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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL gINTomics
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘gINTomics’ ...
** using staged installation
** R
Warning: program compiled against libxml 212 using older 211
[2024-12-24 20:16:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:16:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:16:46] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:16:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-24 20:16:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:16:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:16:47] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:09] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-24 20:17:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-24 20:17:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-24 20:17:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:10] [TRACE]   [OmnipathR] Cache locked: FALSE
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: program compiled against libxml 212 using older 211
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:39] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:17:39] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:18:02] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:18:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-24 20:18:02] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (gINTomics)