[ Started: 2023-12-05 11:51:11 CET ] [ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.18" [3] "/home/omnipath/local/R/4.3" "/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 3.18 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Old packages: 'gert', 'jsonlite', 'xml2' trying URL 'https://cloud.r-project.org/src/contrib/gert_2.0.1.tar.gz' Content type 'application/x-gzip' length 122723 bytes (119 KB) ================================================== downloaded 119 KB trying URL 'https://cloud.r-project.org/src/contrib/jsonlite_1.8.8.tar.gz' Content type 'application/x-gzip' length 1053028 bytes (1.0 MB) ================================================== downloaded 1.0 MB trying URL 'https://cloud.r-project.org/src/contrib/xml2_1.3.6.tar.gz' Content type 'application/x-gzip' length 294715 bytes (287 KB) ================================================== downloaded 287 KB * installing *source* package ‘gert’ ... ** package ‘gert’ successfully unpacked and MD5 sums checked ** using staged installation Found OpenSSL3 Using static libgit2 for Linux x86_64 Using PKG_CFLAGS=-DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include Using PKG_LIBS=-L/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl Configuration OK! ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ rm -f gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 branch.c -o branch.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 clone.c -o clone.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 commit.c -o commit.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 config.c -o config.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 conflicts.c -o conflicts.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 files.c -o files.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 ignore.c -o ignore.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 merge.c -o merge.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 rebase.c -o rebase.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 stash.c -o stash.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 submodules.c -o submodules.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 tag.c -o tag.o gcc -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 -I"/usr/share/R/include" -DNDEBUG -DSTATIC_LIBGIT2 -I/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/include -DR_NO_REMAP -DSTRICT_R_HEADERS -fvisibility=hidden -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 version.c -o version.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o gert.so branch.o clone.o commit.o config.o conflicts.o files.o ignore.o init.o merge.o rebase.o stash.o submodules.o tag.o utils.o version.o -L/tmp/RtmpKdfX9O/R.INSTALL23c23a75ca2a4b/gert/libgit2-1.4.2-x86_64_linux/lib -lstatgit2 -lrt -lpthread -lstatssh2 -lstatssl -lstatcrypto -ldl -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-gert/00new/gert/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gert) * installing *source* package ‘jsonlite’ ... ** package ‘jsonlite’ 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 -Iyajl/api -fvisibility=hidden -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 base64.c -o base64.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 collapse_array.c -o collapse_array.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 collapse_object.c -o collapse_object.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 collapse_pretty.c -o collapse_pretty.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 escape_chars.c -o escape_chars.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 integer64_to_na.c -o integer64_to_na.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 is_datelist.c -o is_datelist.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 is_recordlist.c -o is_recordlist.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 is_scalarlist.c -o is_scalarlist.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 modp_numtoa.c -o modp_numtoa.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 null_to_na.c -o null_to_na.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 num_to_char.c -o num_to_char.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 parse.c -o parse.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 prettify.c -o prettify.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 push_parser.c -o push_parser.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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-base64.c -o r-base64.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 register.c -o register.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 row_collapse.c -o row_collapse.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 transpose_list.c -o transpose_list.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 validate.c -o validate.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl.c -o yajl/yajl.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl_alloc.c -o yajl/yajl_alloc.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl_buf.c -o yajl/yajl_buf.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl_encode.c -o yajl/yajl_encode.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl_gen.c -o yajl/yajl_gen.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl_lex.c -o yajl/yajl_lex.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl_parser.c -o yajl/yajl_parser.o gcc -I"/usr/share/R/include" -DNDEBUG -Iyajl/api -fvisibility=hidden -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 yajl/yajl_tree.c -o yajl/yajl_tree.o ar rcs yajl/libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -Lyajl -lstatyajl -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-jsonlite/00new/jsonlite/libs ** R ** inst ** byte-compile and prepare package for lazy loading in method for ‘asJSON’ with signature ‘"AsIs"’: no definition for class “AsIs” in method for ‘asJSON’ with signature ‘"ITime"’: no definition for class “ITime” in method for ‘asJSON’ with signature ‘"hms"’: no definition for class “hms” in method for ‘asJSON’ with signature ‘"json"’: no definition for class “json” in method for ‘asJSON’ with signature ‘"integer64"’: no definition for class “integer64” in method for ‘asJSON’ with signature ‘"pairlist"’: no definition for class “pairlist” in method for ‘asJSON’ with signature ‘"blob"’: no definition for class “blob” in method for ‘asJSON’ with signature ‘"scalar"’: no definition for class “scalar” in method for ‘asJSON’ with signature ‘"sf"’: no definition for class “sf” in method for ‘asJSON’ with signature ‘"sfc"’: no definition for class “sfc” in method for ‘asJSON’ with signature ‘"vctrs_vctr"’: no definition for class “vctrs_vctr” ** 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 (jsonlite) * installing *source* package ‘xml2’ ... ** package ‘xml2’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/libxml2 Using PKG_LIBS=-lxml2 ** 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 -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 connection.cpp -o connection.o gcc -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -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 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_doc.cpp -o xml2_doc.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_init.cpp -o xml2_init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_namespace.cpp -o xml2_namespace.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_node.cpp -o xml2_node.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_output.cpp -o xml2_output.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_schema.cpp -o xml2_schema.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_url.cpp -o xml2_url.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -fvisibility=hidden -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 xml2_xpath.cpp -o xml2_xpath.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 xml2.so connection.o init.o xml2_doc.o xml2_init.o xml2_namespace.o xml2_node.o xml2_output.o xml2_schema.o xml2_url.o xml2_xpath.o -lxml2 -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.18/00LOCK-xml2/00new/xml2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (xml2) The downloaded source packages are in ‘/tmp/RtmpoLJRhC/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 3.18 (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' Skipping 2 packages ahead of CRAN: jsonlite, xml2 [ Finished: 2023-12-05 11:51:36 CET ]