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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_3.19.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-12-01 02:23:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-01 02:23:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:23:43] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:23:43] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-01 02:23:43] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-30
[2025-12-01 02:23:43] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-30 20:11:49 UTC; unix
[2025-12-01 02:23:43] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.2
[2025-12-01 02:23:43] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-01 02:23:43] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-01 02:23:43] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-01 02:23:44] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.2(2025-11-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-01 02:23:44] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:23:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-01 02:23:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:23:44] [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
[2025-12-01 02:24:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-01 02:24:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:24:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:24:01] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-01 02:24:01] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-30
[2025-12-01 02:24:01] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-30 20:11:49 UTC; unix
[2025-12-01 02:24:01] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.2
[2025-12-01 02:24:01] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-01 02:24:01] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-01 02:24:01] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-01 02:24:02] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.2(2025-11-30); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13)
[2025-12-01 02:24:02] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Contains 1 files.
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:24:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:24:02] [TRACE]   [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
Undefined global functions or variables:
  enzyme_genesymbol
* 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                79.401  0.055  81.578
omnipath-interactions                42.132  5.942  88.828
curated_ligrec_stats                 43.524  2.902 146.449
filter_extra_attrs                   38.610  5.662  57.388
extra_attrs_to_cols                  26.773  1.942  37.270
all_uniprots                         23.937  1.554  41.312
go_annot_download                    19.391  2.409  24.623
uniprot_organisms                    19.756  0.959  24.200
extra_attrs                          16.959  1.728  24.325
giant_component                      17.522  0.990  30.198
nichenet_gr_network_omnipath         17.079  0.978  21.449
has_extra_attrs                      14.864  2.059  22.863
filter_by_resource                   15.613  0.817  21.289
extra_attr_values                    14.486  1.653  21.795
omnipath_for_cosmos                  13.581  1.437  42.676
with_extra_attrs                     13.419  1.549  19.371
nichenet_signaling_network_omnipath  11.603  0.619  16.504
filter_intercell                     11.351  0.568  21.916
find_all_paths                       10.811  0.344  14.181
pivot_annotations                     9.782  0.783  24.810
translate_ids_multi                   8.473  0.358  27.324
curated_ligand_receptor_interactions  7.454  0.826  23.180
static_table                          6.223  0.353  14.778
print_interactions                    6.283  0.262  24.547
hpo_download                          4.905  0.426   7.400
signed_ptms                           4.828  0.093   5.839
kegg_conv                             3.246  0.347  14.539
kegg_picture                          3.107  0.234   8.543
intercell_consensus_filter            2.779  0.339   7.537
print_path_vs                         2.794  0.193   7.016
ensembl_id_mapping_table              2.660  0.192  21.597
enzsub_graph                          2.391  0.119   5.535
metalinksdb_sqlite                    2.060  0.363  17.908
kinasephos                            2.077  0.301  18.584
annotated_network                     1.699  0.086   6.654
kegg_rm_prefix                        1.382  0.120   6.216
kegg_link                             1.317  0.174   7.409
biomart_query                         1.326  0.160   5.550
translate_ids                         1.106  0.043  11.159
uniprot_full_id_mapping_table         1.045  0.044  12.544
omnipath_cache_load                   0.980  0.084   5.151
* 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 re-building of vignette outputs ...