[ Started: 2024-04-04 17:51:12 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-devel/lib/R/library"     
Bioconductor does not yet build and check packages for R version 4.5, using
  unsupported Bioconductor version 3.19; see https://bioconductor.org/install
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-04-01 r86264)
Old packages: 'DT', 'GSVA', 'htmltools', 'wppi'
trying URL 'https://cloud.r-project.org/src/contrib/DT_0.33.tar.gz'
Content type 'application/x-gzip' length 1675674 bytes (1.6 MB)
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downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/GSVA_1.51.8.tar.gz'
Content type 'application/x-gzip' length 2383279 bytes (2.3 MB)
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downloaded 2.3 MB

trying URL 'https://cloud.r-project.org/src/contrib/htmltools_0.5.8.1.tar.gz'
Content type 'application/x-gzip' length 135134 bytes (131 KB)
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downloaded 131 KB

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)
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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"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/opt/R-devel/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c ks_test.c -o ks_test.o
gcc -I"/opt/R-devel/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)
* installing *source* package ‘htmltools’ ...
** package ‘htmltools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
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 template.c -o template.o
gcc -shared -L/usr/local/lib -o htmltools.so init.o template.o
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-htmltools/00new/htmltools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (htmltools)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-04-04 17:51:45] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-04 17:51:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:45] [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
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:47] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:47] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-04 17:51:49] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)
* installing *source* package ‘DT’ ...
** package ‘DT’ 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 (DT)

The downloaded source packages are in
	‘/tmp/Rtmph3u0Ih/downloaded_packages’
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-04-01 r86264)
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: htmltools
[ Finished: 2024-04-04 17:51:54 CEST ]