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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OmnipathR_3.15.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 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 '3.15.0'
* 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
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:00] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 03:29:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:00] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-28 03:29:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:01] [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
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:19] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:19] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-28 03:29:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:20] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-28 03:29:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-28 03:29:20] [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                76.09   0.09   76.77
curated_ligrec_stats                 31.45   1.71   78.66
omnipath-interactions                31.79   1.34   70.59
filter_extra_attrs                   20.17   0.22   20.84
nichenet_gr_network_omnipath         19.06   1.23   20.77
with_extra_attrs                     13.64   0.35   14.48
go_annot_download                    12.23   1.04   11.75
pivot_annotations                    11.97   1.11   36.17
extra_attrs_to_cols                  12.41   0.20   12.61
nichenet_signaling_network_omnipath  11.62   0.87   13.08
extra_attr_values                    12.17   0.25   13.05
omnipath_for_cosmos                  11.55   0.27   36.34
giant_component                      10.27   0.32   11.06
filter_by_resource                    9.51   0.28   10.28
translate_ids_multi                   8.20   0.25   20.77
static_table                          7.10   0.48    8.08
filter_intercell                      6.61   0.34    7.52
extra_attrs                           6.86   0.08    6.94
print_interactions                    6.52   0.27   17.14
has_extra_attrs                       6.21   0.11    6.31
find_all_paths                        6.06   0.11    6.17
signed_ptms                           6.01   0.07    6.55
curated_ligand_receptor_interactions  5.37   0.36   11.89
omnipath_query                        5.10   0.01    5.16
ensembl_id_mapping_table              1.61   0.08   17.92
translate_ids                         1.44   0.10  182.87
uniprot_full_id_mapping_table         1.00   0.07   24.84
all_uniprots                          0.96   0.08   21.78
print_path_es                         0.62   0.11   10.75
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.