[ Started: 2023-04-03 12:20:49 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"     
Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
  cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Warning: unable to access index for repository https://cran.uni-muenster.de/src/contrib:
  cannot open URL 'https://cran.uni-muenster.de/src/contrib/PACKAGES'
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Old packages: 'prodlim', 'ps'
also installing the dependency ‘diagram’

trying URL 'https://cloud.r-project.org/src/contrib/diagram_1.6.5.tar.gz'
Content type 'application/x-gzip' length 536872 bytes (524 KB)
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downloaded 524 KB

trying URL 'https://cloud.r-project.org/src/contrib/prodlim_2023.03.31.tar.gz'
Content type 'application/x-gzip' length 128568 bytes (125 KB)
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downloaded 125 KB

trying URL 'https://cloud.r-project.org/src/contrib/ps_1.7.4.tar.gz'
Content type 'application/x-gzip' length 129226 bytes (126 KB)
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downloaded 126 KB

* installing *source* package ‘diagram’ ...
** package ‘diagram’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (diagram)
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
gcc -g -O2  -L/usr/local/lib -Wall px.c -o px
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c api-common.c -o api-common.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c common.c -o common.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c extra.c -o extra.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c dummy.c -o dummy.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c error-codes.c -o error-codes.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c posix.c -o posix.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c api-posix.c -o api-posix.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c linux.c -o linux.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c api-linux.c -o api-linux.o
gcc -shared -L/usr/local/lib -o ps.so init.o api-common.o common.o extra.o dummy.o error-codes.o posix.o api-posix.o linux.o api-linux.o
installing via 'install.libs.R' to /home/omnipath/local/R/4.3-3.17/00LOCK-ps/00new/ps
** R
** 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 (ps)
* installing *source* package ‘prodlim’ ...
** package ‘prodlim’ successfully unpacked and MD5 sums checked
** 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/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c GMLE.c -o GMLE.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c IntIndex.c -o IntIndex.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c icens_prodlim.c -o icens_prodlim.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c icens_prodlim_ml.c -o icens_prodlim_ml.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c iindex.c -o iindex.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c init.c -o init.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c life_table.c -o life_table.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c loo.c -o loo.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c neighborhood.c -o neighborhood.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c predict.c -o predict.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c predict_individual_survival.c -o predict_individual_survival.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c prodlim.c -o prodlim.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c prodlim_clustersurv.c -o prodlim_clustersurv.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c prodlim_comprisk.c -o prodlim_comprisk.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c prodlim_multistates.c -o prodlim_multistates.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c prodlim_surv.c -o prodlim_surv.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c sindex.c -o sindex.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -c summary_prodlim.c -o summary_prodlim.o
gcc -shared -L/usr/local/lib -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
installing to /home/omnipath/local/R/4.3-3.17/00LOCK-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/RtmpOm7XKs/downloaded_packages’
Bioconductor version 3.17 (BiocManager 1.30.20), R Under development (unstable)
  (2023-03-16 r83996)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 17 packages not available: BiocManager, yaml, rmarkdown, knitr, bookdown, sessioninfo, testthat, covr, RefManageR, rjson, tidyr, tibble, dplyr, igraph, lpSolve, stringr, readr
[ Finished: 2023-04-03 12:21:09 CEST ]