downloading reverse dependencies ... downloading BioM2_1.1.3.tar.gz ... ok downloading calmr_0.8.1.tar.gz ... ok downloading ecostate_0.3.0.tar.gz ... ok downloading genBaRcode_1.2.8.tar.gz ... ok downloading inferCSN_1.1.7.tar.gz ... ok downloading netmap_0.1.4.tar.gz ... ok downloading phyloseqGraphTest_0.1.1.tar.gz ... ok downloading pkggraph_0.2.3.tar.gz ... ok downloading BasketballAnalyzeR_0.8.0.tar.gz ... ok downloading fssemR_0.1.8.tar.gz ... ok downloading mrIML_2.1.0.tar.gz ... ok downloading nosoi_1.1.2.tar.gz ... ok downloading rcausim_0.1.1.tar.gz ... ok installing dependencies ‘CMplot’, ‘finetune’, ‘flashlight’, ‘ggnetwork’, ‘ggpointdensity’, ‘ggstatsplot’, ‘hstats’, ‘MetricsWeighted’, ‘mlr3verse’, ‘MRFcov’, ‘operators’, ‘precrec’, ‘RTMB’, ‘RTransferEntropy’, ‘shapviz’, ‘ShortRead’, ‘themis’ also installing the dependencies ‘stabm’, ‘ggside’, ‘statsExpressions’, ‘mlr3cluster’, ‘mlr3data’, ‘mlr3filters’, ‘mlr3fselect’, ‘mlr3hyperband’, ‘mlr3inferr’, ‘mlr3mbo’, ‘mlr3tuningspaces’, ‘mlr3viz’, ‘ROSE’, ‘gggenes’ begin installing package ‘ggside’ begin installing package ‘stabm’ begin installing package ‘statsExpressions’ begin installing package ‘mlr3cluster’ begin installing package ‘mlr3data’ begin installing package ‘mlr3hyperband’ begin installing package ‘mlr3filters’ begin installing package ‘mlr3inferr’ begin installing package ‘mlr3mbo’ begin installing package ‘mlr3tuningspaces’ begin installing package ‘mlr3viz’ begin installing package ‘ROSE’ begin installing package ‘gggenes’ begin installing package ‘CMplot’ begin installing package ‘RTMB’ begin installing package ‘ShortRead’ begin installing package ‘ggpointdensity’ begin installing package ‘precrec’ begin installing package ‘RTransferEntropy’ begin installing package ‘operators’ begin installing package ‘MetricsWeighted’ begin installing package ‘finetune’ begin installing package ‘hstats’ begin installing package ‘MRFcov’ begin installing package ‘ggnetwork’ * installing *source* package ‘ROSE’ ... ** this is package ‘ROSE’ version ‘0.0-4’ ** package ‘ROSE’ 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 (ROSE) begin installing package ‘themis’ * installing *source* package ‘operators’ ... ** this is package ‘operators’ version ‘0.1-8’ ** package ‘operators’ 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 (operators) * installing *source* package ‘MetricsWeighted’ ... ** this is package ‘MetricsWeighted’ version ‘1.0.4’ ** package ‘MetricsWeighted’ 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 (MetricsWeighted) begin installing package ‘flashlight’ * installing *source* package ‘mlr3hyperband’ ... ** this is package ‘mlr3hyperband’ version ‘1.0.0’ ** package ‘mlr3hyperband’ 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 (mlr3hyperband) * installing *source* package ‘ggpointdensity’ ... ** this is package ‘ggpointdensity’ version ‘0.2.0’ ** package ‘ggpointdensity’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-2) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpAffOft/R.INSTALLe381e7a2ddebf/ggpointdensity/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c count_neighbors.c -o count_neighbors.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o ggpointdensity.so count_neighbors.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpAffOft/R.INSTALLe381e7a2ddebf/ggpointdensity/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ggpointdensity/00new/ggpointdensity/libs ** 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 ** 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 (ggpointdensity) * installing *source* package ‘gggenes’ ... ** this is package ‘gggenes’ version ‘0.5.1’ ** package ‘gggenes’ 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 (gggenes) begin installing package ‘shapviz’ * installing *source* package ‘statsExpressions’ ... ** this is package ‘statsExpressions’ version ‘1.7.1’ ** package ‘statsExpressions’ 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 (statsExpressions) * installing *source* package ‘mlr3viz’ ... ** this is package ‘mlr3viz’ version ‘0.10.1’ ** package ‘mlr3viz’ 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 (mlr3viz) * installing *source* package ‘hstats’ ... ** this is package ‘hstats’ version ‘1.2.1’ ** package ‘hstats’ 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 (hstats) * installing *source* package ‘ggnetwork’ ... ** this is package ‘ggnetwork’ version ‘0.5.14’ ** 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 (ggnetwork) * installing *source* package ‘mlr3inferr’ ... ** this is package ‘mlr3inferr’ version ‘0.2.0’ ** package ‘mlr3inferr’ 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 (mlr3inferr) * installing *source* package ‘mlr3mbo’ ... ** this is package ‘mlr3mbo’ version ‘0.3.1’ ** package ‘mlr3mbo’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-2) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmplOtlNg/R.INSTALLe380c489d3a94/mlr3mbo/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c avl.c -o avl.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hv.c -o hv.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c infill.c -o infill.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o mlr3mbo.so avl.o hv.o infill.o init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmplOtlNg/R.INSTALLe380c489d3a94/mlr3mbo/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mlr3mbo/00new/mlr3mbo/libs ** R ** preparing 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 (mlr3mbo) * installing *source* package ‘stabm’ ... ** this is package ‘stabm’ version ‘1.2.2’ ** package ‘stabm’ 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 (stabm) begin installing package ‘mlr3fselect’ * installing *source* package ‘CMplot’ ... ** this is package ‘CMplot’ version ‘4.5.1’ ** package ‘CMplot’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (CMplot) * installing *source* package ‘flashlight’ ... ** this is package ‘flashlight’ version ‘0.9.0’ ** package ‘flashlight’ 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 (flashlight) * installing *source* package ‘MRFcov’ ... ** this is package ‘MRFcov’ version ‘1.0.39’ ** package ‘MRFcov’ 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 (MRFcov) * installing *source* package ‘mlr3filters’ ... ** this is package ‘mlr3filters’ version ‘0.8.1’ ** package ‘mlr3filters’ 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 (mlr3filters) * installing *source* package ‘ggside’ ... ** this is package ‘ggside’ version ‘0.3.2’ ** package ‘ggside’ 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 (ggside) begin installing package ‘ggstatsplot’ * installing *source* package ‘mlr3tuningspaces’ ... ** this is package ‘mlr3tuningspaces’ version ‘0.6.0’ ** package ‘mlr3tuningspaces’ 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 (mlr3tuningspaces) * installing *source* package ‘mlr3data’ ... ** this is package ‘mlr3data’ version ‘0.9.0’ ** package ‘mlr3data’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mlr3data) * installing *source* package ‘finetune’ ... ** this is package ‘finetune’ version ‘1.2.1’ ** package ‘finetune’ 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 (finetune) * installing *source* package ‘shapviz’ ... ** this is package ‘shapviz’ version ‘0.10.2’ ** package ‘shapviz’ 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 (shapviz) * installing *source* package ‘themis’ ... ** this is package ‘themis’ version ‘1.0.3’ ** package ‘themis’ 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 *** 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 (themis) * installing *source* package ‘RTransferEntropy’ ... ** this is package ‘RTransferEntropy’ version ‘0.2.21’ ** package ‘RTransferEntropy’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-2) 15.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgcVCQL/R.INSTALLe38266ef64259/RTransferEntropy/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calculate_transition_probabilities.cpp -o calculate_transition_probabilities.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cluster_gen.cpp -o cluster_gen.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c freq_table.cpp -o freq_table.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RTransferEntropy.so RcppExports.o calculate_transition_probabilities.o cluster_gen.o freq_table.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgcVCQL/R.INSTALLe38266ef64259/RTransferEntropy/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RTransferEntropy/00new/RTransferEntropy/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 (RTransferEntropy) * installing *source* package ‘ggstatsplot’ ... ** this is package ‘ggstatsplot’ version ‘0.13.1’ ** package ‘ggstatsplot’ 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 (ggstatsplot) * installing *source* package ‘mlr3fselect’ ... ** this is package ‘mlr3fselect’ version ‘1.4.0’ ** package ‘mlr3fselect’ 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 (mlr3fselect) * installing *source* package ‘mlr3cluster’ ... ** this is package ‘mlr3cluster’ version ‘0.1.11’ ** package ‘mlr3cluster’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (mlr3cluster) begin installing package ‘mlr3verse’ * installing *source* package ‘precrec’ ... ** this is package ‘precrec’ version ‘0.14.5’ ** package ‘precrec’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-2) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGKZFHZ/R.INSTALLe382c1ed5c41b/precrec/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c precrec_misc.cpp -o precrec_misc.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c precrec_mmx.cpp -o precrec_mmx.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c precrec_plx.cpp -o precrec_plx.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o precrec.so RcppExports.o precrec_misc.o precrec_mmx.o precrec_plx.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGKZFHZ/R.INSTALLe382c1ed5c41b/precrec/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-precrec/00new/precrec/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 (precrec) * installing *source* package ‘mlr3verse’ ... ** this is package ‘mlr3verse’ version ‘0.3.1’ ** package ‘mlr3verse’ 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 (mlr3verse) * installing *source* package ‘ShortRead’ ... ** this is package ‘ShortRead’ version ‘1.66.0’ ** using staged installation checking for gcc... gcc-15 checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc-15 accepts -g... yes checking for gcc-15 option to accept ISO C89... none needed checking for gzeof in -lz... yes checking how to run the C preprocessor... gcc-15 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking size of unsigned long... 8 configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-2) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-2) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8reb8h/R.INSTALLe3818349c4533/ShortRead/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Biostrings_stubs.c -o Biostrings_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c IRanges_stubs.c -o IRanges_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c R_init_ShortRead.c -o R_init_ShortRead.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c XVector_stubs.c -o XVector_stubs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c alphabet.c -o alphabet.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c count.c -o count.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io.c -o io.o io.c: In function ‘read_prb_as_character’: io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but argument 2 has type ‘const char *’ [-Wformat=] 227 | error("could not read file '%f'", translateChar(STRING_ELT(fname, 0))); | ~^ | | | double | %s io.c: In function ‘_read_solexa_export_file’: io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 658 | error("invalid 'strand' field '%s', %s:%d", | ~^ | | | char * | %d 659 | *elt[13], fname, lineno); | ~~~~~~~~ | | | int io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but argument 2 has type ‘int’ [-Wformat=] 676 | error("invalid 'filtering' field '%s', %s:%d", | ~^ | | | char * | %d 677 | *elt[21], fname, lineno); | ~~~~~~~~ | | | int gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_bowtie.c -o io_bowtie.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c io_soap.c -o io_soap.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c readBfaToc.cc -o readBfaToc.o readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’: readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 35 | (void) fread( seq_name, sizeof(char), name_len, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 37 | (void) fread( &seq_len, sizeof(int), 1, fp ); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_maq_map.cc -o read_maq_map.o In file included from read_maq_map.cc:13: maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 128]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 128]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ maqmap_m.h: In function ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’: maqmap_m.h:102:21: warning: pointer ‘mm’ used after ‘void free(void*)’ [-Wuse-after-free] 102 | Rf_error("MAQ format '%d' not supported", mm->format); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’, inlined from ‘void maq_delete_maqmap(maqmap_T*) [with int max_readlen = 64]’ at maqmap_m.h:74:35, inlined from ‘maqmap_T* maqmap_read_header(gzFile) [with int max_readlen = 64]’ at maqmap_m.h:101:30: maqmap_m.h:84:14: note: call to ‘void free(void*)’ here 84 | std::free(mm); | ~~~~~~~~~^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sampler.c -o sampler.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c trim.c -o trim.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c util.c -o util.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/S4Vectors/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/IRanges/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/XVector/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Biostrings/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rhtslib/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c xsnap.c -o xsnap.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o count.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8reb8h/R.INSTALLe3818349c4533/ShortRead/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-ShortRead/00new/ShortRead/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ShortRead) * installing *source* package ‘RTMB’ ... ** this is package ‘RTMB’ version ‘1.7’ ** package ‘RTMB’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-2) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpyRcS9E/R.INSTALLe381c3b22bb0b/RTMB/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RTMB.cpp -o RTMB.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RTMB_tape.cpp -o RTMB_tape.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TMB.cpp -o TMB.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distributions.cpp -o distributions.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interpol.cpp -o interpol.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c lapack.cpp -o lapack.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c math.cpp -o math.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c math_complex.cpp -o math_complex.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.cpp -o misc.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c poshess.cpp -o poshess.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RTMB.so RTMB.o RTMB_tape.o RcppExports.o TMB.o distributions.o interpol.o lapack.o math.o math_complex.o misc.o poshess.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpyRcS9E/R.INSTALLe381c3b22bb0b/RTMB/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RTMB/00new/RTMB/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘fft’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘colSums’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘diag’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘dexp’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dweibull’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dbeta’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘df’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dt’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dnbinom’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dgamma’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pgamma’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pexp’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pweibull’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pbeta’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qgamma’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qexp’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qweibull’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qbeta’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘besselK’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘besselI’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘besselJ’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘besselY’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘eigen’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘svd’ from ‘base’ in package ‘RTMB’ (from the saved implicit definition) Creating a generic function for ‘svd’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘cov2cor’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dlnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘matrix’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘apply’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘sapply’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dmultinom’ from package ‘stats’ in package ‘RTMB’ ** 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 (RTMB) checking ggnetwork_0.5.14.tar.gz ... checking calmr_0.8.1.tar.gz ... checking BioM2_1.1.3.tar.gz ... checking ecostate_0.3.0.tar.gz ... checking genBaRcode_1.2.8.tar.gz ... checking inferCSN_1.1.7.tar.gz ... checking netmap_0.1.4.tar.gz ... checking pkggraph_0.2.3.tar.gz ... checking phyloseqGraphTest_0.1.1.tar.gz ... checking BasketballAnalyzeR_0.8.0.tar.gz ... checking fssemR_0.1.8.tar.gz ... checking mrIML_2.1.0.tar.gz ... checking nosoi_1.1.2.tar.gz ... checking rcausim_0.1.1.tar.gz ... Depends: Package: ggnetwork Depends: R (>= 3.5), ggplot2 (>= 2.0.0) Imports: ggrepel (>= 0.5), network, igraph, sna, utils Timings: user system elapsed ggnetwork 61.016 4.753 69.033 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 2 11 Check results summary: ggnetwork ... OK rdepends_BasketballAnalyzeR ... OK rdepends_BioM2 ... OK rdepends_calmr ... OK rdepends_ecostate ... OK rdepends_fssemR ... NOTE * checking C++ specification ... NOTE rdepends_genBaRcode ... OK rdepends_inferCSN ... OK rdepends_mrIML ... OK rdepends_netmap ... OK rdepends_nosoi ... OK rdepends_phyloseqGraphTest ... OK rdepends_pkggraph ... NOTE * checking package subdirectories ... NOTE rdepends_rcausim ... OK Check results changes: Package: fssemR Check: CRAN incoming feasibility Old result: NOTE Package: phyloseqGraphTest Check: CRAN incoming feasibility Old result: NOTE Package: rcausim Check: CRAN incoming feasibility Old result: NOTE