[ Started: 2024-05-03 15:18:11 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: 'AnnotationDbi', 'GenomicRanges', 'SpatialExperiment',
  'SummarizedExperiment', 'wppi'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/AnnotationDbi_1.66.0.tar.gz'
Content type 'application/x-gzip' length 4359386 bytes (4.2 MB)
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downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/GenomicRanges_1.56.0.tar.gz'
Content type 'application/x-gzip' length 1140266 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SpatialExperiment_1.14.0.tar.gz'
Content type 'application/x-gzip' length 5406870 bytes (5.2 MB)
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downloaded 5.2 MB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SummarizedExperiment_1.34.0.tar.gz'
Content type 'application/x-gzip' length 688177 bytes (672 KB)
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downloaded 672 KB

trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.12.0.tar.gz'
Content type 'application/x-gzip' length 661086 bytes (645 KB)
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* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’
** 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 (AnnotationDbi)
* installing *source* package ‘GenomicRanges’ ...
** 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'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG  -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I/usr/local/include    -fpic  -g -O2  -c transcript_utils.c -o transcript_utils.o
gcc -shared -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-GenomicRanges/00new/GenomicRanges/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 (GenomicRanges)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-05-03 15:18:45] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:45] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 15:18:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:45] [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
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:47] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:47] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:49] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 15:18:49] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)
* installing *source* package ‘SummarizedExperiment’ ...
** 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 (SummarizedExperiment)
* installing *source* package ‘SpatialExperiment’ ...
** 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 (SpatialExperiment)

The downloaded source packages are in
	‘/tmp/RtmprgPfNl/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: 2024-05-03 15:19:26 CEST ]