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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
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:44:49] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:44:49] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 04:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:44:49] [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
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:45:10] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:45:10] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 04:45:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 04:45:10] [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                65.61   0.05   66.50
curated_ligrec_stats                 32.50   1.64   78.19
filter_extra_attrs                   27.67   0.30   29.91
omnipath-interactions                25.94   1.19   39.58
nichenet_gr_network_omnipath         14.01   1.07   23.89
go_annot_download                    13.59   1.13   14.69
extra_attr_values                    13.81   0.31   15.47
giant_component                      13.44   0.31   14.74
extra_attrs_to_cols                  13.01   0.12   13.82
pivot_annotations                    11.00   0.80   13.68
nichenet_signaling_network_omnipath   9.74   0.72   11.06
with_extra_attrs                     10.04   0.27   10.88
omnipath_for_cosmos                   9.52   0.23   34.70
has_extra_attrs                       8.68   0.06    9.47
extra_attrs                           8.49   0.02    8.87
translate_ids_multi                   7.71   0.26   35.42
static_table                          7.05   0.33    7.83
filter_by_resource                    7.19   0.16    8.18
filter_intercell                      7.02   0.28    9.06
print_interactions                    6.05   0.22    7.92
find_all_paths                        5.89   0.22    6.23
signed_ptms                           5.55   0.05    6.00
curated_ligand_receptor_interactions  5.07   0.35   11.67
hpo_download                          2.48   0.14    5.06
ensembl_id_mapping_table              1.83   0.09   24.20
translate_ids                         1.34   0.11  192.16
uniprot_full_id_mapping_table         0.98   0.13  336.42
all_uniprots                          0.91   0.08  192.41
intercell                             0.58   0.03    5.53
* 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.