Denes Turei
| Snapshot Date: 2025-11-30 13:40 -0500 (Sun, 30 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: 0f1c5d0 |
| git_last_commit_date: 2025-11-17 12:47:44 -0500 (Mon, 17 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-01 11:35 -0500 (Mon, 01 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4572 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1488/2328 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.2 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.19.2 |
| Command: /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 |
| StartedAt: 2025-12-01 02:23:01 -0500 (Mon, 01 Dec 2025) |
| EndedAt: 2025-12-01 03:03:02 -0500 (Mon, 01 Dec 2025) |
| EllapsedTime: 2400.6 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /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 ...
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.2’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-11-30 15:12:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-30 15:12:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:02] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-11-30 15:12:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-30 15:12:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-30 [2025-11-30 15:12:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-30 20:11:49 UTC; unix [2025-11-30 15:12:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-11-30 15:12:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-30 15:12:03] [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=2025-11-30; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-11-30 15:12:03] [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] [2025-11-30 15:12:03] [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) [2025-11-30 15:12:03] [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 [2025-11-30 15:12:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-30 15:12:03] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-11-30 15:12:03] [TRACE] [OmnipathR] Contains 9 files. [2025-11-30 15:12:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-30 15:12:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-30 15:12:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-11-30 15:12:03] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-11-30 15:12:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-30 15:12:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-30 15:12:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-30 15:12:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-30 15:12:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:03] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-11-30 15:12:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-30 15:12:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-11-30 15:12:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-30 15:12:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-30 [2025-11-30 15:12:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-30 20:11:49 UTC; unix [2025-11-30 15:12:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-11-30 15:12:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-30 15:12:06] [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=2025-11-30; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-11-30 15:12:06] [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] [2025-11-30 15:12:06] [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) [2025-11-30 15:12:06] [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 [2025-11-30 15:12:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-30 15:12:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-11-30 15:12:06] [TRACE] [OmnipathR] Contains 1 files. [2025-11-30 15:12:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-30 15:12:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-30 15:12:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-11-30 15:12:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-11-30 15:12:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-30 15:12:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-30 15:12:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-30 15:12:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-30 15:12:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-30 15:12:06] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-12-01 02:43:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-01 02:43:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:43:35] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:43:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-01 02:43:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-30
[2025-12-01 02:43:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-30 20:11:49 UTC; unix
[2025-12-01 02:43:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2
[2025-12-01 02:43:35] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-01 02:43:36] [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=C; 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 02:43:36] [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 02:43:36] [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); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); 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); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); 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); testthat 3.3.1(2025-11-25); 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); 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 02:43:36] [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 02:43:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-01 02:43:36] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:43:36] [TRACE] [OmnipathR] Contains 22 files.
[2025-12-01 02:43:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-01 02:43:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-01 02:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:43:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-01 02:43:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-01 02:43:36] [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 02:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:43:36] [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 02:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:43:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-01 02:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:43:36] [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 02:43:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-01 02:43:37] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
46.513 3.998 93.588
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.017 | 0.002 | 0.020 | |
| all_uniprots | 23.937 | 1.554 | 41.312 | |
| ancestors | 0.009 | 0.000 | 0.009 | |
| annotated_network | 1.699 | 0.086 | 6.654 | |
| annotation_categories | 79.401 | 0.055 | 81.578 | |
| annotation_resources | 0.123 | 0.014 | 1.110 | |
| annotations | 0.657 | 0.051 | 1.964 | |
| biomart_query | 1.326 | 0.160 | 5.550 | |
| bioplex1 | 0.008 | 0.002 | 0.010 | |
| bioplex2 | 0.005 | 0.004 | 0.009 | |
| bioplex3 | 0.009 | 0.000 | 0.009 | |
| bioplex_all | 0.009 | 0.001 | 0.010 | |
| bioplex_hct116_1 | 0.008 | 0.000 | 0.009 | |
| bma_motif_es | 0.720 | 0.133 | 2.128 | |
| bma_motif_vs | 0.286 | 0.017 | 1.239 | |
| chalmers_gem | 0.007 | 0.002 | 0.009 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.008 | 0.000 | 0.009 | |
| chalmers_gem_network | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_raw | 0.006 | 0.002 | 0.008 | |
| chalmers_gem_reactions | 0.007 | 0.001 | 0.008 | |
| common_name | 0.132 | 0.005 | 0.137 | |
| complex_genes | 0.912 | 0.043 | 3.470 | |
| complex_resources | 0.155 | 0.005 | 1.015 | |
| complexes | 0.296 | 0.008 | 1.265 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.000 | |
| consensuspathdb_raw_table | 0.009 | 0.000 | 0.009 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 7.454 | 0.826 | 23.180 | |
| curated_ligrec_stats | 43.524 | 2.902 | 146.449 | |
| database_summary | 1.751 | 0.083 | 4.080 | |
| descendants | 0.008 | 0.001 | 0.010 | |
| ensembl_dataset | 0.053 | 0.000 | 0.053 | |
| ensembl_id_mapping_table | 2.660 | 0.192 | 21.597 | |
| ensembl_id_type | 0.002 | 0.001 | 0.002 | |
| ensembl_name | 0.305 | 0.002 | 0.306 | |
| ensembl_organisms | 0.108 | 0.011 | 0.119 | |
| ensembl_organisms_raw | 0.106 | 0.011 | 0.117 | |
| ensembl_orthology | 0.001 | 0.000 | 0.001 | |
| enzsub_graph | 2.391 | 0.119 | 5.535 | |
| enzsub_resources | 0.141 | 0.009 | 1.014 | |
| enzyme_substrate | 1.111 | 0.031 | 2.081 | |
| evex_download | 0.01 | 0.00 | 0.01 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 14.486 | 1.653 | 21.795 | |
| extra_attrs | 16.959 | 1.728 | 24.325 | |
| extra_attrs_to_cols | 26.773 | 1.942 | 37.270 | |
| filter_by_resource | 15.613 | 0.817 | 21.289 | |
| filter_extra_attrs | 38.610 | 5.662 | 57.388 | |
| filter_intercell | 11.351 | 0.568 | 21.916 | |
| filter_intercell_network | 0.039 | 0.007 | 0.065 | |
| find_all_paths | 10.811 | 0.344 | 14.181 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0.000 | 0.001 | 0.000 | |
| get_ontology_db | 0.009 | 0.000 | 0.009 | |
| giant_component | 17.522 | 0.990 | 30.198 | |
| go_annot_download | 19.391 | 2.409 | 24.623 | |
| go_annot_slim | 0.001 | 0.000 | 0.001 | |
| go_ontology_download | 0.009 | 0.001 | 0.010 | |
| guide2pharma_download | 0.008 | 0.001 | 0.009 | |
| harmonizome_download | 0.009 | 0.000 | 0.009 | |
| has_extra_attrs | 14.864 | 2.059 | 22.863 | |
| hmdb_id_mapping_table | 0.032 | 0.004 | 0.100 | |
| hmdb_id_type | 0.006 | 0.002 | 0.027 | |
| hmdb_metabolite_fields | 0.003 | 0.001 | 0.006 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.005 | |
| hmdb_table | 0.022 | 0.004 | 0.042 | |
| homologene_download | 0.016 | 0.005 | 0.021 | |
| homologene_raw | 0.121 | 0.019 | 0.201 | |
| homologene_uniprot_orthology | 0.021 | 0.003 | 0.032 | |
| hpo_download | 4.905 | 0.426 | 7.400 | |
| htridb_download | 0.019 | 0.001 | 0.019 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.072 | 0.008 | 0.080 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 1.399 | 0.196 | 2.114 | |
| interaction_graph | 0.513 | 0.108 | 1.579 | |
| interaction_resources | 0.149 | 0.018 | 1.231 | |
| interaction_types | 0.160 | 0.019 | 0.178 | |
| intercell | 1.694 | 0.357 | 3.992 | |
| intercell_categories | 1.363 | 0.255 | 3.380 | |
| intercell_consensus_filter | 2.779 | 0.339 | 7.537 | |
| intercell_generic_categories | 0.152 | 0.009 | 0.240 | |
| intercell_network | 0.022 | 0.002 | 0.043 | |
| intercell_resources | 0.182 | 0.009 | 1.290 | |
| intercell_summary | 0.160 | 0.032 | 0.387 | |
| is_ontology_id | 0.001 | 0.000 | 0.001 | |
| is_swissprot | 0.128 | 0.025 | 0.305 | |
| is_trembl | 0.237 | 0.042 | 0.555 | |
| is_uniprot | 0.020 | 0.005 | 0.049 | |
| kegg_api_templates | 0.003 | 0.004 | 0.014 | |
| kegg_conv | 3.246 | 0.347 | 14.539 | |
| kegg_databases | 0.003 | 0.001 | 0.006 | |
| kegg_ddi | 1.715 | 0.208 | 3.878 | |
| kegg_find | 1.290 | 0.152 | 3.455 | |
| kegg_info | 0.019 | 0.001 | 0.019 | |
| kegg_link | 1.317 | 0.174 | 7.409 | |
| kegg_list | 1.410 | 0.082 | 2.383 | |
| kegg_open | 0.018 | 0.002 | 0.020 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.019 | 0.108 | 0.127 | |
| kegg_organisms | 0.044 | 0.004 | 0.049 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.020 | 0.002 | 0.021 | |
| kegg_pathway_list | 0.018 | 0.002 | 0.020 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 3.107 | 0.234 | 8.543 | |
| kegg_process | 0.051 | 0.003 | 0.111 | |
| kegg_query | 0.019 | 0.000 | 0.037 | |
| kegg_request | 0.148 | 0.002 | 0.299 | |
| kegg_rm_prefix | 1.382 | 0.120 | 6.216 | |
| kinasephos | 2.077 | 0.301 | 18.584 | |
| latin_name | 0.487 | 0.028 | 0.537 | |
| load_db | 0.136 | 0.021 | 0.157 | |
| metalinksdb_sqlite | 2.060 | 0.363 | 17.908 | |
| metalinksdb_table | 0.286 | 0.051 | 0.336 | |
| metalinksdb_tables | 0.023 | 0.005 | 0.028 | |
| ncbi_taxid | 0.303 | 0.018 | 0.320 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.009 | 0.003 | 0.012 | |
| nichenet_gr_network | 0.028 | 0.001 | 0.029 | |
| nichenet_gr_network_evex | 0.010 | 0.000 | 0.009 | |
| nichenet_gr_network_harmonizome | 0.010 | 0.000 | 0.011 | |
| nichenet_gr_network_htridb | 0.008 | 0.002 | 0.011 | |
| nichenet_gr_network_omnipath | 17.079 | 0.978 | 21.449 | |
| nichenet_gr_network_pathwaycommons | 0.009 | 0.000 | 0.009 | |
| nichenet_gr_network_regnetwork | 0.007 | 0.001 | 0.008 | |
| nichenet_gr_network_remap | 0.008 | 0.001 | 0.008 | |
| nichenet_gr_network_trrust | 0.007 | 0.001 | 0.008 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.025 | 0.000 | 0.026 | |
| nichenet_lr_network_guide2pharma | 0.008 | 0.001 | 0.008 | |
| nichenet_lr_network_omnipath | 0.023 | 0.001 | 0.023 | |
| nichenet_lr_network_ramilowski | 0.052 | 0.002 | 0.053 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.038 | 0.002 | 0.040 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.020 | 0.004 | 0.023 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.024 | 0.001 | 0.024 | |
| nichenet_signaling_network_cpdb | 0.008 | 0.001 | 0.008 | |
| nichenet_signaling_network_evex | 0.007 | 0.002 | 0.008 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.001 | 0.008 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network_omnipath | 11.603 | 0.619 | 16.504 | |
| nichenet_signaling_network_pathwaycommons | 0.008 | 0.003 | 0.011 | |
| nichenet_signaling_network_vinayagam | 0.008 | 0.001 | 0.009 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.155 | 0.034 | 0.680 | |
| oma_code | 0.138 | 0.011 | 0.149 | |
| oma_organisms | 0.065 | 0.005 | 0.070 | |
| oma_pairwise | 0.009 | 0.001 | 0.010 | |
| oma_pairwise_genesymbols | 0.007 | 0.002 | 0.010 | |
| oma_pairwise_translated | 0.006 | 0.003 | 0.009 | |
| omnipath-interactions | 42.132 | 5.942 | 88.828 | |
| omnipath_cache_autoclean | 0.000 | 0.001 | 0.000 | |
| omnipath_cache_clean | 0.015 | 0.000 | 0.015 | |
| omnipath_cache_clean_db | 0.163 | 0.017 | 0.180 | |
| omnipath_cache_download_ready | 0.934 | 0.132 | 1.087 | |
| omnipath_cache_filter_versions | 0.275 | 0.023 | 0.312 | |
| omnipath_cache_get | 0.134 | 0.014 | 0.149 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.003 | |
| omnipath_cache_latest_or_new | 0.107 | 0.013 | 0.120 | |
| omnipath_cache_load | 0.980 | 0.084 | 5.151 | |
| omnipath_cache_move_in | 0.248 | 0.071 | 0.421 | |
| omnipath_cache_remove | 0.217 | 0.066 | 0.396 | |
| omnipath_cache_save | 0.311 | 0.026 | 0.645 | |
| omnipath_cache_search | 0.000 | 0.001 | 0.000 | |
| omnipath_cache_set_ext | 0.129 | 0.018 | 0.214 | |
| omnipath_cache_update_status | 0.138 | 0.018 | 0.157 | |
| omnipath_cache_wipe | 0.001 | 0.000 | 0.001 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 13.581 | 1.437 | 42.676 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.000 | 0.001 | 0.000 | |
| omnipath_logfile | 0.001 | 0.001 | 0.002 | |
| omnipath_msg | 0.005 | 0.000 | 0.005 | |
| omnipath_query | 3.571 | 0.170 | 3.747 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.021 | 0.004 | 0.025 | |
| omnipath_set_console_loglevel | 0.002 | 0.001 | 0.003 | |
| omnipath_set_logfile_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_set_loglevel | 0.001 | 0.001 | 0.002 | |
| omnipath_show_db | 0.055 | 0.009 | 0.064 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.000 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.000 | |
| ontology_name_id | 0.001 | 0.001 | 0.001 | |
| organism_for | 0.173 | 0.007 | 0.181 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 9.782 | 0.783 | 24.810 | |
| preppi_download | 0.000 | 0.001 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.702 | 0.062 | 2.006 | |
| print_bma_motif_vs | 0.242 | 0.013 | 1.205 | |
| print_interactions | 6.283 | 0.262 | 24.547 | |
| print_path_es | 0.915 | 0.112 | 3.346 | |
| print_path_vs | 2.794 | 0.193 | 7.016 | |
| pubmed_open | 3.718 | 0.121 | 3.838 | |
| query_info | 0.469 | 0.003 | 0.776 | |
| ramilowski_download | 0.000 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.001 | 0.001 | |
| ramp_id_type | 0.002 | 0.000 | 0.002 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0.001 | 0.000 | 0.000 | |
| ramp_tables | 0.000 | 0.000 | 0.001 | |
| recon3d | 0.001 | 0.001 | 0.002 | |
| recon3d_raw | 0.001 | 0.000 | 0.001 | |
| recon3d_raw_vmh | 0.001 | 0.000 | 0.001 | |
| regnetwork_directions | 0.000 | 0.001 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.001 | |
| relations_list_to_table | 0.143 | 0.019 | 0.842 | |
| relations_table_to_graph | 0.001 | 0.000 | 0.000 | |
| relations_table_to_list | 0.094 | 0.021 | 0.239 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
| remap_filtered | 0.001 | 0.000 | 0.000 | |
| remap_tf_target_download | 0.001 | 0.000 | 0.000 | |
| resource_info | 0.443 | 0.062 | 0.811 | |
| resources | 0.158 | 0.009 | 1.132 | |
| resources_colname | 1.260 | 0.053 | 4.986 | |
| resources_in | 3.555 | 0.141 | 3.698 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 4.828 | 0.093 | 5.839 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 6.223 | 0.353 | 14.778 | |
| static_tables | 0.050 | 0.007 | 0.065 | |
| stitch_actions | 0.000 | 0.000 | 0.001 | |
| stitch_links | 0.000 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.006 | 0.001 | 0.007 | |
| swap_relations | 0.125 | 0.031 | 0.279 | |
| swissprots_only | 0.142 | 0.003 | 0.145 | |
| tfcensus_download | 0.652 | 0.019 | 1.291 | |
| translate_ids | 1.106 | 0.043 | 11.159 | |
| translate_ids_multi | 8.473 | 0.358 | 27.324 | |
| trembls_only | 0.140 | 0.001 | 0.141 | |
| trrust_download | 0.001 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.045 | 0.044 | 12.544 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.000 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.002 | 0.000 | 0.002 | |
| uniprot_idmapping_id_types | 0.552 | 0.016 | 1.701 | |
| uniprot_organisms | 19.756 | 0.959 | 24.200 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0.001 | 0.000 | 0.000 | |
| uploadlists_id_type | 0.002 | 0.000 | 0.002 | |
| vinayagam_download | 0.000 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.000 | 0.000 | 0.001 | |
| with_extra_attrs | 13.419 | 1.549 | 19.371 | |
| with_references | 1.048 | 0.088 | 3.538 | |
| zenodo_download | 0.000 | 0.001 | 0.002 | |