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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
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:22] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 04:17:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:22] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-20 04:17:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:23] [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
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:41] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:41] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-20 04:17:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-20 04:17:41] [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                70.81   0.06   71.52
omnipath-interactions                32.48   1.48   85.06
curated_ligrec_stats                 31.58   1.54   77.24
filter_extra_attrs                   20.99   0.16   21.58
nichenet_gr_network_omnipath         13.91   0.80   15.22
go_annot_download                    11.92   0.85   11.44
pivot_annotations                    11.28   0.95   29.89
nichenet_signaling_network_omnipath  11.12   0.83   13.13
extra_attr_values                    11.72   0.19   12.61
extra_attrs_to_cols                  11.55   0.08   11.63
giant_component                      10.46   0.40   11.28
omnipath_for_cosmos                  10.38   0.22   21.22
with_extra_attrs                      9.92   0.33   10.67
translate_ids_multi                   7.30   0.19   17.13
extra_attrs                           6.92   0.04    7.03
static_table                          6.58   0.30    7.31
print_interactions                    6.53   0.28   13.97
filter_intercell                      6.35   0.38    6.62
filter_by_resource                    6.45   0.17    7.22
has_extra_attrs                       6.44   0.03    6.47
find_all_paths                        5.58   0.06    5.64
curated_ligand_receptor_interactions  5.03   0.38   11.90
signed_ptms                           4.98   0.00    5.49
ensembl_id_mapping_table              1.77   0.11   12.07
translate_ids                         1.15   0.12   18.47
uniprot_full_id_mapping_table         1.11   0.13   22.39
all_uniprots                          0.76   0.12   20.58
print_path_es                         0.58   0.11    9.90
print_bma_motif_es                    0.30   0.11    5.67
* 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.