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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_3.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.7
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 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
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-09 09:02:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:36] [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
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-09 09:02:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-09 09:02:41] [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                34.389  0.022  35.994
curated_ligrec_stats                  8.123  0.373  71.706
omnipath-interactions                 7.892  0.285  32.651
filter_extra_attrs                    5.154  0.023   5.750
pivot_annotations                     3.950  0.222  13.445
nichenet_gr_network_omnipath          3.704  0.292   6.296
extra_attr_values                     3.238  0.051   5.885
giant_component                       2.913  0.107   5.818
with_extra_attrs                      2.808  0.069   5.688
translate_ids_multi                   2.769  0.060  15.591
nichenet_signaling_network_omnipath   2.647  0.147   5.486
omnipath_for_cosmos                   2.646  0.063  18.125
static_table                          2.264  0.112   8.425
filter_intercell                      2.073  0.121   6.968
print_interactions                    1.732  0.045   6.323
curated_ligand_receptor_interactions  1.295  0.077  10.834
ensembl_id_mapping_table              0.683  0.021  15.998
translate_ids                         0.390  0.036  17.199
uniprot_full_id_mapping_table         0.336  0.089  21.063
all_uniprots                          0.231  0.020  19.108
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.