[ Started: 2023-08-28 23:21:35 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"             
Bioconductor version '3.16' is out-of-date; the current release version '3.17'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: 'prodlim'
trying URL 'https://cloud.r-project.org/src/contrib/prodlim_2023.08.28.tar.gz'
Content type 'application/x-gzip' length 128725 bytes (125 KB)
==================================================
downloaded 125 KB

* installing *source* package ‘prodlim’ ...
** package ‘prodlim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 GMLE.c -o GMLE.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 IntIndex.c -o IntIndex.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 icens_prodlim.c -o icens_prodlim.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 icens_prodlim_ml.c -o icens_prodlim_ml.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 iindex.c -o iindex.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 life_table.c -o life_table.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 loo.c -o loo.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 neighborhood.c -o neighborhood.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 predict.c -o predict.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 predict_individual_survival.c -o predict_individual_survival.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 prodlim.c -o prodlim.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 prodlim_clustersurv.c -o prodlim_clustersurv.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 prodlim_comprisk.c -o prodlim_comprisk.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 prodlim_multistates.c -o prodlim_multistates.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 prodlim_surv.c -o prodlim_surv.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 sindex.c -o sindex.o
gcc -I"/usr/share/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.2-3.16/Rcpp/include'    -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 summary_prodlim.c -o summary_prodlim.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o prodlim.so GMLE.o IntIndex.o icens_prodlim.o icens_prodlim_ml.o iindex.o init.o life_table.o loo.o neighborhood.o predict.o predict_individual_survival.o prodlim.o prodlim_clustersurv.o prodlim_comprisk.o prodlim_multistates.o prodlim_surv.o sindex.o summary_prodlim.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.2-3.16/00LOCK-prodlim/00new/prodlim/libs
** R
** 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 (prodlim)

The downloaded source packages are in
	‘/tmp/RtmpX3VGtR/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: 2023-08-28 23:21:58 CEST ]