[ Started: 2023-02-07 01:00:35 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 '?repositories' for details replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 Patched (2022-11-10 r83330) Old packages: 'fs' trying URL 'https://cloud.r-project.org/src/contrib/fs_1.6.1.tar.gz' Content type 'application/x-gzip' length 1185417 bytes (1.1 MB) ================================================== downloaded 1.1 MB * installing *source* package ‘fs’ ... ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 dir.cc -o dir.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 error.cc -o error.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 file.cc -o file.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 fs.cc -o fs.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 getmode.cc -o getmode.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 id.cc -o id.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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.cc -o init.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 link.cc -o link.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 path.cc -o path.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 utils.cc -o utils.o g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 unix/getmode.cc -o unix/getmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 bsd/setmode.c -o bsd/setmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 bsd/strmode.c -o bsd/strmode.o gcc -I"/usr/share/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -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 bsd/reallocarray.c -o bsd/reallocarray.o (cd libuv-1.44.2 \ && CC="gcc" CFLAGS="-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 -fpic -fvisibility=hidden -std=c99" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -Wl,-z,relro" ./configure --quiet) make --directory=libuv-1.44.2 \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/Rtmp5Ukqf9/R.INSTALL10af314832dbe1/fs/src/libuv-1.44.2' CC src/libuv_la-fs-poll.lo CC src/libuv_la-idna.lo CC src/libuv_la-inet.lo CC src/libuv_la-random.lo CC src/libuv_la-strscpy.lo CC src/libuv_la-threadpool.lo CC src/libuv_la-timer.lo CC src/libuv_la-uv-data-getter-setters.lo CC src/libuv_la-uv-common.lo CC src/libuv_la-version.lo CC src/libuv_la-strtok.lo CC src/unix/libuv_la-async.lo CC src/unix/libuv_la-core.lo CC src/unix/libuv_la-dl.lo CC src/unix/libuv_la-fs.lo CC src/unix/libuv_la-getaddrinfo.lo CC src/unix/libuv_la-getnameinfo.lo CC src/unix/libuv_la-loop-watcher.lo CC src/unix/libuv_la-loop.lo CC src/unix/libuv_la-pipe.lo CC src/unix/libuv_la-poll.lo CC src/unix/libuv_la-process.lo CC src/unix/libuv_la-random-devurandom.lo CC src/unix/libuv_la-signal.lo CC src/unix/libuv_la-stream.lo CC src/unix/libuv_la-tcp.lo CC src/unix/libuv_la-thread.lo CC src/unix/libuv_la-tty.lo CC src/unix/libuv_la-udp.lo CC src/unix/libuv_la-linux-core.lo CC src/unix/libuv_la-linux-inotify.lo CC src/unix/libuv_la-linux-syscalls.lo CC src/unix/libuv_la-procfs-exepath.lo CC src/unix/libuv_la-proctitle.lo CC src/unix/libuv_la-random-getrandom.lo CC src/unix/libuv_la-random-sysctl-linux.lo CC src/unix/libuv_la-epoll.lo CCLD libuv.la make[1]: Leaving directory '/tmp/Rtmp5Ukqf9/R.INSTALL10af314832dbe1/fs/src/libuv-1.44.2' g++ -std=gnu++14 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o fs.so dir.o error.o file.o fs.o getmode.o id.o init.o link.o path.o utils.o unix/getmode.o bsd/setmode.o bsd/strmode.o bsd/reallocarray.o ./libuv-1.44.2/.libs/libuv.a -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.2-3.16/00LOCK-fs/00new/fs/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 (fs) The downloaded source packages are in ‘/tmp/RtmpVKu55L/downloaded_packages’ Skipping 1 packages ahead of CRAN: fs [ Finished: 2023-02-07 01:01:06 CET ]