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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
[2025-01-28 00:48:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 00:48:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:45] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-28 00:48:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-28 00:48:45] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-28 00:48:45] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-28 00:48:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-28 00:48:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:46] [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
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-28 00:48:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 00:48:58] [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                79.416  0.096  81.072
omnipath-interactions                39.626  1.865  69.699
curated_ligrec_stats                 34.009  1.546 108.669
nichenet_gr_network_omnipath         26.331  0.493  37.662
extra_attrs_to_cols                  23.838  0.127  24.307
nichenet_signaling_network_omnipath  21.734  0.355  27.646
filter_extra_attrs                   21.431  0.040  22.258
extra_attr_values                    19.438  0.278  26.250
go_annot_download                    15.212  0.851  18.864
giant_component                      11.523  0.283  15.597
has_extra_attrs                      11.494  0.091  11.802
filter_by_resource                   11.331  0.154  13.810
find_all_paths                       10.644  0.188  13.745
filter_intercell                      9.794  0.527  17.173
with_extra_attrs                     10.046  0.273  12.947
omnipath_for_cosmos                   9.458  0.319  23.786
pivot_annotations                     9.112  0.495  18.683
extra_attrs                           6.349  0.078   6.427
translate_ids_multi                   6.022  0.214  17.390
static_table                          5.360  0.315  11.992
curated_ligand_receptor_interactions  4.950  0.678  16.037
print_interactions                    5.262  0.291   9.726
enzsub_graph                          3.951  0.141   6.863
database_summary                      2.347  0.055   5.257
ensembl_id_mapping_table              1.924  0.205  16.272
translate_ids                         1.186  0.026 222.506
uniprot_full_id_mapping_table         1.088  0.108 267.832
all_uniprots                          0.956  0.185 143.380
* 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 ...