[ Started: 2022-05-05 14:09:21 ]
tibble    (3.1.6        -> 3.1.7       ) [CRAN]
cli       (3.2.0        -> 3.3.0       ) [CRAN]
ps        (1.6.0        -> 1.7.0       ) [CRAN]
dplyr     (1.0.8        -> 1.0.9       ) [CRAN]
knitr     (1.38         -> 1.39        ) [CRAN]
httr      (1.4.2        -> 1.4.3       ) [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... -> af4c471ed...) [GitHub]
Installing 9 packages: tibble, cli, ps, dplyr, knitr, httr, checkmate, rmarkdown, testthat
trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.1.7.tar.gz'
Content type 'application/x-gzip' length 674873 bytes (659 KB)
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downloaded 659 KB

trying URL 'https://cloud.r-project.org/src/contrib/cli_3.3.0.tar.gz'
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downloaded 484 KB

trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.0.tar.gz'
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downloaded 122 KB

trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.0.9.tar.gz'
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downloaded 935 KB

trying URL 'https://cloud.r-project.org/src/contrib/knitr_1.39.tar.gz'
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downloaded 877 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.3.tar.gz'
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downloaded 157 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)
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downloaded 166 KB

trying URL 'https://cloud.r-project.org/src/contrib/rmarkdown_2.14.tar.gz'
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downloaded 3.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/testthat_3.1.4.tar.gz'
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* installing *source* package ‘tibble’ ...
** package ‘tibble’ 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 attributes.c -o attributes.o
gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -std=gnu99 -Wall -pedantic  -c coerce.c -o coerce.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 matrixToDataFrame.c -o matrixToDataFrame.o
gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o -L/opt/R-rc/lib/R/lib -lR
installing to /home/omnipath/local/R/00LOCK-tibble/00new/tibble/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 (tibble)
* 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 ‘knitr’ ...
** package ‘knitr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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 (knitr)
* installing *source* package ‘httr’ ...
** package ‘httr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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 (httr)
* 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 ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c chop.cpp -o chop.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c filter.cpp -o filter.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c funs.cpp -o funs.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c group_by.cpp -o group_by.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c group_data.cpp -o group_data.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c imports.cpp -o imports.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c init.cpp -o init.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c mask.cpp -o mask.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c mutate.cpp -o mutate.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c slice.cpp -o slice.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c summarise.cpp -o summarise.o
g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o -L/opt/R-rc/lib/R/lib -lR
installing to /home/omnipath/local/R/00LOCK-dplyr/00new/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (dplyr)
* 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/RtmpaCjC5Q/downloaded_packages’
Downloading GitHub repo saezlab/OmnipathR@HEAD
cli       (3.2.0 -> 3.3.0) [CRAN]
tibble    (3.1.6 -> 3.1.7) [CRAN]
dplyr     (1.0.8 -> 1.0.9) [CRAN]
httr      (1.4.2 -> 1.4.3) [CRAN]
checkmate (2.0.0 -> 2.1.0) [CRAN]
Installing 5 packages: cli, tibble, dplyr, httr, 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)
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downloaded 484 KB

trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.1.7.tar.gz'
Content type 'application/x-gzip' length 674873 bytes (659 KB)
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downloaded 659 KB

trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.0.9.tar.gz'
Content type 'application/x-gzip' length 957637 bytes (935 KB)
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downloaded 935 KB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.3.tar.gz'
Content type 'application/x-gzip' length 161122 bytes (157 KB)
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downloaded 157 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)
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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 ‘tibble’ ...
** package ‘tibble’ 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 attributes.c -o attributes.o
gcc -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -std=gnu99 -Wall -pedantic  -c coerce.c -o coerce.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 matrixToDataFrame.c -o matrixToDataFrame.o
gcc -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o tibble.so attributes.o coerce.o init.o matrixToDataFrame.o -L/opt/R-rc/lib/R/lib -lR
installing to /home/omnipath/local/R/00LOCK-tibble/00new/tibble/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 (tibble)
* installing *source* package ‘httr’ ...
** package ‘httr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** demo
** 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 (httr)
* 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 ‘dplyr’ ...
** package ‘dplyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c chop.cpp -o chop.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c filter.cpp -o filter.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c funs.cpp -o funs.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c group_by.cpp -o group_by.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c group_data.cpp -o group_data.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c imports.cpp -o imports.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c init.cpp -o init.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c mask.cpp -o mask.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c mutate.cpp -o mutate.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c slice.cpp -o slice.o
g++ -std=gnu++14 -I"/opt/R-rc/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -Wall -pedantic  -c summarise.cpp -o summarise.o
g++ -std=gnu++14 -shared -L/opt/R-rc/lib/R/lib -L/usr/local/lib -o dplyr.so chop.o filter.o funs.o group_by.o group_data.o imports.o init.o mask.o mutate.o slice.o summarise.o -L/opt/R-rc/lib/R/lib -lR
installing to /home/omnipath/local/R/00LOCK-dplyr/00new/dplyr/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (dplyr)

The downloaded source packages are in
	‘/tmp/RtmpaCjC5Q/downloaded_packages’
* checking for file ‘/tmp/RtmpaCjC5Q/remotes1690c14f512162/saezlab-OmnipathR-af4c471/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_3.5.0.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
[2022-05-05 14:12:12] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2022-05-05 14:12:12] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-05-05 14:12:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-05-05 14:12:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2022-05-05 14:12:12] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-05-05 14:12:12] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2022-05-05 14:12:14] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-05-05 14:12:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-05-05 14:12:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2022-05-05 14:12:14] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-05-05 14:12:14] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2022-05-05 14:12:14 ]