##############################################################################
##############################################################################
###
### 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_3.12.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-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 13.6.6
* 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 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 ... 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
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-15 06:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:04:54] [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
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:08] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-10-15 06:05:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-10-15 06:05:09] [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                            106.923  0.938 110.918
annotation_categories                 96.350  0.362  98.282
dorothea                              58.511  0.376  62.195
curated_ligrec_stats                  25.698  1.454  32.654
filter_extra_attrs                    18.056  0.100  18.470
go_annot_download                     12.192  0.635  12.822
nichenet_gr_network_omnipath          11.293  0.944  12.432
extra_attr_values                     11.448  0.155  11.800
pivot_annotations                     10.088  0.757  10.973
giant_component                        9.962  0.414  10.747
extra_attrs_to_cols                    9.461  0.078   9.849
nichenet_signaling_network_omnipath    9.058  0.324   9.628
with_extra_attrs                       7.652  0.135   8.060
filter_intercell                       6.982  0.352   7.746
static_table                           6.939  0.298   7.215
extra_attrs                            6.464  0.044   6.650
has_extra_attrs                        6.039  0.076   6.160
find_all_paths                         5.637  0.146   5.871
curated_ligand_receptor_interactions   5.062  0.272   6.410
filter_by_resource                     5.209  0.096   5.495
get_signed_ptms                        5.226  0.063   5.398
print_interactions                     4.784  0.317   5.451
ensembl_id_mapping_table               1.176  0.076  71.327
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.