[ Started: 2022-04-23 18:27:27 ]
checkmate (2.0.0        -> 2.1.0       ) [CRAN]
OmnipathR (178582759... -> 4b6b9ba11...) [GitHub]
Installing 1 packages: checkmate
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 ‘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/Rtmp3IKeaQ/downloaded_packages’
Downloading GitHub repo saezlab/OmnipathR@HEAD
checkmate (2.0.0 -> 2.1.0) [CRAN]
Installing 1 packages: checkmate
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 ‘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/Rtmp3IKeaQ/downloaded_packages’
* checking for file ‘/tmp/Rtmp3IKeaQ/remotes3442592cc7b8b0/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
[2022-04-23 18:28:05] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2022-04-23 18:28:05] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-04-23 18:28:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-04-23 18:28:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2022-04-23 18:28:05] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-23 18:28:05] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2022-04-23 18:28:06] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2022-04-23 18:28:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-04-23 18:28:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2022-04-23 18:28:07] [INFO]    [OmnipathR] Welcome to OmnipathR!
[2022-04-23 18:28:07] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
[ Finished: 2022-04-23 18:28:07 ]