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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 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 whether startup messages can be suppressed ... NOTE
[2025-01-20 02:55:00] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 02:55:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:00] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-20 02:55:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 02:55:00] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-20 02:55:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-20 02:55:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 02:55:00] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:01] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 02:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:01] [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
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:19] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 02:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:19] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 02:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 02:55:20] [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                69.62   0.08   70.45
curated_ligrec_stats                 32.35   1.66   78.25
omnipath-interactions                25.43   1.03   39.83
filter_extra_attrs                   24.50   0.16   28.14
go_annot_download                    13.95   0.87   24.72
extra_attr_values                    13.81   0.35   15.28
nichenet_gr_network_omnipath         12.27   1.01   14.20
extra_attrs_to_cols                  13.08   0.19   13.58
giant_component                      11.72   0.39   13.17
pivot_annotations                    10.64   0.73   13.33
with_extra_attrs                     10.44   0.29   11.25
nichenet_signaling_network_omnipath   9.81   0.69   10.97
omnipath_for_cosmos                   8.87   0.19   36.70
has_extra_attrs                       8.20   0.05    8.40
extra_attrs                           8.11   0.07    8.41
translate_ids_multi                   7.86   0.16   36.06
filter_intercell                      7.14   0.64   10.29
filter_by_resource                    7.22   0.28    8.48
find_all_paths                        7.19   0.30    7.57
print_interactions                    6.27   0.18    8.55
static_table                          6.06   0.38    6.93
curated_ligand_receptor_interactions  5.37   0.48   12.07
signed_ptms                           5.27   0.01    5.71
enzsub_graph                          3.02   0.08    8.53
ensembl_id_mapping_table              1.97   0.11   35.65
biomart_query                         1.30   0.03   17.73
uniprot_full_id_mapping_table         1.11   0.16   25.61
translate_ids                         1.14   0.09   20.41
all_uniprots                          0.80   0.14  153.27
intercell                             0.63   0.06    5.56
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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