[ Started: 2022-04-26 15:57:10 ]
cli          (3.2.0        -> 3.3.0       ) [CRAN]
ps           (1.6.0        -> 1.7.0       ) [CRAN]
GenomeInfoDb (1.31.7       -> 1.31.10     ) [CRAN]
gplots       (3.1.1        -> 3.1.3       ) [CRAN]
rmarkdown    (2.13         -> 2.14        ) [CRAN]
testthat     (3.1.3        -> 3.1.4       ) [CRAN]
CARNIVAL     (14057d13a... -> 8b3f0dff8...) [GitHub]
Installing 6 packages: cli, ps, GenomeInfoDb, gplots, 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)
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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)
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downloaded 122 KB

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/GenomeInfoDb_1.31.10.tar.gz'
Content type 'application/x-gzip' length 3452600 bytes (3.3 MB)
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downloaded 3.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/gplots_3.1.3.tar.gz'
Content type 'application/x-gzip' length 520683 bytes (508 KB)
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downloaded 508 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)
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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)
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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 ‘GenomeInfoDb’ ...
** 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 (GenomeInfoDb)
* installing *source* package ‘gplots’ ...
** package ‘gplots’ 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 (gplots)
* 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/RtmpA8oxUi/downloaded_packages’
Downloading GitHub repo saezlab/CARNIVAL@HEAD
cli       (3.2.0 -> 3.3.0) [CRAN]
rmarkdown (2.13  -> 2.14 ) [CRAN]
Installing 2 packages: cli, rmarkdown
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)
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downloaded 484 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)
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downloaded 3.1 MB

* 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 ‘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)

The downloaded source packages are in
	‘/tmp/RtmpA8oxUi/downloaded_packages’
* checking for file ‘/tmp/RtmpA8oxUi/remotes3d237f620c1c3c/saezlab-CARNIVAL-8b3f0df/DESCRIPTION’ ... OK
* preparing ‘CARNIVAL’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘CARNIVAL_2.5.1.tar.gz’

* installing *source* package ‘CARNIVAL’ ...
** 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 (CARNIVAL)
[ Finished: 2022-04-26 15:59:05 ]