checking Rd cross-references ... NOTE rdepends_ggfigdone ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_golem ... OK rdepends_googleVis ... OK rdepends_httr ... NOTE * checking for unstated dependencies in ‘demo’ ... NOTE rdepends_httr2 ... OK rdepends_JBrowseR ... OK rdepends_jrc ... OK rdepends_learnr ... OK rdepends_mlflow ... OK rdepends_opencpu ... OK rdepends_osmapiR ... OK rdepends_pagedown ... OK rdepends_plotscaper ... OK rdepends_plumber ... OK rdepends_plumbertableau ... OK rdepends_Rfacebook ... OK rdepends_rfigshare ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_rlc ... NOTE * checking Rd cross-references ... NOTE rdepends_Rlinkedin ... OK rdepends_rorcid ... OK rdepends_servr ... OK rdepends_shiny ... OK rdepends_shinylight ... OK rdepends_shinylive ... OK rdepends_shinyloadtest ... OK rdepends_shinytest ... OK rdepends_sleepwalk ... OK rdepends_sship ... OK rdepends_telegram.bot ... NOTE * checking Rd files ... [1s/1s] NOTE * checking Rd cross-references ... NOTE rdepends_tfdeploy ... OK rdepends_tidyllm ... OK rdepends_tricolore ... OK rdepends_urlshorteneR ... OK rdepends_vetiver ... OK rdepends_vkR ... OK rdepends_VOSONDash ... OK rdepends_vosonSML ... NOTE * checking Rd cross-references ... NOTE rdepends_webdav ... OK rdepends_webdeveloper ... OK rdepends_webfakes ... OK rdepends_webglobe ... OK rdepends_webshot ... OK rdepends_webshot2 ... OK rdepends_websocket ... OK rdepends_webutils ... OK rdepends_workflowr ... NOTE * checking Rd cross-references ... NOTE