[ Started: 2023-08-09 22:10:28 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/BiocManager_1.30.22.tar.gz'
Content type 'application/x-gzip' length 582690 bytes (569 KB)
==================================================
downloaded 569 KB

* 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)

The downloaded source packages are in
	‘/tmp/RtmpJO1thZ/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Bioconductor version '3.16' is out-of-date; the current release version '3.17'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)
Old packages: 'nlme'
trying URL 'https://cloud.r-project.org/src/contrib/nlme_3.1-163.tar.gz'
Content type 'application/x-gzip' length 848981 bytes (829 KB)
==================================================
downloaded 829 KB

* installing *source* package ‘nlme’ ...
** package ‘nlme’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong  -c chol.f -o chol.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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 corStruct.c -o corStruct.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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 gnls.c -o gnls.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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     -fvisibility=hidden -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 matrix.c -o matrix.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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 nlOptimizer.c -o nlOptimizer.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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 nlme.c -o nlme.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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 nlmefit.c -o nlmefit.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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 pdMat.c -o pdMat.o
gcc -I"/usr/share/R/include" -DNDEBUG     -fvisibility=hidden -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 pythag.c -o pythag.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -ffile-prefix-map=/build/r-base-LhKvHL/r-base-4.2.3=. -fstack-protector-strong  -c rs.f -o rs.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-nlme/00new/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (nlme)

The downloaded source packages are in
	‘/tmp/RtmpJO1thZ/downloaded_packages’
'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: 2023-08-09 22:10:58 CEST ]