[ Started: 2024-03-28 13:15:09 CET ]
[ decoupleR v2.9.6 for BioC-3.18 from https://github.com/saezlab/decoupleR@master (68bf5f6 2024-03-24 13:38:34) ]

* using log directory ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.18/2024-03-28_1311/decoupleR/decoupleR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.9.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc       6.6Mb
    extdata   1.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-28 13:15:34] [INFO]    [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Contains 6 files.
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-28 13:15:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.3-3.18/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-28 13:15:34] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'run_gsva.Rd':
  ‘GSVA::gsva’ ‘GeneSetCollection’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘decoupleR.Rmd’ using ‘UTF-8’... OK
  ‘pw_bk.Rmd’ using ‘UTF-8’... OK
  ‘pw_sc.Rmd’ using ‘UTF-8’... OK
  ‘tf_bk.Rmd’ using ‘UTF-8’... OK
  ‘tf_sc.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/mnt/disk0/build/bioc-check/decoupler/bioc-3.18/2024-03-28_1311/decoupleR/decoupleR.Rcheck/00check.log’
for details.


[ Finished: 2024-03-28 13:36:03 CET ]