[ Started: 2023-11-29 11:53:37 CET ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/bslib_0.6.1.tar.gz' Content type 'application/x-gzip' length 6059587 bytes (5.8 MB) ================================================== downloaded 5.8 MB trying URL 'https://cran.uni-muenster.de/src/contrib/distances_0.1.10.tar.gz' Content type 'application/x-gzip' length 87660 bytes (85 KB) ================================================== downloaded 85 KB trying URL 'https://cran.uni-muenster.de/src/contrib/stringdist_0.9.12.tar.gz' Content type 'application/x-gzip' length 862306 bytes (842 KB) ================================================== downloaded 842 KB * installing *source* package ‘bslib’ ... ** package ‘bslib’ 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 (bslib) * installing *source* package ‘distances’ ... ** package ‘distances’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c distances-init.c -o distances-init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c error.c -o error.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c get_dists.c -o get_dists.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c internal.c -o internal.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c max_dists.c -o max_dists.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nn_search.c -o nn_search.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nn_search_ann.cpp -o nn_search_ann.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o (cd libann && R_AR="ar" R_CXX="g++ -std=gnu++17" R_CPPFLAGS="-DNDEBUG " R_CXXFLAGS="-fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 " make) || exit 1; make[1]: Entering directory '/tmp/RtmpWP0GLK/R.INSTALL38576971ad0549/distances/src/libann' g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/ANN.cpp -o src/ANN.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/brute.cpp -o src/brute.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/kd_tree.cpp -o src/kd_tree.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/kd_util.cpp -o src/kd_util.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/kd_split.cpp -o src/kd_split.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/kd_dump.cpp -o src/kd_dump.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/kd_search.cpp -o src/kd_search.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/kd_pr_search.cpp -o src/kd_pr_search.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/kd_fix_rad_search.cpp -o src/kd_fix_rad_search.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/bd_tree.cpp -o src/bd_tree.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/bd_search.cpp -o src/bd_search.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/bd_pr_search.cpp -o src/bd_pr_search.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/bd_fix_rad_search.cpp -o src/bd_fix_rad_search.o g++ -std=gnu++17 -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Iinclude -c src/perf.cpp -o src/perf.o ar -rcs libann.a src/ANN.o src/brute.o src/kd_tree.o src/kd_util.o src/kd_split.o src/kd_dump.o src/kd_search.o src/kd_pr_search.o src/kd_fix_rad_search.o src/bd_tree.o src/bd_search.o src/bd_pr_search.o src/bd_fix_rad_search.o src/perf.o make[1]: Leaving directory '/tmp/RtmpWP0GLK/R.INSTALL38576971ad0549/distances/src/libann' g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o distances.so distances-init.o error.o get_dists.o internal.o max_dists.o nn_search.o nn_search_ann.o utils.o libann/libann.a -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-distances/00new/distances/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (distances) * installing *source* package ‘stringdist’ ... ** package ‘stringdist’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c R_register_native.c -o R_register_native.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rstringdist.c -o Rstringdist.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dl.c -o dl.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hamming.c -o hamming.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c jaro.c -o jaro.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lcs.c -o lcs.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lv.c -o lv.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c osa.c -o osa.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qgram.c -o qgram.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c soundex.c -o soundex.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c stringdist.c -o stringdist.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utf8ToInt.c -o utf8ToInt.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.c -o utils.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o stringdist.so R_register_native.o Rstringdist.o dl.o hamming.o jaro.o lcs.o lv.o osa.o qgram.o soundex.o stringdist.o utf8ToInt.o utils.o -fopenmp -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-stringdist/00new/stringdist/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 (stringdist) The downloaded source packages are in ‘/tmp/RtmpKx7dIk/downloaded_packages’ Bioconductor version '3.17' is out-of-date; the current release version '3.18' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Old packages: 'spatstat.random' trying URL 'https://cloud.r-project.org/src/contrib/spatstat.random_3.2-2.tar.gz' Content type 'application/x-gzip' length 263605 bytes (257 KB) ================================================== downloaded 257 KB * installing *source* package ‘spatstat.random’ ... ** package ‘spatstat.random’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Perfect.cc -o Perfect.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c areaint.c -o areaint.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c badgey.c -o badgey.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dgs.c -o dgs.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c diggra.c -o diggra.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dist2.c -o dist2.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fiksel.c -o fiksel.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getcif.c -o getcif.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c geyer.c -o geyer.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hardcore.c -o hardcore.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lennard.c -o lennard.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lookup.c -o lookup.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c methas.c -o methas.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mhsnoop.c -o mhsnoop.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multihard.c -o multihard.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c penttinen.c -o penttinen.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rcauchy.c -o rcauchy.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rmatclus.c -o rmatclus.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rthin.c -o rthin.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rthomas.c -o rthomas.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rtruncpois.c -o rtruncpois.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sftcr.c -o sftcr.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c straush.c -o straush.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c straushm.c -o straushm.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c strauss.c -o strauss.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c straussm.c -o straussm.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c triplets.c -o triplets.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o spatstat.random.so Perfect.o areaint.o badgey.o dgs.o diggra.o dist2.o fiksel.o getcif.o geyer.o hardcore.o init.o lennard.o lookup.o methas.o mhsnoop.o multihard.o penttinen.o rcauchy.o rmatclus.o rthin.o rthomas.o rtruncpois.o sftcr.o straush.o straushm.o strauss.o straussm.o triplets.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-spatstat.random/00new/spatstat.random/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (spatstat.random) The downloaded source packages are in ‘/tmp/RtmpKx7dIk/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2023-11-29 11:54:20 CET ]