[ Started: 2023-03-03 01:00:49 CET ] [ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 Patched (2022-11-10 r83330) Old packages: 'mgcv', 'rgeos' trying URL 'https://cloud.r-project.org/src/contrib/mgcv_1.8-42.tar.gz' Content type 'application/x-gzip' length 1076221 bytes (1.0 MB) ================================================== downloaded 1.0 MB trying URL 'https://cloud.r-project.org/src/contrib/rgeos_0.6-2.tar.gz' Content type 'application/x-gzip' length 290935 bytes (284 KB) ================================================== downloaded 284 KB * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c coxph.c -o coxph.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c davies.c -o davies.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c discrete.c -o discrete.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gdi.c -o gdi.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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 -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c magic.c -o magic.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mat.c -o mat.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c matrix.c -o matrix.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mgcv.c -o mgcv.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c misc.c -o misc.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mvn.c -o mvn.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ncv.c -o ncv.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c qp.c -o qp.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c soap.c -o soap.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sparse-smooth.c -o sparse-smooth.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sparse.c -o sparse.o gcc -I"/usr/share/R/include" -DNDEBUG -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tprs.c -o tprs.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o mgcv.so coxph.o davies.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o ncv.o qp.o soap.o sparse-smooth.o sparse.o tprs.o -llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-mgcv/00new/mgcv/libs ** 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 ** 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 (mgcv) * installing *source* package ‘rgeos’ ... ** package ‘rgeos’ successfully unpacked and MD5 sums checked ** using staged installation configure: CC: gcc configure: CXX: g++ -std=gnu++14 configure: rgeos: 0.6-2 checking for /usr/bin/svnversion... yes configure: svn revision: 693 checking for geos-config... /usr/bin/geos-config checking geos-config usability... yes configure: GEOS version: 3.10.2 checking geos version at least 3.2.0... yes checking geos-config clibs... yes checking geos_c.h presence and usability... yes checking geos: linking with libgeos_c... yes configure: PKG_CPPFLAGS: -I/usr/include configure: PKG_LIBS: -L/usr/lib/x86_64-linux-gnu -lgeos_c configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dummy.cc -o dummy.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -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 -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c local_stubs.c -o local_stubs.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos.c -o rgeos.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_R2geos.c -o rgeos_R2geos.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_R2geosMP.c -o rgeos_R2geosMP.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_bbox.c -o rgeos_bbox.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_buffer.c -o rgeos_buffer.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_coord.c -o rgeos_coord.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_geos2R.c -o rgeos_geos2R.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_linearref.c -o rgeos_linearref.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_misc.c -o rgeos_misc.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_poly2nb.c -o rgeos_poly2nb.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_predicate_binary.c -o rgeos_predicate_binary.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_predicate_unary.c -o rgeos_predicate_unary.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_topology.c -o rgeos_topology.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_topology_binary.c -o rgeos_topology_binary.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_validate.c -o rgeos_validate.o gcc -I"/usr/share/R/include" -DNDEBUG -I/usr/include -I'/home/omnipath/local/R/4.2-3.16/sp/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rgeos_wkt.c -o rgeos_wkt.o g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o rgeos.so dummy.o init.o local_stubs.o rgeos.o rgeos_R2geos.o rgeos_R2geosMP.o rgeos_bbox.o rgeos_buffer.o rgeos_coord.o rgeos_geos2R.o rgeos_linearref.o rgeos_misc.o rgeos_poly2nb.o rgeos_predicate_binary.o rgeos_predicate_unary.o rgeos_topology.o rgeos_topology_binary.o rgeos_validate.o rgeos_wkt.o -L/usr/lib/x86_64-linux-gnu -lgeos_c -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-rgeos/00new/rgeos/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 (rgeos) The downloaded source packages are in ‘/tmp/RtmpzI9WY7/downloaded_packages’ [ Finished: 2023-03-03 01:01:49 CET ]