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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.7.15’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 08:00:55] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
annotation_categories                77.983  0.039  79.521
curated_ligrec_stats                 39.454  1.201 112.729
filter_extra_attrs                   38.637  0.195  40.034
has_extra_attrs                      10.294 25.066 183.932
with_extra_attrs                     21.843  0.157  33.965
giant_component                      20.007  0.176  45.807
go_annot_download                    16.019  4.042  71.163
extra_attr_values                    17.487  0.420  20.293
nichenet_gr_network_omnipath         16.685  0.196  21.095
pivot_annotations                    15.883  0.414  31.758
extra_attrs_to_cols                  15.193  0.172  15.366
find_all_paths                       12.865  0.111  27.223
extra_attrs                          10.858  0.160  11.039
get_signed_ptms                      10.581  0.012  19.871
nichenet_signaling_network_omnipath  10.443  0.137  13.060
filter_intercell                      9.601  0.328  23.244
pubmed_open                           9.221  0.172  12.087
filter_by_resource                    8.301  0.142  10.706
print_interactions                    7.187  0.179  11.201
curated_ligand_receptor_interactions  6.476  0.229  16.600
collectri                             4.607  0.120   6.447
print_path_vs                         3.442  0.134   7.048
import_transcriptional_interactions   2.824  0.061   7.126
enzsub_graph                          2.558  0.108   5.104
intercell_consensus_filter            2.380  0.088   7.081
dorothea                              2.202  0.104   5.001
biomart_query                         1.742  0.056   9.511
ensembl_id_mapping_table              1.248  0.040  21.631
kegg_picture                          0.135  0.023   5.593
* 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 ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.