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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:54] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:40:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:40:55] [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
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.1/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 10:41:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 10:41:12] [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                103.965  0.052 105.571
curated_ligrec_stats                  33.238  0.761 129.534
omnipath-interactions                 29.387  1.069  74.238
filter_extra_attrs                    25.706  0.176  27.998
nichenet_gr_network_omnipath          15.630  0.344  26.874
extra_attr_values                     14.657  0.419  17.580
go_annot_download                     13.863  0.511  27.881
extra_attrs_to_cols                   12.950  0.108  13.092
giant_component                       12.112  0.484  14.230
pivot_annotations                     11.173  0.313  22.058
with_extra_attrs                      10.994  0.127  12.633
nichenet_signaling_network_omnipath   10.493  0.071  14.170
omnipath_for_cosmos                   10.246  0.191  63.700
extra_attrs                            8.260  0.119   8.401
translate_ids_multi                    8.236  0.028  17.533
has_extra_attrs                        7.883  0.087   8.375
filter_by_resource                     7.221  0.136   8.708
filter_intercell                       6.877  0.202  10.634
static_table                           6.677  0.147  11.387
find_all_paths                         6.429  0.032   6.472
print_interactions                     6.349  0.092  10.288
signed_ptms                            5.569  0.004   6.620
curated_ligand_receptor_interactions   5.354  0.176  17.879
hpo_download                           2.437  0.226  25.027
enzsub_graph                           2.406  0.096   5.060
print_path_vs                          2.295  0.024   5.623
translate_ids                          1.347  0.004  20.189
ensembl_id_mapping_table               1.284  0.048  10.621
biomart_query                          0.969  0.020   5.515
all_uniprots                           0.878  0.055  26.050
uniprot_full_id_mapping_table          0.911  0.016  96.042
* 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 ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! Package textcomp Error: Symbol \textrightarrow not provided by
(textcomp)                font family ptm in TS1 encoding.
(textcomp)                Default family used instead.

See the textcomp package documentation for explanation.
* checking PDF version of manual without index ... ERROR
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.