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### Running command:
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###   E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings OmnipathR_3.12.4.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '3.12.4'
* 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 ... NOTE
License stub is invalid DCF.
* 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
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:22] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:22] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 04:07:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:22] [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
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:36] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-17 04:07:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:37] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-17 04:07:37] [TRACE]   [OmnipathR] Cache locked: FALSE
oma_organisms: no visible binding for global variable 'ncbi_tax_id'
Undefined global functions or variables:
  ncbi_tax_id
* 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
collectri                            131.53   1.55  133.30
dorothea                              77.03   0.94   80.24
annotation_categories                 74.90   0.03   75.64
curated_ligrec_stats                  29.15   1.92   75.96
filter_extra_attrs                    23.05   0.12   23.57
extra_attr_values                     15.00   0.23   16.33
nichenet_gr_network_omnipath          13.71   0.66   14.82
go_annot_download                     13.47   0.71   15.48
giant_component                       13.59   0.49   16.60
extra_attrs_to_cols                   13.03   0.07   13.41
pivot_annotations                     12.22   0.75   14.39
with_extra_attrs                      11.16   0.17   11.93
nichenet_signaling_network_omnipath   10.14   0.57   11.41
extra_attrs                            7.91   0.06    8.21
has_extra_attrs                        7.64   0.09    8.47
filter_intercell                       6.81   0.55    7.43
filter_by_resource                     7.13   0.11    7.75
find_all_paths                         6.96   0.20    7.42
static_table                           6.29   0.36    7.14
print_interactions                     5.56   0.09    7.39
get_signed_ptms                        5.55   0.01    6.18
curated_ligand_receptor_interactions   4.83   0.50   11.04
pubmed_open                            4.67   0.15    5.34
hpo_download                           2.38   0.25   12.63
ensembl_id_mapping_table               2.10   0.13   46.46
annotated_network                      1.71   0.16    5.64
get_complex_genes                      1.54   0.11    5.54
biomart_query                          1.11   0.09   10.47
* 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: 3 NOTEs
See
  'E:/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.