[ Started: 2023-10-17 09:39:21 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.16 from https://github.com/saezlab/CARNIVAL@master ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.2-3.16"
[3] "/home/omnipath/local/R/4.2"      "/usr/lib/R/library"             
trying URL 'https://cran.uni-muenster.de/src/contrib/bookdown_0.36.tar.gz'
Content type 'application/x-gzip' length 859015 bytes (838 KB)
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downloaded 838 KB

trying URL 'https://cran.uni-muenster.de/src/contrib/sp_2.1-1.tar.gz'
Content type 'application/x-gzip' length 1244612 bytes (1.2 MB)
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downloaded 1.2 MB

* installing *source* package ‘bookdown’ ...
** package ‘bookdown’ 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 (bookdown)
* installing *source* package ‘sp’ ...
** package ‘sp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c Rcentroid.c -o Rcentroid.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c gcdist.c -o gcdist.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c pip.c -o pip.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c pip2.c -o pip2.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c sp_xports.c -o sp_xports.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c surfaceArea.c -o surfaceArea.o
gcc -I"/usr/share/R/include" -DNDEBUG      -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c zerodist.c -o zerodist.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-sp/00new/sp/libs
** R
** data
** 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
** 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 (sp)

The downloaded source packages are in
	‘/tmp/Rtmpy9rkjH/downloaded_packages’
Bioconductor version '3.16' is out-of-date; the current release version '3.17'
  is available with R version '4.3'; see https://bioconductor.org/install
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
Bioconductor version 3.16 (BiocManager 1.30.22), R 4.2.3 (2023-03-15)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

[ Finished: 2023-10-17 09:39:46 CEST ]