[ Started: 2022-04-25 13:08:19 ] cli (3.2.0 -> 3.3.0 ) [CRAN] ps (1.6.0 -> 1.7.0 ) [CRAN] BiocManager (1.30.16 -> 1.30.17) [CRAN] Installing 3 packages: cli, ps, BiocManager 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/BiocManager_1.30.17.tar.gz' Content type 'application/x-gzip' length 287948 bytes (281 KB) ================================================== downloaded 281 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 ‘BiocManager’ ... ** package ‘BiocManager’ successfully unpacked and MD5 sums checked ** 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 (BiocManager) The downloaded source packages are in ‘/tmp/Rtmp57sBFW/downloaded_packages’ [ Finished: 2022-04-25 13:08:44 ]