[ Started: 2023-05-15 23:55:09 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.17"
[3] "/home/omnipath/local/R/4.3"      "/opt/R-devel/lib/R/library"     
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Old packages: 'biocViews', 'clock', 'S4Arrays'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/biocViews_1.68.1.tar.gz'
Content type 'application/x-gzip' length 518266 bytes (506 KB)
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downloaded 506 KB

trying URL 'https://cloud.r-project.org/src/contrib/clock_0.7.0.tar.gz'
Content type 'application/x-gzip' length 558040 bytes (544 KB)
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downloaded 544 KB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/S4Arrays_1.0.4.tar.gz'
Content type 'application/x-gzip' length 277646 bytes (271 KB)
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downloaded 271 KB

* installing *source* package ‘biocViews’ ...
** 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 (biocViews)
* installing *source* package ‘clock’ ...
** package ‘clock’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c duration.cpp -o duration.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c enums.cpp -o enums.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c format.cpp -o format.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c gregorian-year-day.cpp -o gregorian-year-day.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c gregorian-year-month-day.cpp -o gregorian-year-month-day.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c gregorian-year-month-weekday.cpp -o gregorian-year-month-weekday.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c iso-year-week-day.cpp -o iso-year-week-day.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c limits.cpp -o limits.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c naive-time.cpp -o naive-time.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c quarterly-year-quarter-day.cpp -o quarterly-year-quarter-day.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c rcrd.cpp -o rcrd.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c sys-time.cpp -o sys-time.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c time-point.cpp -o time-point.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c utils.cpp -o utils.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c week-year-week-day.cpp -o week-year-week-day.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c weekday.cpp -o weekday.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c zone.cpp -o zone.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -I/usr/local/include    -fpic  -g -O2  -c zoned-time.cpp -o zoned-time.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o clock.so cpp11.o duration.o enums.o format.o gregorian-year-day.o gregorian-year-month-day.o gregorian-year-month-weekday.o iso-year-week-day.o limits.o naive-time.o quarterly-year-quarter-day.o rcrd.o sys-time.o time-point.o utils.o week-year-week-day.o weekday.o zone.o zoned-time.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-clock/00new/clock/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 (clock)
* installing *source* package ‘S4Arrays’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c R_init_S4Arrays.c -o R_init_S4Arrays.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c abind.c -o abind.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c array_selection.c -o array_selection.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/S4Vectors/include' -I/usr/local/include    -fpic  -g -O2  -c dim_tuning_utils.c -o dim_tuning_utils.o
gcc -shared -L/usr/local/lib -o S4Arrays.so R_init_S4Arrays.o S4Vectors_stubs.o abind.o array_selection.o dim_tuning_utils.o
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-S4Arrays/00new/S4Arrays/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowsum’ in package ‘S4Arrays’
** 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 (S4Arrays)

The downloaded source packages are in
	‘/tmp/RtmpuLBjfb/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R 4.3.0 (2023-04-21)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

[ Finished: 2023-05-15 23:57:03 CEST ]