[ Started: 2024-04-06 17:01:31 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.18 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.3-3.18"
[3] "/home/omnipath/local/R/4.3"      "/usr/lib/R/library"             
trying URL 'https://cran.uni-muenster.de/src/contrib/RcppArmadillo_0.12.8.2.0.tar.gz'
Content type 'application/x-gzip' length 1405964 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking whether we have a suitable tempdir... /tmp
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking LAPACK_LIBS... system LAPACK found
configure: creating ./config.status
config.status: creating inst/include/RcppArmadillo/config/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include'    -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include'    -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.3-3.18/Rcpp/include'    -fopenmp -fpic  -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c fastLm.cpp -o fastLm.o
g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.18/00LOCK-RcppArmadillo/00new/RcppArmadillo/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 (RcppArmadillo)

The downloaded source packages are in
	‘/tmp/RtmpY5WrwG/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 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29)
Old packages: 'GSVA', 'wppi'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/GSVA_1.50.2.tar.gz'
Content type 'application/x-gzip' length 2265957 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/wppi_1.10.0.tar.gz'
Content type 'application/x-gzip' length 662114 bytes (646 KB)
==================================================
downloaded 646 KB

* installing *source* package ‘GSVA’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c ks_test.c -o ks_test.o
gcc -I"/usr/share/R/include" -DNDEBUG       -fpic  -g -O2 -ffile-prefix-map=/build/r-base-14Q6vq/r-base-4.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2  -c register_cmethods.c -o register_cmethods.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.18/00LOCK-GSVA/00new/GSVA/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 (GSVA)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-04-06 17:02:24] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:24] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:24] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:26] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:26] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:28] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-06 17:02:28] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

The downloaded source packages are in
	‘/tmp/RtmpY5WrwG/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 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29)
Warning message:
package(s) not installed when version(s) same as or greater than current; use
  `force = TRUE` to re-install: 'BiocCheck' 

Skipping 1 packages ahead of CRAN: BiocStyle
[ Finished: 2024-04-06 17:02:36 CEST ]