##############################################################################
##############################################################################
###
### Running command:
###
###   /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_3.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:29] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 20:32:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:29] [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
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:34] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 20:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 20:32:34] [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                35.265  0.026  36.746
curated_ligrec_stats                  9.230  0.492  81.693
omnipath-interactions                 8.168  0.416  43.867
filter_extra_attrs                    5.933  0.033   6.701
nichenet_gr_network_omnipath          5.324  0.375   8.099
extra_attr_values                     4.575  0.088   9.305
nichenet_signaling_network_omnipath   4.202  0.301  10.731
pivot_annotations                     4.079  0.260  22.131
with_extra_attrs                      3.575  0.066   6.317
giant_component                       3.176  0.098   9.996
static_table                          2.701  0.144   9.225
omnipath_for_cosmos                   2.696  0.088  19.015
filter_by_resource                    2.650  0.049   5.125
translate_ids_multi                   2.367  0.105  18.242
filter_intercell                      2.252  0.145   7.143
print_interactions                    1.804  0.085   7.699
curated_ligand_receptor_interactions  1.455  0.110  13.327
ensembl_id_mapping_table              0.485  0.065  14.361
biomart_query                         0.388  0.032   6.285
uniprot_full_id_mapping_table         0.341  0.077  21.222
translate_ids                         0.312  0.057  18.064
all_uniprots                          0.244  0.031  19.983
* 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-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.