[ Started: 2024-05-16 15:19:35 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"             
Bioconductor version '3.18' is out-of-date; the current release version '3.19'
  is available with R version '4.4'; 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 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29)
Old packages: 'cachem', 'wppi'
trying URL 'https://cloud.r-project.org/src/contrib/cachem_1.1.0.tar.gz'
Content type 'application/x-gzip' length 27192 bytes (26 KB)
==================================================
downloaded 26 KB

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)
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downloaded 646 KB

* installing *source* package ‘cachem’ ...
** package ‘cachem’ 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"/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 cache.c -o cache.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 init.c -o init.o
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o cachem.so cache.o init.o -L/usr/lib/R/lib -lR
installing to /home/omnipath/local/R/4.3-3.18/00LOCK-cachem/00new/cachem/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 (cachem)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-05-16 15:19:47] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:47] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-16 15:19:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:47] [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
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-16 15:19:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-16 15:19:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-16 15:19:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:50] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-16 15:19:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:50] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:51] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-16 15:19:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-16 15:19:51] [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/RtmpsHNeO2/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 1.30.23), 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 2 packages ahead of CRAN: cachem, BiocStyle
[ Finished: 2024-05-16 15:19:59 CEST ]