[ Started: 2023-05-24 23:59:44 CEST ] [ 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"/home/omnipath/local/R/4.2-3.16" [3] "/home/omnipath/local/R/4.2" "/usr/lib/R/library" Bioconductor version '3.16' is out-of-date; the current release version '3.17' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard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 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15) Old packages: 'rgeos', 'statnet.common' trying URL 'https://cloud.r-project.org/src/contrib/rgeos_0.6-3.tar.gz' Content type 'application/x-gzip' length 290912 bytes (284 KB) ================================================== downloaded 284 KB trying URL 'https://cloud.r-project.org/src/contrib/statnet.common_4.9.0.tar.gz' Content type 'application/x-gzip' length 339323 bytes (331 KB) ================================================== downloaded 331 KB * 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: 0.6-3 checking for /usr/bin/svnversion... yes configure: svn revision: 696 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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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 -flto=auto -ffat-lto-objects -flto=auto -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) * installing *source* package ‘statnet.common’ ... ** package ‘statnet.common’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -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-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c logspace_utils.c -o logspace_utils.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o statnet.common.so init.o logspace_utils.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-statnet.common/00new/statnet.common/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 (statnet.common) The downloaded source packages are in ‘/tmp/RtmpTC1SEi/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 3.16 (BiocManager 1.30.20), R 4.2.3 (2023-03-15) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' [ Finished: 2023-05-25 00:00:05 CEST ]