downloading reverse dependencies ... downloading ecospat_4.1.1.tar.gz ... ok downloading ENMeval_2.0.4.tar.gz ... ok downloading ENMTools_1.1.2.tar.gz ... ok downloading gbm.auto_2024.10.01.tar.gz ... ok downloading hemispheR_1.1.4.tar.gz ... ok downloading NicheBarcoding_1.0.tar.gz ... ok downloading PopGenReport_3.1.tar.gz ... ok downloading red_1.6.1.tar.gz ... ok downloading SDMtune_1.3.1.tar.gz ... ok downloading SSDM_0.2.9.tar.gz ... ok downloading webSDM_1.1-5.tar.gz ... ok downloading BiodiversityR_2.16-1.tar.gz ... ok downloading biomod2_4.2-5-2.tar.gz ... ok downloading ctmcmove_1.2.9.tar.gz ... ok downloading dartR_2.9.7.tar.gz ... ok downloading dartR.base_0.98.tar.gz ... ok downloading dartR.spatial_0.78.tar.gz ... ok downloading maskRangeR_1.1.tar.gz ... ok downloading maxlike_0.1-11.tar.gz ... ok downloading rangeModelMetadata_0.1.5.tar.gz ... ok downloading sdm_1.2-46.tar.gz ... ok downloading wallace_2.1.3.tar.gz ... ok installing dependencies ‘adehabitatHR’, ‘autothresholdr’, ‘BAT’, ‘BIEN’, ‘biomod2’, ‘blockCV’, ‘CalibratR’, ‘crawl’, ‘dartR.base’, ‘dartR.data’, ‘dismo’, ‘ecodist’, ‘ecospat’, ‘ENMeval’, ‘envirem’, ‘fastshap’, ‘genetics’, ‘geodata’, ‘ggtern’, ‘HardyWeinberg’, ‘hierfstat’, ‘hypervolume’, ‘iterpc’, ‘knitcitations’, ‘leaflet.minicharts’, ‘mapplots’, ‘maxlike’, ‘maxnet’, ‘mmod’, ‘occCite’, ‘plotROC’, ‘poibin’, ‘PopGenReport’, ‘poppr’, ‘predicts’, ‘rangeModelMetadata’, ‘red’, ‘ResourceSelection’, ‘Rlof’, ‘sdm’, ‘SIBER’, ‘SNPassoc’, ‘SNPRelate’, ‘spider’, ‘spocc’, ‘spThin’, ‘StAMPP’, ‘starsExtra’, ‘vegan3d’, ‘wallace’ also installing the dependencies ‘arsenal’, ‘humaniformat’, ‘rebird’, ‘rvertnet’, ‘ridigbio’, ‘nngeo’, ‘ijtiff’, ‘palinsol’, ‘gdsfmt’, ‘polysat’, ‘haplo.stats’, ‘poisbinom’, ‘bib2df’, ‘waffle’ begin installing package ‘humaniformat’ begin installing package ‘arsenal’ begin installing package ‘rebird’ begin installing package ‘rvertnet’ begin installing package ‘ridigbio’ begin installing package ‘nngeo’ begin installing package ‘ijtiff’ begin installing package ‘palinsol’ begin installing package ‘gdsfmt’ begin installing package ‘polysat’ begin installing package ‘poisbinom’ begin installing package ‘waffle’ begin installing package ‘adehabitatHR’ begin installing package ‘biomod2’ begin installing package ‘ecodist’ begin installing package ‘poibin’ begin installing package ‘maxnet’ begin installing package ‘blockCV’ begin installing package ‘hypervolume’ begin installing package ‘CalibratR’ begin installing package ‘ResourceSelection’ begin installing package ‘fastshap’ begin installing package ‘mapplots’ begin installing package ‘spider’ begin installing package ‘genetics’ begin installing package ‘mmod’ begin installing package ‘predicts’ begin installing package ‘plotROC’ * installing *source* package ‘maxnet’ ... ** package ‘maxnet’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maxnet) begin installing package ‘spThin’ * installing *source* package ‘ridigbio’ ... ** package ‘ridigbio’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ridigbio) begin installing package ‘sdm’ * installing *source* package ‘mapplots’ ... ** package ‘mapplots’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mapplots) begin installing package ‘vegan3d’ * installing *source* package ‘poibin’ ... ** package ‘poibin’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMnGAES/R.INSTALL85eae3366534e/poibin/src' gcc-14 -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 dftcf.c -o dftcf.o gcc-14 -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 poibin_init.c -o poibin_init.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o poibin.so dftcf.o poibin_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMnGAES/R.INSTALL85eae3366534e/poibin/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poibin/00new/poibin/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 (poibin) begin installing package ‘maxlike’ * installing *source* package ‘palinsol’ ... ** package ‘palinsol’ 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 (palinsol) begin installing package ‘Rlof’ * installing *source* package ‘rebird’ ... ** package ‘rebird’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rebird) begin installing package ‘crawl’ * installing *source* package ‘spider’ ... ** package ‘spider’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spider) begin installing package ‘dartR.data’ * installing *source* package ‘genetics’ ... ** package ‘genetics’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (genetics) begin installing package ‘StAMPP’ * installing *source* package ‘Rlof’ ... ** package ‘Rlof’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpfA8yn6/R.INSTALL862b733f9a071/Rlof/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c distance.c -o distance.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o Rlof.so distance.o -fopenmp -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpfA8yn6/R.INSTALL862b733f9a071/Rlof/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rlof/00new/Rlof/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 (Rlof) begin installing package ‘ggtern’ * installing *source* package ‘rvertnet’ ... ** package ‘rvertnet’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rvertnet) begin installing package ‘HardyWeinberg’ * installing *source* package ‘nngeo’ ... ** package ‘nngeo’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpx8qmIc/R.INSTALL85e6c4015f216/nngeo/src' gcc-14 -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 dist.c -o dist.o gcc-14 -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 geodesic.c -o geodesic.o gcc-14 -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 nngeo_init.c -o nngeo_init.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o nngeo.so dist.o geodesic.o nngeo_init.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpx8qmIc/R.INSTALL85e6c4015f216/nngeo/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-nngeo/00new/nngeo/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nngeo) begin installing package ‘hierfstat’ * installing *source* package ‘plotROC’ ... ** package ‘plotROC’ 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 (plotROC) begin installing package ‘iterpc’ * installing *source* package ‘waffle’ ... ** package ‘waffle’ 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 (waffle) begin installing package ‘leaflet.minicharts’ * installing *source* package ‘ecodist’ ... ** package ‘ecodist’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuKGu8m/R.INSTALL85ea546448170/ecodist/src' gcc-14 -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 ecodist.c -o ecodist.o gcc-14 -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 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o ecodist.so ecodist.o init.o -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/RtmpuKGu8m/R.INSTALL85ea546448170/ecodist/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ecodist/00new/ecodist/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ecodist) begin installing package ‘SIBER’ * installing *source* package ‘spThin’ ... ** package ‘spThin’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spThin) begin installing package ‘BIEN’ * installing *source* package ‘ResourceSelection’ ... ** package ‘ResourceSelection’ 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 (ResourceSelection) begin installing package ‘geodata’ * installing *source* package ‘ijtiff’ ... ** package ‘ijtiff’ successfully unpacked and MD5 sums checked ** using staged installation ** preparing to configure package 'ijtiff' ... Found pkg-config! Found pkg-config cflags and/or libs for libtiff! Using PKG_CFLAGS=-I/usr/include/x86_64-linux-gnu -I/usr/include/webp Using PKG_LIBS=-ltiff -lwebp -lm -lsharpyuv -lzstd -pthread -llzma -lpthread -ljpeg -ldeflate -lz ** finished configure for package 'ijtiff' ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpG49yB3/R.INSTALL85e61662bcf97/ijtiff/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c common.c -o common.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -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 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c read.c -o read.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -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 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/include/x86_64-linux-gnu -I/usr/include/webp -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c write.c -o write.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o ijtiff.so common.o init.o read.o utils.o write.o -ltiff -lwebp -lm -lsharpyuv -lzstd -pthread -llzma -lpthread -ljpeg -ldeflate -lz -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpG49yB3/R.INSTALL85e61662bcf97/ijtiff/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ijtiff/00new/ijtiff/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 (ijtiff) begin installing package ‘knitcitations’ * installing *source* package ‘arsenal’ ... ** package ‘arsenal’ 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 (arsenal) begin installing package ‘dismo’ * installing *source* package ‘iterpc’ ... ** package ‘iterpc’ 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 (iterpc) begin installing package ‘haplo.stats’ * installing *source* package ‘leaflet.minicharts’ ... ** package ‘leaflet.minicharts’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (leaflet.minicharts) begin installing package ‘spocc’ * installing *source* package ‘hierfstat’ ... ** package ‘hierfstat’ 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 (hierfstat) begin installing package ‘starsExtra’ * installing *source* package ‘mmod’ ... ** package ‘mmod’ 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 (mmod) begin installing package ‘autothresholdr’ * installing *source* package ‘vegan3d’ ... ** package ‘vegan3d’ 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 (vegan3d) begin installing package ‘envirem’ * installing *source* package ‘knitcitations’ ... ** package ‘knitcitations’ 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 (knitcitations) * installing *source* package ‘adehabitatHR’ ... ** package ‘adehabitatHR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8aROqJ/R.INSTALL85e8a4529600c/adehabitatHR/src' gcc-14 -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 -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 tests.c -o tests.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o adehabitatHR.so init.o tests.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8aROqJ/R.INSTALL85e8a4529600c/adehabitatHR/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-adehabitatHR/00new/adehabitatHR/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (adehabitatHR) * installing *source* package ‘poisbinom’ ... ** package ‘poisbinom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpQRNSyB/R.INSTALL85e886afeb043/poisbinom/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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/4.5/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 -DR_NO_REMAP -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/RtmpQRNSyB/R.INSTALL85e886afeb043/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) * installing *source* package ‘CalibratR’ ... ** package ‘CalibratR’ 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 (CalibratR) * installing *source* package ‘SIBER’ ... ** package ‘SIBER’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SIBER) * installing *source* package ‘blockCV’ ... ** package ‘blockCV’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpI2qs9y/R.INSTALL85eb328118866/blockCV/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -c nndm.cpp -o nndm.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o blockCV.so RcppExports.o nndm.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpI2qs9y/R.INSTALL85eb328118866/blockCV/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-blockCV/00new/blockCV/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 (blockCV) * installing *source* package ‘StAMPP’ ... ** package ‘StAMPP’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (StAMPP) * installing *source* package ‘starsExtra’ ... ** package ‘starsExtra’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmphUurHh/R.INSTALL8674e375541ed/starsExtra/src' gcc-14 -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 CI.c -o CI.o gcc-14 -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 aspect.c -o aspect.o gcc-14 -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 focal2.c -o focal2.o gcc-14 -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 max.c -o max.o gcc-14 -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 mean.c -o mean.o gcc-14 -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 min.c -o min.o gcc-14 -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 mode.c -o mode.o gcc-14 -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 slope.c -o slope.o gcc-14 -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 starsExtra_init.c -o starsExtra_init.o gcc-14 -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 sum.c -o sum.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o starsExtra.so CI.o aspect.o focal2.o max.o mean.o min.o mode.o slope.o starsExtra_init.o sum.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmphUurHh/R.INSTALL8674e375541ed/starsExtra/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-starsExtra/00new/starsExtra/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (starsExtra) * installing *source* package ‘polysat’ ... ** package ‘polysat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHEZVxD/R.INSTALL85e9545713c7a/polysat/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -c deSilvaFuncs.cpp -o deSilvaFuncs.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o polysat.so RcppExports.o deSilvaFuncs.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHEZVxD/R.INSTALL85e9545713c7a/polysat/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-polysat/00new/polysat/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 (polysat) begin installing package ‘poppr’ * installing *source* package ‘spocc’ ... ** package ‘spocc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spocc) * installing *source* package ‘ggtern’ ... ** 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 ‘fastshap’ ... ** package ‘fastshap’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpBUh8re/R.INSTALL85ebe422773c7/fastshap/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DARMA_DONT_USE_OPENMP -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastshap.cpp -o fastshap.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o fastshap.so RcppExports.o fastshap.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/RtmpBUh8re/R.INSTALL85ebe422773c7/fastshap/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-fastshap/00new/fastshap/libs ** 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 ** 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 (fastshap) * installing *source* package ‘humaniformat’ ... ** package ‘humaniformat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRTddP7/R.INSTALL85e661d619e13/humaniformat/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -c human_format.cpp -o human_format.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -c human_getset.cpp -o human_getset.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -c human_parse.cpp -o human_parse.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -c humaniformat.cpp -o humaniformat.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o humaniformat.so RcppExports.o human_format.o human_getset.o human_parse.o humaniformat.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpRTddP7/R.INSTALL85e661d619e13/humaniformat/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-humaniformat/00new/humaniformat/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 (humaniformat) begin installing package ‘bib2df’ * installing *source* package ‘haplo.stats’ ... ** package ‘haplo.stats’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpYpOb7d/R.INSTALL866032ab09c4c/haplo.stats/src' gcc-14 -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 groupsum.c -o groupsum.o gcc-14 -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 haplo.stats_init.c -o haplo.stats_init.o gcc-14 -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 haplo_em_pin.c -o haplo_em_pin.o gcc-14 -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 louis_info.c -o louis_info.o gcc-14 -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 seqhap.c -o seqhap.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o haplo.stats.so groupsum.o haplo.stats_init.o haplo_em_pin.o louis_info.o seqhap.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpYpOb7d/R.INSTALL866032ab09c4c/haplo.stats/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-haplo.stats/00new/haplo.stats/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 (haplo.stats) begin installing package ‘SNPassoc’ * installing *source* package ‘maxlike’ ... ** package ‘maxlike’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (maxlike) * installing *source* package ‘predicts’ ... ** package ‘predicts’ 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 (predicts) * installing *source* package ‘bib2df’ ... ** package ‘bib2df’ 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 (bib2df) * installing *source* package ‘geodata’ ... ** package ‘geodata’ 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 (geodata) * installing *source* package ‘envirem’ ... ** package ‘envirem’ 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 (envirem) * installing *source* package ‘autothresholdr’ ... ** package ‘autothresholdr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3IWG3g/R.INSTALL867d46e330321/autothresholdr/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -c AutoThreshold.cpp -o AutoThreshold.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -c pillar_stats.cpp -o pillar_stats.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o autothresholdr.so AutoThreshold.o RcppExports.o pillar_stats.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3IWG3g/R.INSTALL867d46e330321/autothresholdr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-autothresholdr/00new/autothresholdr/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 (autothresholdr) * installing *source* package ‘BIEN’ ... ** package ‘BIEN’ 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 (BIEN) begin installing package ‘rangeModelMetadata’ begin installing package ‘occCite’ * installing *source* package ‘HardyWeinberg’ ... ** package ‘HardyWeinberg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpinq5Ec/R.INSTALL8648f9667b61/HardyWeinberg/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -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/Rtmpinq5Ec/R.INSTALL8648f9667b61/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 ‘biomod2’ ... ** package ‘biomod2’ 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 Checking Models arguments... ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘mda’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘gam’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘earth’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘randomForest’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘xgboost’ ** testing if installed package can be loaded from final location Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘mda’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘gam’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘earth’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘randomForest’ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘xgboost’ ** testing if installed package keeps a record of temporary installation path * DONE (biomod2) * installing *source* package ‘SNPassoc’ ... ** 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 ‘poppr’ ... ** package ‘poppr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpaqF0yQ/R.INSTALL86998c322157/poppr/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c adjust_missing.c -o adjust_missing.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bitwise_distance.c -o bitwise_distance.o bitwise_distance.c: In function ‘association_index_haploid’: bitwise_distance.c:823:7: warning: unused variable ‘only_differences’ [-Wunused-variable] 823 | int only_differences; | ^~~~~~~~~~~~~~~~ bitwise_distance.c:815:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable] 815 | int chr_length; | ^~~~~~~~~~ bitwise_distance.c:808:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable] 808 | SEXP R_chr2_1; | ^~~~~~~~ bitwise_distance.c: In function ‘association_index_diploid’: bitwise_distance.c:1190:7: warning: variable ‘chr_length’ set but not used [-Wunused-but-set-variable] 1190 | int chr_length; | ^~~~~~~~~~ bitwise_distance.c:1182:8: warning: unused variable ‘R_chr2_2’ [-Wunused-variable] 1182 | SEXP R_chr2_2; | ^~~~~~~~ bitwise_distance.c:1181:8: warning: unused variable ‘R_chr2_1’ [-Wunused-variable] 1181 | SEXP R_chr2_1; | ^~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mlg_clustering.c -o mlg_clustering.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mlg_counter.c -o mlg_counter.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c msn.c -o msn.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c omp_test.c -o omp_test.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c permut_shuffler.c -o permut_shuffler.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c poppr_distance.c -o poppr_distance.o poppr_distance.c: In function ‘bruvo_between’: poppr_distance.c:428:13: warning: variable ‘numel’ set but not used [-Wunused-but-set-variable] 428 | int numel; // Number of elements in returned matrix | ^~~~~ gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o poppr.so adjust_missing.o bitwise_distance.o init.o mlg_clustering.o mlg_counter.o msn.o omp_test.o permut_shuffler.o poppr_distance.o -fopenmp -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpaqF0yQ/R.INSTALL86998c322157/poppr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poppr/00new/poppr/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘as.genambig’ in package ‘poppr’ ** 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 (poppr) * installing *source* package ‘occCite’ ... ** package ‘occCite’ 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 (occCite) * installing *source* package ‘dartR.data’ ... ** package ‘dartR.data’ 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 ** 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 (dartR.data) * installing *source* package ‘dismo’ ... ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpiwmd4N/R.INSTALL865ba3cacb6c5/dismo/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/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 -DR_NO_REMAP -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/4.5/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 -DR_NO_REMAP -c percRank.cpp -o percRank.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o dismo.so RcppExports.o percRank.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpiwmd4N/R.INSTALL865ba3cacb6c5/dismo/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-dismo/00new/dismo/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 (dismo) begin installing package ‘ecospat’ begin installing package ‘PopGenReport’ * installing *source* package ‘hypervolume’ ... ** package ‘hypervolume’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpU8cxqg/R.INSTALL85eb5535bd3a3/hypervolume/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c convert.cpp -o convert.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c fastPdist2.cpp -o fastPdist2.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o hypervolume.so RcppExports.o convert.o fastPdist2.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/RtmpU8cxqg/R.INSTALL85eb5535bd3a3/hypervolume/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-hypervolume/00new/hypervolume/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 (hypervolume) begin installing package ‘BAT’ * installing *source* package ‘ecospat’ ... ** package ‘ecospat’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ecospat) * installing *source* package ‘rangeModelMetadata’ ... ** package ‘rangeModelMetadata’ 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 (rangeModelMetadata) begin installing package ‘ENMeval’ * installing *source* package ‘sdm’ ... ** package ‘sdm’ 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 (sdm) * installing *source* package ‘PopGenReport’ ... ** package ‘PopGenReport’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PopGenReport) * installing *source* package ‘BAT’ ... ** package ‘BAT’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BAT) begin installing package ‘red’ * installing *source* package ‘ENMeval’ ... ** package ‘ENMeval’ 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 (ENMeval) begin installing package ‘wallace’ * installing *source* package ‘wallace’ ... ** package ‘wallace’ 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 (wallace) * installing *source* package ‘crawl’ ... ** package ‘crawl’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpSQjBa9/R.INSTALL8631f3878c36c/crawl/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CTCRWN2LL.cpp -o CTCRWN2LL.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CTCRWN2LL_DRIFT.cpp -o CTCRWN2LL_DRIFT.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CTCRWPREDICT.cpp -o CTCRWPREDICT.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CTCRWPREDICT_DRIFT.cpp -o CTCRWPREDICT_DRIFT.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CTCRWSAMPLE.cpp -o CTCRWSAMPLE.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CTCRWSAMPLE_DRIFT.cpp -o CTCRWSAMPLE_DRIFT.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -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/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c SMM_MATS.cpp -o SMM_MATS.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/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 init.c -o init.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o crawl.so CTCRWN2LL.o CTCRWN2LL_DRIFT.o CTCRWPREDICT.o CTCRWPREDICT_DRIFT.o CTCRWSAMPLE.o CTCRWSAMPLE_DRIFT.o RcppExports.o SMM_MATS.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/RtmpSQjBa9/R.INSTALL8631f3878c36c/crawl/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-crawl/00new/crawl/libs ** 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 ** 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 (crawl) * installing *source* package ‘red’ ... ** package ‘red’ 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 (red) * installing *source* package ‘gdsfmt’ ... ** package ‘gdsfmt’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c R_CoreArray.cpp -o R_CoreArray.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c gdsfmt.cpp -o gdsfmt.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c digest.cpp -o digest.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dAny.cpp -o CoreArray/dAny.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dBase.cpp -o CoreArray/dBase.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dFile.cpp -o CoreArray/dFile.o CoreArray/dFile.cpp: In member function ‘void CoreArray::CdObjAttr::Delete(int)’: CoreArray/dFile.cpp:129:17: warning: ignoring return value of ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::at(size_type) [with _Tp = CoreArray::CdObjAttr::TdPair*; _Alloc = std::allocator; reference = CoreArray::CdObjAttr::TdPair*&; size_type = long unsigned int]’, declared with attribute ‘nodiscard’ [-Wunused-result] 129 | fList.at(Index); // check range | ~~~~~~~~^~~~~~~ In file included from /usr/include/c++/14/vector:66, from CoreArray/dPlatform.h:48, from CoreArray/dEndian.h:40, from CoreArray/dBase.h:41, from CoreArray/dFile.h:40, from CoreArray/dFile.cpp:28: /usr/include/c++/14/bits/stl_vector.h:1180:7: note: declared here 1180 | at(size_type __n) | ^~ g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dRealGDS.cpp -o CoreArray/dRealGDS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dStrGDS.cpp -o CoreArray/dStrGDS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dStream.cpp -o CoreArray/dStream.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dSparse.cpp -o CoreArray/dSparse.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c CoreArray/dVLIntGDS.cpp -o CoreArray/dVLIntGDS.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/adler32.c -o ZLIB/adler32.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/compress.c -o ZLIB/compress.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/crc32.c -o ZLIB/crc32.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/deflate.c -o ZLIB/deflate.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/infback.c -o ZLIB/infback.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/inffast.c -o ZLIB/inffast.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/inflate.c -o ZLIB/inflate.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/inftrees.c -o ZLIB/inftrees.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/trees.c -o ZLIB/trees.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/uncompr.c -o ZLIB/uncompr.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c -g0 ZLIB/zutil.c -o ZLIB/zutil.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/lz4.c -o LZ4/lz4.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/lz4hc.c -o LZ4/lz4hc.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/lz4frame.c -o LZ4/lz4frame.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c LZ4/xxhash.c -o LZ4/xxhash.o cd XZ && tar -xzf xz-5.2.9.tar.gz cd XZ/xz-5.2.9 && \ ./configure CC="gcc-14 " CPP="gcc-14 -E" CXX="g++-14 -std=gnu++17" CXXCPP="" --build="" \ --with-pic --enable-silent-rules --quiet --disable-xz --disable-shared > /dev/null cd XZ/xz-5.2.9/src/liblzma && make make[2]: Entering directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' Making all in api make[3]: Entering directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src/XZ/xz-5.2.9/src/liblzma/api' make[3]: Entering directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' CC liblzma_la-tuklib_physmem.lo CC liblzma_la-tuklib_cpucores.lo CC liblzma_la-common.lo CC liblzma_la-block_util.lo CC liblzma_la-easy_preset.lo CC liblzma_la-filter_common.lo CC liblzma_la-hardware_physmem.lo CC liblzma_la-index.lo CC liblzma_la-stream_flags_common.lo CC liblzma_la-vli_size.lo CC liblzma_la-hardware_cputhreads.lo CC liblzma_la-alone_encoder.lo CC liblzma_la-block_buffer_encoder.lo CC liblzma_la-block_encoder.lo CC liblzma_la-block_header_encoder.lo CC liblzma_la-easy_buffer_encoder.lo CC liblzma_la-easy_encoder.lo CC liblzma_la-easy_encoder_memusage.lo CC liblzma_la-filter_buffer_encoder.lo CC liblzma_la-filter_encoder.lo CC liblzma_la-filter_flags_encoder.lo CC liblzma_la-index_encoder.lo CC liblzma_la-stream_buffer_encoder.lo CC liblzma_la-stream_encoder.lo CC liblzma_la-stream_flags_encoder.lo CC liblzma_la-vli_encoder.lo CC liblzma_la-outqueue.lo CC liblzma_la-stream_encoder_mt.lo CC liblzma_la-alone_decoder.lo CC liblzma_la-auto_decoder.lo CC liblzma_la-block_buffer_decoder.lo CC liblzma_la-block_decoder.lo CC liblzma_la-block_header_decoder.lo CC liblzma_la-easy_decoder_memusage.lo CC liblzma_la-filter_buffer_decoder.lo CC liblzma_la-filter_decoder.lo CC liblzma_la-filter_flags_decoder.lo CC liblzma_la-index_decoder.lo CC liblzma_la-index_hash.lo CC liblzma_la-stream_buffer_decoder.lo CC liblzma_la-stream_decoder.lo CC liblzma_la-stream_flags_decoder.lo CC liblzma_la-vli_decoder.lo CC liblzma_la-check.lo CC liblzma_la-crc32_table.lo CC liblzma_la-crc32_fast.lo CC liblzma_la-crc64_table.lo CC liblzma_la-crc64_fast.lo CC liblzma_la-sha256.lo CC liblzma_la-lz_encoder.lo CC liblzma_la-lz_encoder_mf.lo CC liblzma_la-lz_decoder.lo CC liblzma_la-lzma_encoder_presets.lo CC liblzma_la-lzma_encoder.lo CC liblzma_la-lzma_encoder_optimum_fast.lo CC liblzma_la-lzma_encoder_optimum_normal.lo CC liblzma_la-fastpos_table.lo CC liblzma_la-lzma_decoder.lo CC liblzma_la-lzma2_encoder.lo CC liblzma_la-lzma2_decoder.lo CC liblzma_la-price_table.lo CC liblzma_la-delta_common.lo CC liblzma_la-delta_encoder.lo CC liblzma_la-delta_decoder.lo CC liblzma_la-simple_coder.lo CC liblzma_la-simple_encoder.lo CC liblzma_la-simple_decoder.lo CC liblzma_la-x86.lo CC liblzma_la-powerpc.lo CC liblzma_la-ia64.lo CC liblzma_la-arm.lo CC liblzma_la-armthumb.lo CC liblzma_la-sparc.lo CCLD liblzma.la PC liblzma.pc make[3]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' make[2]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src/XZ/xz-5.2.9/src/liblzma' cp XZ/xz-5.2.9/src/liblzma/.libs/liblzma.a . rm -rf XZ/xz-5.2.9/dos rm -rf XZ/xz-5.2.9/po g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o gdsfmt.so R_CoreArray.o gdsfmt.o digest.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dRealGDS.o CoreArray/dSerial.o CoreArray/dStrGDS.o CoreArray/dStream.o CoreArray/dStruct.o CoreArray/dSparse.o CoreArray/dVLIntGDS.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o ./liblzma.a -lpthread -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp7EKDXc/R.INSTALL85e7d558c628f/gdsfmt/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-gdsfmt/00new/gdsfmt/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 (gdsfmt) begin installing package ‘SNPRelate’ * installing *source* package ‘SNPRelate’ ... ** package ‘SNPRelate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpStCCLN/R.INSTALL8890c388f5fc9/SNPRelate/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c ConvToGDS.cpp -o ConvToGDS.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_SNPRelate.c -o R_SNPRelate.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c SNPRelate.cpp -o SNPRelate.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c ThreadPool.cpp -o ThreadPool.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dGenGWAS.cpp -o dGenGWAS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c dVect.cpp -o dVect.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genBeta.cpp -o genBeta.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genEIGMIX.cpp -o genEIGMIX.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genFst.cpp -o genFst.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genHWE.cpp -o genHWE.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genIBD.cpp -o genIBD.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genIBS.cpp -o genIBS.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genKING.cpp -o genKING.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genLD.cpp -o genLD.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genPCA.cpp -o genPCA.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -DUSING_R -DUSE_FC_LEN_T -I. -I'/home/hornik/tmp/CRAN_recheck/Library/gdsfmt/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -DR_NO_REMAP -c genSlideWin.cpp -o genSlideWin.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o SNPRelate.so ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -lpthread -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/RtmpStCCLN/R.INSTALL8890c388f5fc9/SNPRelate/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-SNPRelate/00new/SNPRelate/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SNPRelate) begin installing package ‘dartR.base’ * installing *source* package ‘dartR.base’ ... ** package ‘dartR.base’ 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 (dartR.base) checking ecospat_4.1.1.tar.gz ... checking dismo_1.3-16.tar.gz ... checking ENMeval_2.0.4.tar.gz ... checking ENMTools_1.1.2.tar.gz ... checking gbm.auto_2024.10.01.tar.gz ... checking hemispheR_1.1.4.tar.gz ... checking NicheBarcoding_1.0.tar.gz ... checking PopGenReport_3.1.tar.gz ... checking red_1.6.1.tar.gz ... checking SDMtune_1.3.1.tar.gz ... checking SSDM_0.2.9.tar.gz ... checking webSDM_1.1-5.tar.gz ... checking BiodiversityR_2.16-1.tar.gz ... checking biomod2_4.2-5-2.tar.gz ... checking ctmcmove_1.2.9.tar.gz ... checking dartR_2.9.7.tar.gz ... checking dartR.base_0.98.tar.gz ... checking dartR.spatial_0.78.tar.gz ... checking maskRangeR_1.1.tar.gz ... checking maxlike_0.1-11.tar.gz ... checking rangeModelMetadata_0.1.5.tar.gz ... checking wallace_2.1.3.tar.gz ... checking sdm_1.2-46.tar.gz ... Depends: Package: dismo Depends: R (>= 3.6.3), raster (>= 3.5-21), sp (>= 1.4-5) Imports: Rcpp, methods, terra (>= 1.5-34) LinkingTo: Rcpp Timings: user system elapsed dismo 233.056 11.166 248.818 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 7 15 Check results summary: dismo ... OK rdepends_BiodiversityR ... OK rdepends_biomod2 ... OK rdepends_ctmcmove ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_dartR.base ... OK rdepends_dartR ... NOTE * checking Rd files ... [1s/1s] NOTE * checking Rd cross-references ... NOTE rdepends_dartR.spatial ... NOTE * checking Rd cross-references ... NOTE rdepends_ecospat ... OK rdepends_ENMeval ... OK rdepends_ENMTools ... OK rdepends_gbm.auto ... OK rdepends_hemispheR ... OK rdepends_maskRangeR ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_maxlike ... NOTE * checking Rd cross-references ... NOTE rdepends_NicheBarcoding ... OK rdepends_PopGenReport ... NOTE * checking Rd cross-references ... NOTE rdepends_rangeModelMetadata ... OK rdepends_red ... OK rdepends_sdm ... OK rdepends_SDMtune ... NOTE * checking Rd cross-references ... NOTE rdepends_SSDM ... OK rdepends_wallace ... OK rdepends_webSDM ... OK