[ Started: 2023-10-12 08:16:27 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"     
trying URL 'https://cran.uni-muenster.de/src/contrib/svglite_2.1.2.tar.gz'
Content type 'application/x-gzip' length 124525 bytes (121 KB)
==================================================
downloaded 121 KB

* installing *source* package ‘svglite’ ...
** package ‘svglite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -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/systemfonts/include' -I/usr/local/include    -fpic  -g -O2  -c cpp11.cpp -o cpp11.o
g++ -std=gnu++11 -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/systemfonts/include' -I/usr/local/include    -fpic  -g -O2  -c devSVG.cpp -o devSVG.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o svglite.so cpp11.o devSVG.o -lpng -lz
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-svglite/00new/svglite/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 (svglite)

The downloaded source packages are in
	‘/tmp/RtmpQCikR7/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.0 (2023-04-21)
Old packages: 'scuttle'
trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/scuttle_1.10.3.tar.gz'
Content type 'application/x-gzip' length 1029617 bytes (1005 KB)
==================================================
downloaded 1005 KB

* installing *source* package ‘scuttle’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c cumulative_prop.cpp -o cumulative_prop.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c downsample_counts.cpp -o downsample_counts.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c fit_linear_model.cpp -o fit_linear_model.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c pool_size_factors.cpp -o pool_size_factors.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c sparse_summarize.cpp -o sparse_summarize.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c sum_counts.cpp -o sum_counts.o
g++ -std=gnu++11 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include/ -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I'/home/omnipath/local/R/4.3-3.17/beachmat/include' -I/usr/local/include    -fpic  -g -O2  -c utils.cpp -o utils.o
g++ -std=gnu++11 -shared -L/usr/local/lib -o scuttle.so RcppExports.o cumulative_prop.o downsample_counts.o fit_linear_model.o pool_size_factors.o sparse_summarize.o sum_counts.o utils.o -llapack -L/opt/R-devel/lib/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-scuttle/00new/scuttle/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 (scuttle)

The downloaded source packages are in
	‘/tmp/RtmpQCikR7/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.22), 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: 2023-10-12 08:17:41 CEST ]