[ Started: 2024-04-05 16:58:21 CEST ]
[ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ]

[1] "Libraries: "                     "/home/omnipath/local/R/4.4-3.19"
[3] "/home/omnipath/local/R/4.4"      "/opt/R-alpha/lib/R/library"     
Warning message:
package ‘remotes’ was built under R version 4.5.0 
Warning message:
package ‘BiocManager’ was built under R version 4.5.0 
Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04
  r86334)
Old packages: 'GenomeInfoDb', 'GSVA', 'wppi'
also installing the dependency ‘SpatialExperiment’

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SpatialExperiment_1.13.1.tar.gz'
Content type 'application/x-gzip' length 5409939 bytes (5.2 MB)
==================================================
downloaded 5.2 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/GenomeInfoDb_1.39.11.tar.gz'
Content type 'application/x-gzip' length 3582327 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/GSVA_1.51.9.tar.gz'
Content type 'application/x-gzip' length 2383724 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.11.0.tar.gz'
Content type 'application/x-gzip' length 662120 bytes (646 KB)
==================================================
downloaded 646 KB

* installing *source* package ‘SpatialExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: package ‘SingleCellExperiment’ was built under R version 4.5.0 
2: package ‘SummarizedExperiment’ was built under R version 4.5.0 
3: package ‘MatrixGenerics’ was built under R version 4.5.0 
4: package ‘matrixStats’ was built under R version 4.5.0 
5: package ‘GenomicRanges’ was built under R version 4.5.0 
6: package ‘BiocGenerics’ was built under R version 4.5.0 
7: package ‘S4Vectors’ was built under R version 4.5.0 
8: package ‘IRanges’ was built under R version 4.5.0 
9: package ‘GenomeInfoDb’ was built under R version 4.5.0 
10: package ‘Biobase’ was built under R version 4.5.0 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package ‘SingleCellExperiment’ was built under R version 4.5.0
Warning: package ‘SummarizedExperiment’ was built under R version 4.5.0
Warning: package ‘MatrixGenerics’ was built under R version 4.5.0
Warning: package ‘matrixStats’ was built under R version 4.5.0
Warning: package ‘GenomicRanges’ was built under R version 4.5.0
Warning: package ‘BiocGenerics’ was built under R version 4.5.0
Warning: package ‘S4Vectors’ was built under R version 4.5.0
Warning: package ‘IRanges’ was built under R version 4.5.0
Warning: package ‘GenomeInfoDb’ was built under R version 4.5.0
Warning: package ‘Biobase’ was built under R version 4.5.0
** testing if installed package can be loaded from final location
Warning: package ‘SingleCellExperiment’ was built under R version 4.5.0
Warning: package ‘SummarizedExperiment’ was built under R version 4.5.0
Warning: package ‘MatrixGenerics’ was built under R version 4.5.0
Warning: package ‘matrixStats’ was built under R version 4.5.0
Warning: package ‘GenomicRanges’ was built under R version 4.5.0
Warning: package ‘BiocGenerics’ was built under R version 4.5.0
Warning: package ‘S4Vectors’ was built under R version 4.5.0
Warning: package ‘IRanges’ was built under R version 4.5.0
Warning: package ‘GenomeInfoDb’ was built under R version 4.5.0
Warning: package ‘Biobase’ was built under R version 4.5.0
** testing if installed package keeps a record of temporary installation path
* DONE (SpatialExperiment)
* installing *source* package ‘GenomeInfoDb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: package ‘BiocGenerics’ was built under R version 4.5.0 
2: package ‘S4Vectors’ was built under R version 4.5.0 
3: package ‘IRanges’ was built under R version 4.5.0 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package ‘BiocGenerics’ was built under R version 4.5.0
Warning: package ‘S4Vectors’ was built under R version 4.5.0
Warning: package ‘IRanges’ was built under R version 4.5.0
** testing if installed package can be loaded from final location
Warning: package ‘BiocGenerics’ was built under R version 4.5.0
Warning: package ‘S4Vectors’ was built under R version 4.5.0
Warning: package ‘IRanges’ was built under R version 4.5.0
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDb)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-04-05 16:58:53] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:53] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-05 16:58:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-05 16:58:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:54] [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
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:56] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:56] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:57] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-05 16:58:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-05 16:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-05 16:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:58] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-05 16:58:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-05 16:58:58] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)
* installing *source* package ‘GSVA’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ks_test.c -o ks_test.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c register_cmethods.c -o register_cmethods.o
gcc -shared -L/usr/local/lib -o GSVA.so kernel_estimation.o ks_test.o register_cmethods.o
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-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)

The downloaded source packages are in
	‘/tmp/RtmpQnJQPw/downloaded_packages’
Bioconductor version 3.19 (BiocManager 1.30.22), R 4.4.0 alpha (2024-04-04
  r86334)
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: 2024-04-05 16:59:24 CEST ]