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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* 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 code 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 whether startup messages can be suppressed ... NOTE
[2025-04-01 00:37:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 00:37:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:12] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:24] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-01 00:37:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-01 00:37:24] [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                95.959  0.083  97.465
omnipath-interactions                34.997  1.597  68.327
curated_ligrec_stats                 30.941  2.814 107.291
go_annot_download                    21.932  0.948  31.546
omnipath_for_cosmos                  19.487  0.512  39.571
pivot_annotations                    16.516  1.068  31.048
nichenet_gr_network_omnipath         17.040  0.320  22.166
nichenet_signaling_network_omnipath  16.414  0.086  25.670
filter_extra_attrs                   15.623  0.219  16.606
with_extra_attrs                     11.693  0.504  16.291
extra_attr_values                     9.670  0.265  12.766
print_interactions                    9.506  0.263  23.789
giant_component                       8.375  0.141  11.563
extra_attrs_to_cols                   8.191  0.028   8.219
signed_ptms                           7.657  0.100  10.158
translate_ids_multi                   7.059  0.336  18.746
has_extra_attrs                       6.631  0.107   7.108
static_table                          6.147  0.389  12.373
omnipath_query                        5.772  0.014  12.256
pubmed_open                           5.510  0.141   6.090
filter_intercell                      5.233  0.416   9.904
extra_attrs                           5.323  0.090   5.413
curated_ligand_receptor_interactions  4.756  0.476  15.605
print_path_vs                         4.662  0.402   8.956
filter_by_resource                    4.755  0.172   7.300
uniprot_full_id_mapping_table         1.352  0.078  22.420
ensembl_id_mapping_table              1.263  0.090  13.814
translate_ids                         1.019  0.051  84.948
all_uniprots                          0.868  0.108  20.269
kegg_picture                          0.341  0.011   5.216
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.