[ Started: 2022-04-26 18:56:14 ] cli (3.2.0 -> 3.3.0 ) [CRAN] ps (1.6.0 -> 1.7.0 ) [CRAN] checkmate (2.0.0 -> 2.1.0 ) [CRAN] rmarkdown (2.13 -> 2.14 ) [CRAN] testthat (3.1.3 -> 3.1.4 ) [CRAN] OmnipathR (178582759... -> 4b6b9ba11...) [GitHub] Installing 5 packages: cli, ps, checkmate, rmarkdown, testthat trying URL 'https://cloud.r-project.org/src/contrib/cli_3.3.0.tar.gz' Content type 'application/x-gzip' length 495823 bytes (484 KB) ================================================== downloaded 484 KB trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.0.tar.gz' Content type 'application/x-gzip' length 125455 bytes (122 KB) ================================================== downloaded 122 KB trying URL 'https://cloud.r-project.org/src/contrib/checkmate_2.1.0.tar.gz' Content type 'application/x-gzip' length 170034 bytes (166 KB) ================================================== downloaded 166 KB trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.14.tar.gz' Content type 'application/x-gzip' length 3241807 bytes (3.1 MB) ================================================== downloaded 3.1 MB trying URL 'https://cloud.r-project.org/src/contrib/testthat_3.1.4.tar.gz' Content type 'application/x-gzip' length 700919 bytes (684 KB) ================================================== downloaded 684 KB * installing *source* package ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c ansi.c -o ansi.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c cleancall.c -o cleancall.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c diff.c -o diff.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c errors.c -o errors.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c md5.c -o md5.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress-altrep.c -o progress-altrep.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress.c -o progress.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c sha256.c -o sha256.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c thread.c -o thread.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c tty.c -o tty.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c utf8.c -o utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c win-utf8.c -o win-utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c winfiles.c -o winfiles.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o init.o md5.o progress-altrep.o progress.o sha256.o thread.o tty.o utf8.o win-utf8.o winfiles.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-cli/00new/cli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (cli) * installing *source* package ‘ps’ ... ** package ‘ps’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -std=gnu99 -Wall -pedantic -L/usr/local/lib -Wall px.c -o px gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-common.c -o api-common.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c common.c -o common.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c extra.c -o extra.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c dummy.c -o dummy.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c error-codes.c -o error-codes.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c posix.c -o posix.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-posix.c -o api-posix.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c linux.c -o linux.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c api-linux.c -o api-linux.o api-linux.c: In function ‘psll_get_cpu_aff’: api-linux.c:1139:9: warning: ‘pid’ may be used uninitialized in this function [-Wmaybe-uninitialized] 1139 | if (sched_getaffinity(pid, setsize, mask) == 0) { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o posix.o api-posix.o linux.o api-linux.o -L/opt/R-rc/lib/R/lib -lR installing via 'install.libs.R' to /home/omnipath/local/R/00LOCK-ps/00new/ps ** 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 (ps) * installing *source* package ‘checkmate’ ... ** package ‘checkmate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c all_missing.c -o all_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_infinite.c -o any_infinite.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_missing.c -o any_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_nan.c -o any_nan.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c checks.c -o checks.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c find_nchar.c -o find_nchar.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c guess_type.c -o guess_type.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c helper.c -o helper.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c integerish.c -o integerish.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c is_sorted.c -o is_sorted.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c qassert.c -o qassert.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c which_first.c -o which_first.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o checkmate.so all_missing.o any_infinite.o any_missing.o any_nan.o checks.o find_nchar.o guess_type.o helper.o init.o integerish.o is_sorted.o qassert.o which_first.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-checkmate/00new/checkmate/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 (checkmate) * installing *source* package ‘rmarkdown’ ... ** package ‘rmarkdown’ 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 (rmarkdown) * installing *source* package ‘testthat’ ... ** package ‘testthat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c reassign.c -o reassign.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-catch.cpp -o test-catch.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-example.cpp -o test-example.o g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG -I../inst/include -DCOMPILING_TESTTHAT -I/usr/local/include -fpic -Wall -pedantic -c test-runner.cpp -o test-runner.o g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o testthat.so init.o reassign.o test-catch.o test-example.o test-runner.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-testthat/00new/testthat/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 (testthat) The downloaded source packages are in ‘/tmp/RtmpzP1DAg/downloaded_packages’ Downloading GitHub repo saezlab/OmnipathR@HEAD cli (3.2.0 -> 3.3.0) [CRAN] checkmate (2.0.0 -> 2.1.0) [CRAN] Installing 2 packages: cli, checkmate trying URL 'https://cloud.r-project.org/src/contrib/cli_3.3.0.tar.gz' Content type 'application/x-gzip' length 495823 bytes (484 KB) ================================================== downloaded 484 KB trying URL 'https://cloud.r-project.org/src/contrib/checkmate_2.1.0.tar.gz' Content type 'application/x-gzip' length 170034 bytes (166 KB) ================================================== downloaded 166 KB * installing *source* package ‘cli’ ... ** package ‘cli’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c ansi.c -o ansi.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c cleancall.c -o cleancall.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c diff.c -o diff.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c errors.c -o errors.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c md5.c -o md5.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress-altrep.c -o progress-altrep.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c progress.c -o progress.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c sha256.c -o sha256.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c thread.c -o thread.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c tty.c -o tty.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c utf8.c -o utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c win-utf8.c -o win-utf8.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c winfiles.c -o winfiles.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o cli.so ansi.o cleancall.o diff.o errors.o init.o md5.o progress-altrep.o progress.o sha256.o thread.o tty.o utf8.o win-utf8.o winfiles.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-cli/00new/cli/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (cli) * installing *source* package ‘checkmate’ ... ** package ‘checkmate’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c all_missing.c -o all_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_infinite.c -o any_infinite.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_missing.c -o any_missing.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c any_nan.c -o any_nan.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c checks.c -o checks.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c find_nchar.c -o find_nchar.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c guess_type.c -o guess_type.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c helper.c -o helper.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c init.c -o init.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c integerish.c -o integerish.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c is_sorted.c -o is_sorted.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c qassert.c -o qassert.o gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -std=gnu99 -Wall -pedantic -c which_first.c -o which_first.o gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o checkmate.so all_missing.o any_infinite.o any_missing.o any_nan.o checks.o find_nchar.o guess_type.o helper.o init.o integerish.o is_sorted.o qassert.o which_first.o -L/opt/R-rc/lib/R/lib -lR installing to /home/omnipath/local/R/00LOCK-checkmate/00new/checkmate/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 (checkmate) The downloaded source packages are in ‘/tmp/RtmpzP1DAg/downloaded_packages’ * checking for file ‘/tmp/RtmpzP1DAg/remotes3fb56e2efae95d/saezlab-OmnipathR-4b6b9ba/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.3.25.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** 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 [2022-04-26 18:57:55] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2022-04-26 18:57:55] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-04-26 18:57:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-04-26 18:57:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-04-26 18:57:56] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-04-26 18:57:56] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2022-04-26 18:57:57] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2022-04-26 18:57:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-04-26 18:57:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2022-04-26 18:57:57] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-04-26 18:57:57] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) [ Finished: 2022-04-26 18:57:58 ]