[ Started: 2022-05-05 09:44:41 ]
tibble      (3.1.6   -> 3.1.7  ) [CRAN]
cli         (3.2.0   -> 3.3.0  ) [CRAN]
ps          (1.6.0   -> 1.7.0  ) [CRAN]
knitr       (1.38    -> 1.39   ) [CRAN]
rmarkdown   (2.13    -> 2.14   ) [CRAN]
httr        (1.4.2   -> 1.4.3  ) [CRAN]
BiocManager (1.30.16 -> 1.30.17) [CRAN]
dplyr       (1.0.8   -> 1.0.9  ) [CRAN]
testthat    (3.1.3   -> 3.1.4  ) [CRAN]
BiocStyle   (2.23.1  -> 2.24.0 ) [CRAN]
Installing 10 packages: tibble, cli, ps, knitr, rmarkdown, httr, BiocManager, dplyr, testthat, BiocStyle
trying URL 'https://cloud.r-project.org/src/contrib/tibble_3.1.7.tar.gz'
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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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trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.0.tar.gz'
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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/rmarkdown_2.14.tar.gz'
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downloaded 3.1 MB

trying URL 'https://cloud.r-project.org/src/contrib/httr_1.4.3.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/BiocManager_1.30.17.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/dplyr_1.0.9.tar.gz'
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trying URL 'https://cloud.r-project.org/src/contrib/testthat_3.1.4.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/BiocStyle_2.24.0.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 ‘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)
* 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 ‘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 ‘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)
* installing *source* package ‘BiocStyle’ ...
** 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 (BiocStyle)

The downloaded source packages are in
	‘/tmp/Rtmpfpf5Cr/downloaded_packages’
[ Finished: 2022-05-05 09:46:27 ]