[ Started: 2024-03-30 12:25:12 CET ]
[ 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 version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-03-23 r86179)
Old packages: 'beachmat', 'wppi'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/beachmat_2.19.4.tar.gz'
Content type 'application/x-gzip' length 512255 bytes (500 KB)
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downloaded 500 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 ‘beachmat’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c delayed_isometric_binary.cpp -o delayed_isometric_binary.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c delayed_isometric_math.cpp -o delayed_isometric_math.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c delayed_isometric_unary.cpp -o delayed_isometric_unary.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c delayed_other.cpp -o delayed_other.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c dense_matrix.cpp -o dense_matrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c fragment_sparse_rows.cpp -o fragment_sparse_rows.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c sparse_matrix.cpp -o sparse_matrix.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c tatami_utils.cpp -o tatami_utils.o
g++ -std=gnu++17 -I"/opt/R-devel/lib/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.4-3.19/Rcpp/include' -I/usr/local/include    -fpic  -g -O2   -c unknown_matrix.cpp -o unknown_matrix.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o beachmat.so RcppExports.o delayed_isometric_binary.o delayed_isometric_math.o delayed_isometric_unary.o delayed_other.o dense_matrix.o fragment_sparse_rows.o sparse_matrix.o tatami_utils.o unknown_matrix.o
installing to /home/omnipath/local/R/4.4-3.19/00LOCK-beachmat/00new/beachmat/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 (beachmat)
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
[2024-03-30 12:29:13] [INFO]    [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:13] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-30 12:29:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:13] [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
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:15] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-30 12:29:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-30 12:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:16] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-30 12:29:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:16] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:17] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-30 12:29:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-30 12:29:17] [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/Rtmp0q7rmY/downloaded_packages’
Bioconductor version 3.19 (BiocManager 1.30.22), R Under development (unstable)
  (2024-03-23 r86179)
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: 2024-03-30 12:29:20 CET ]