[ Started: 2023-04-26 00:08:20 CEST ] [ 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" "/opt/R-devel/lib/R/library" Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib: cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES' Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Old packages: 'fitdistrplus', 'fs', 'recipes', 'scater' trying URL 'https://cloud.r-project.org/src/contrib/fitdistrplus_1.1-11.tar.gz' Content type 'application/x-gzip' length 1551868 bytes (1.5 MB) ================================================== downloaded 1.5 MB trying URL 'https://cloud.r-project.org/src/contrib/fs_1.6.2.tar.gz' Content type 'application/x-gzip' length 1185454 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cloud.r-project.org/src/contrib/recipes_1.0.6.tar.gz' Content type 'application/x-gzip' length 799246 bytes (780 KB) ================================================== downloaded 780 KB trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/scater_1.27.9.tar.gz' Content type 'application/x-gzip' length 4089452 bytes (3.9 MB) ================================================== downloaded 3.9 MB * installing *source* package ‘fitdistrplus’ ... ** package ‘fitdistrplus’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fitdistrplus) * installing *source* package ‘fs’ ... ** package ‘fs’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c dir.cc -o dir.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c error.cc -o error.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c file.cc -o file.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c fs.cc -o fs.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c getmode.cc -o getmode.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c id.cc -o id.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c init.cc -o init.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c link.cc -o link.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c path.cc -o path.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c utils.cc -o utils.o g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c unix/getmode.cc -o unix/getmode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/setmode.c -o bsd/setmode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/strmode.c -o bsd/strmode.o gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG -I./libuv-1.44.2/include -I. -pthread -I/usr/local/include -fpic -g -O2 -c bsd/reallocarray.c -o bsd/reallocarray.o (cd libuv-1.44.2 \ && CC="gcc" CFLAGS="-g -O2 -I/usr/local/include -fpic -fvisibility=hidden -std=c99" AR="ar" RANLIB="ranlib" LDFLAGS="-L/usr/local/lib" ./configure --quiet) make --directory=libuv-1.44.2 \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/Rtmpr2NKlp/R.INSTALL10d4792fb987a9/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/Rtmpr2NKlp/R.INSTALL10d4792fb987a9/fs/src/libuv-1.44.2' g++ -std=gnu++17 -shared -L/usr/local/lib -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 installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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) * installing *source* package ‘recipes’ ... ** package ‘recipes’ 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 ** installing vignettes ** 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 (recipes) * installing *source* package ‘scater’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (scater) The downloaded source packages are in ‘/tmp/RtmphDQPkl/downloaded_packages’ Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr [ Finished: 2023-04-26 00:09:32 CEST ]