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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.10.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.10.1’
* 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 for sufficient/correct file permissions ... 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 R 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 startup messages can be suppressed ... NOTE
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 22:18:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:24] [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
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-03 22:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-03 22:18:39] [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
collectri                            94.563  1.413  99.506
annotation_categories                63.386  0.644  66.063
dorothea                             49.632  1.105  64.423
curated_ligrec_stats                 28.746  8.388 122.133
filter_extra_attrs                   25.033  0.904  38.342
nichenet_gr_network_omnipath         12.740  0.643  15.735
pivot_annotations                    10.896  1.129  20.382
extra_attrs_to_cols                  11.273  0.131  24.581
nichenet_signaling_network_omnipath  10.257  0.678  13.690
giant_component                      10.243  0.390  13.423
go_annot_download                     8.823  1.037   9.338
extra_attr_values                     8.587  0.397  17.672
with_extra_attrs                      8.500  0.261  11.139
filter_intercell                      6.019  0.594  14.431
has_extra_attrs                       6.345  0.159   6.562
extra_attrs                           6.229  0.175   7.288
filter_by_resource                    5.849  0.430  15.277
find_all_paths                        5.975  0.182   8.584
print_interactions                    5.834  0.279  10.317
static_table                          5.665  0.433  11.889
get_signed_ptms                       5.151  0.082   5.836
curated_ligand_receptor_interactions  4.384  0.356  14.292
pubmed_open                           4.535  0.197   6.983
enzsub_graph                          2.491  0.131   6.279
annotated_network                     1.657  0.199  10.939
ensembl_id_mapping_table              1.140  0.126  17.216
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.