Denes Turei
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_21 |
| git_last_commit: e923fc4 |
| git_last_commit_date: 2025-08-30 05:55:56 -0400 (Sat, 30 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1484/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.16.2 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.16.2 |
| Command: /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_3.16.2.tar.gz |
| StartedAt: 2025-10-14 12:09:14 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 12:33:23 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 1448.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /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_3.16.2.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (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 ‘3.16.2’
* 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
[2025-10-14 12:10:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-14 12:10:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:00] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:10:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-14 12:10:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-14 12:10:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-13 20:19:57 UTC; unix
[2025-10-14 12:10:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-14 12:10:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-14 12:10:01] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-14; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-10-14 12:10:01] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-10-14 12:10:01] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-10-14 12:10:02] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-14 12:10:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-14 12:10:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-14 12:10:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-14 12:10:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-14 12:10:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:02] [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
[2025-10-14 12:10:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-14 12:10:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:31] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:10:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-14 12:10:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-14 12:10:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-13 20:19:57 UTC; unix
[2025-10-14 12:10:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-14 12:10:31] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-14 12:10:32] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-14; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-10-14 12:10:32] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-10-14 12:10:32] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-10-14 12:10:32] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Contains 1 files.
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-14 12:10:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-14 12:10:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-14 12:10:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-14 12:10:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-14 12:10:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:10:32] [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 109.221 0.004 122.800
curated_ligrec_stats 42.046 5.093 183.000
filter_extra_attrs 37.985 3.776 78.248
omnipath-interactions 36.435 3.268 78.589
nichenet_gr_network_omnipath 20.853 1.159 27.305
extra_attrs_to_cols 19.471 1.303 22.586
extra_attr_values 16.564 1.406 21.023
with_extra_attrs 16.119 1.826 19.734
go_annot_download 15.793 0.527 38.422
nichenet_signaling_network_omnipath 15.347 0.793 19.467
giant_component 13.448 0.369 23.025
omnipath_for_cosmos 12.068 1.164 39.431
pivot_annotations 11.704 0.442 28.323
filter_by_resource 11.770 0.336 22.022
translate_ids_multi 10.630 1.228 33.525
has_extra_attrs 10.500 1.123 11.675
extra_attrs 9.365 1.064 12.056
filter_intercell 8.516 0.413 29.617
print_interactions 7.792 1.033 15.206
curated_ligand_receptor_interactions 7.506 0.835 28.341
find_all_paths 7.682 0.231 10.996
static_table 6.783 0.552 12.650
signed_ptms 6.420 0.386 8.288
pubmed_open 5.097 0.227 5.336
resources_in 4.811 0.318 5.179
omnipath_query 4.745 0.249 5.018
hpo_download 3.205 0.722 27.624
print_path_vs 2.913 0.397 6.548
ensembl_id_mapping_table 2.689 0.139 22.813
enzsub_graph 2.610 0.123 7.410
all_uniprots 1.747 0.115 15.212
metalinksdb_sqlite 1.060 0.548 13.206
translate_ids 1.393 0.178 11.559
annotated_network 1.349 0.135 5.934
uniprot_full_id_mapping_table 1.065 0.064 15.497
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.16.2’ ** 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 [2025-10-13 20:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:18] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-13 20:20:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-13 20:20:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13 [2025-10-13 20:20:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-13 20:19:57 UTC; unix [2025-10-13 20:20:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:20:18] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-10-13 20:20:18] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-10-13 20:20:18] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-10-13 20:20:18] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-10-13 20:20:18] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-10-13 20:20:18] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:20:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-13 20:20:18] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:20:18] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-13 20:20:18] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-10-13 20:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:20:18] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:18] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-10-13 20:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:20:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:22] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-10-13 20:20:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-10-13 20:20:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13 [2025-10-13 20:20:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-13 20:19:57 UTC; unix [2025-10-13 20:20:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2 [2025-10-13 20:20:22] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-10-13 20:20:22] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-10-13 20:20:22] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-10-13 20:20:22] [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 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-10-13 20:20:22] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-10-13 20:20:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-10-13 20:20:22] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-10-13 20:20:22] [TRACE] [OmnipathR] Contains 1 files. [2025-10-13 20:20:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-10-13 20:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-10-13 20:20:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-10-13 20:20:22] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-10-13 20:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-10-13 20:20:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-10-13 20:20:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:22] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-10-13 20:20:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-10-13 20:20:23] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-10-13 20:20:23] [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) (2025-02-19 r87757) -- "Unsuffered Consequences"
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Platform: aarch64-unknown-linux-gnu
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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)
[2025-10-14 12:30:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-14 12:30:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:30:12] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:30:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-14 12:30:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-10-13
[2025-10-14 12:30:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-10-13 20:19:57 UTC; unix
[2025-10-14 12:30:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-14 12:30:12] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-14 12:30:12] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-10-14; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-10-14 12:30:13] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-10-14 12:30:13] [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 2.3.2(2024-07-29); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-13); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); testthat 3.2.3(2025-01-13); tibble 3.2.1(2023-03-20); 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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-10-14 12:30:13] [INFO] [OmnipathR] CURL: version: 8.12.1; headers: 8.4.0; ssl_version: OpenSSL/3.4.1; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Contains 21 files.
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-14 12:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:30:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-14 12:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-14 12:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-14 12:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-14 12:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-10-14 12:30:13] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
17.704 2.779 181.938
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.000 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.024 | 0.000 | 0.025 | |
| all_uniprots | 1.747 | 0.115 | 15.212 | |
| ancestors | 0.021 | 0.005 | 0.050 | |
| annotated_network | 1.349 | 0.135 | 5.934 | |
| annotation_categories | 109.221 | 0.004 | 122.800 | |
| annotation_resources | 0.078 | 0.020 | 1.104 | |
| annotations | 0.610 | 0.061 | 2.687 | |
| biomart_query | 1.285 | 0.120 | 3.582 | |
| bioplex1 | 0.012 | 0.000 | 0.012 | |
| bioplex2 | 0.012 | 0.000 | 0.012 | |
| bioplex3 | 0.012 | 0.000 | 0.012 | |
| bioplex_all | 0.011 | 0.000 | 0.011 | |
| bioplex_hct116_1 | 0.012 | 0.000 | 0.011 | |
| bma_motif_es | 0.674 | 0.088 | 2.736 | |
| bma_motif_vs | 0.207 | 0.060 | 1.264 | |
| chalmers_gem | 0.009 | 0.004 | 0.014 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.004 | 0.013 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_metabolites | 0.008 | 0.004 | 0.012 | |
| chalmers_gem_network | 0.008 | 0.004 | 0.012 | |
| chalmers_gem_raw | 0.012 | 0.000 | 0.012 | |
| chalmers_gem_reactions | 0.012 | 0.000 | 0.012 | |
| common_name | 0.038 | 0.004 | 0.043 | |
| complex_genes | 0.734 | 0.065 | 3.279 | |
| complex_resources | 0.090 | 0.000 | 1.088 | |
| complexes | 0.189 | 0.036 | 3.216 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.014 | 0.000 | 0.014 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.506 | 0.835 | 28.341 | |
| curated_ligrec_stats | 42.046 | 5.093 | 183.000 | |
| database_summary | 1.953 | 0.158 | 3.608 | |
| descendants | 0.009 | 0.005 | 0.014 | |
| ensembl_dataset | 0.013 | 0.004 | 0.017 | |
| ensembl_id_mapping_table | 2.689 | 0.139 | 22.813 | |
| ensembl_id_type | 0.003 | 0.000 | 0.003 | |
| ensembl_name | 0.073 | 0.008 | 0.081 | |
| ensembl_organisms | 0.195 | 0.016 | 0.212 | |
| ensembl_organisms_raw | 0.147 | 0.008 | 0.156 | |
| ensembl_orthology | 0.000 | 0.000 | 0.001 | |
| enzsub_graph | 2.610 | 0.123 | 7.410 | |
| enzsub_resources | 0.094 | 0.006 | 1.115 | |
| enzyme_substrate | 1.369 | 0.062 | 2.521 | |
| evex_download | 0.015 | 0.000 | 0.015 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 16.564 | 1.406 | 21.023 | |
| extra_attrs | 9.365 | 1.064 | 12.056 | |
| extra_attrs_to_cols | 19.471 | 1.303 | 22.586 | |
| filter_by_resource | 11.770 | 0.336 | 22.022 | |
| filter_extra_attrs | 37.985 | 3.776 | 78.248 | |
| filter_intercell | 8.516 | 0.413 | 29.617 | |
| filter_intercell_network | 0.025 | 0.005 | 0.034 | |
| find_all_paths | 7.682 | 0.231 | 10.996 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.013 | 0.000 | 0.013 | |
| giant_component | 13.448 | 0.369 | 23.025 | |
| go_annot_download | 15.793 | 0.527 | 38.422 | |
| go_annot_slim | 0.001 | 0.000 | 0.001 | |
| go_ontology_download | 0.014 | 0.000 | 0.014 | |
| guide2pharma_download | 0.010 | 0.004 | 0.013 | |
| harmonizome_download | 0.013 | 0.000 | 0.014 | |
| has_extra_attrs | 10.500 | 1.123 | 11.675 | |
| hmdb_id_mapping_table | 0.012 | 0.000 | 0.012 | |
| hmdb_id_type | 0.003 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_table | 0.012 | 0.000 | 0.013 | |
| homologene_download | 0.012 | 0.000 | 0.013 | |
| homologene_raw | 0.022 | 0.004 | 0.026 | |
| homologene_uniprot_orthology | 0.012 | 0.000 | 0.013 | |
| hpo_download | 3.205 | 0.722 | 27.624 | |
| htridb_download | 0.013 | 0.000 | 0.014 | |
| id_translation_resources | 0.001 | 0.000 | 0.000 | |
| id_types | 0.056 | 0.008 | 0.064 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.757 | 0.137 | 1.396 | |
| interaction_graph | 0.414 | 0.122 | 1.517 | |
| interaction_resources | 0.083 | 0.016 | 1.049 | |
| interaction_types | 0.108 | 0.012 | 0.121 | |
| intercell | 0.885 | 0.292 | 2.241 | |
| intercell_categories | 0.687 | 0.219 | 1.409 | |
| intercell_consensus_filter | 1.629 | 0.280 | 4.361 | |
| intercell_generic_categories | 0.053 | 0.016 | 0.070 | |
| intercell_network | 0.015 | 0.000 | 0.015 | |
| intercell_resources | 0.081 | 0.013 | 1.017 | |
| intercell_summary | 0.066 | 0.004 | 0.071 | |
| is_ontology_id | 0.000 | 0.000 | 0.001 | |
| is_swissprot | 0.041 | 0.000 | 0.041 | |
| is_trembl | 0.041 | 0.000 | 0.041 | |
| is_uniprot | 0.016 | 0.000 | 0.015 | |
| kegg_api_templates | 0.001 | 0.000 | 0.001 | |
| kegg_conv | 1.430 | 0.568 | 4.688 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.651 | 0.074 | 1.590 | |
| kegg_find | 0.634 | 0.373 | 2.097 | |
| kegg_info | 0.013 | 0.000 | 0.014 | |
| kegg_link | 0.752 | 0.094 | 2.399 | |
| kegg_list | 0.668 | 0.044 | 1.224 | |
| kegg_open | 0.013 | 0.000 | 0.014 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.012 | 0.013 | 0.024 | |
| kegg_organisms | 0.03 | 0.00 | 0.03 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.013 | 0.000 | 0.014 | |
| kegg_pathway_list | 0.009 | 0.004 | 0.013 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 1.025 | 0.042 | 1.837 | |
| kegg_process | 0.021 | 0.004 | 0.025 | |
| kegg_query | 0.012 | 0.000 | 0.012 | |
| kegg_request | 0.082 | 0.000 | 0.082 | |
| kegg_rm_prefix | 0.844 | 0.082 | 2.254 | |
| latin_name | 0.088 | 0.000 | 0.088 | |
| load_db | 0.105 | 0.029 | 0.135 | |
| metalinksdb_sqlite | 1.060 | 0.548 | 13.206 | |
| metalinksdb_table | 0.273 | 0.063 | 0.335 | |
| metalinksdb_tables | 0.026 | 0.004 | 0.030 | |
| ncbi_taxid | 0.091 | 0.004 | 0.095 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.015 | 0.000 | 0.016 | |
| nichenet_gr_network | 0.027 | 0.022 | 0.049 | |
| nichenet_gr_network_evex | 0.008 | 0.008 | 0.016 | |
| nichenet_gr_network_harmonizome | 0.017 | 0.000 | 0.017 | |
| nichenet_gr_network_htridb | 0.013 | 0.004 | 0.018 | |
| nichenet_gr_network_omnipath | 20.853 | 1.159 | 27.305 | |
| nichenet_gr_network_pathwaycommons | 0.013 | 0.000 | 0.012 | |
| nichenet_gr_network_regnetwork | 0.012 | 0.000 | 0.012 | |
| nichenet_gr_network_remap | 0.012 | 0.000 | 0.013 | |
| nichenet_gr_network_trrust | 0.012 | 0.000 | 0.012 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.033 | 0.002 | 0.035 | |
| nichenet_lr_network_guide2pharma | 0.011 | 0.000 | 0.011 | |
| nichenet_lr_network_omnipath | 0.030 | 0.004 | 0.034 | |
| nichenet_lr_network_ramilowski | 0.012 | 0.000 | 0.012 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.054 | 0.004 | 0.058 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.035 | 0.000 | 0.035 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.000 | |
| nichenet_signaling_network | 0.038 | 0.000 | 0.038 | |
| nichenet_signaling_network_cpdb | 0.012 | 0.000 | 0.012 | |
| nichenet_signaling_network_evex | 0.009 | 0.004 | 0.013 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.004 | 0.012 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 15.347 | 0.793 | 19.467 | |
| nichenet_signaling_network_pathwaycommons | 0.014 | 0.000 | 0.014 | |
| nichenet_signaling_network_vinayagam | 0.013 | 0.000 | 0.013 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.001 | 0.000 | 0.001 | |
| obo_parser | 0.117 | 0.004 | 0.867 | |
| oma_code | 0.038 | 0.004 | 0.042 | |
| oma_organisms | 0.090 | 0.004 | 0.096 | |
| oma_pairwise | 0.013 | 0.000 | 0.013 | |
| oma_pairwise_genesymbols | 0.013 | 0.000 | 0.014 | |
| oma_pairwise_translated | 0.013 | 0.000 | 0.014 | |
| omnipath-interactions | 36.435 | 3.268 | 78.589 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.007 | 0.007 | 0.013 | |
| omnipath_cache_clean_db | 0.136 | 0.012 | 0.148 | |
| omnipath_cache_download_ready | 0.652 | 0.134 | 0.811 | |
| omnipath_cache_filter_versions | 0.136 | 0.021 | 0.188 | |
| omnipath_cache_get | 0.117 | 0.016 | 0.135 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.139 | 0.033 | 0.175 | |
| omnipath_cache_load | 0.527 | 0.054 | 3.864 | |
| omnipath_cache_move_in | 0.190 | 0.037 | 0.238 | |
| omnipath_cache_remove | 0.118 | 0.020 | 0.147 | |
| omnipath_cache_save | 0.188 | 0.025 | 0.230 | |
| omnipath_cache_search | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.101 | 0.015 | 0.127 | |
| omnipath_cache_update_status | 0.111 | 0.013 | 0.125 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.001 | |
| omnipath_for_cosmos | 12.068 | 1.164 | 39.431 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.001 | 0.000 | 0.000 | |
| omnipath_logfile | 0.000 | 0.002 | 0.002 | |
| omnipath_msg | 0.049 | 0.001 | 0.051 | |
| omnipath_query | 4.745 | 0.249 | 5.018 | |
| omnipath_reset_config | 0.001 | 0.000 | 0.000 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.036 | 0.000 | 0.037 | |
| omnipath_set_console_loglevel | 0.005 | 0.000 | 0.006 | |
| omnipath_set_logfile_loglevel | 0.005 | 0.000 | 0.006 | |
| omnipath_set_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_show_db | 0.079 | 0.012 | 0.091 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.001 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.060 | 0.005 | 0.064 | |
| pathwaycommons_download | 0.000 | 0.000 | 0.001 | |
| pivot_annotations | 11.704 | 0.442 | 28.323 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.001 | 0.001 | |
| print_bma_motif_es | 0.494 | 0.031 | 1.969 | |
| print_bma_motif_vs | 0.144 | 0.017 | 1.100 | |
| print_interactions | 7.792 | 1.033 | 15.206 | |
| print_path_es | 0.915 | 0.226 | 3.299 | |
| print_path_vs | 2.913 | 0.397 | 6.548 | |
| pubmed_open | 5.097 | 0.227 | 5.336 | |
| query_info | 0.420 | 0.028 | 0.953 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| ramp_id_type | 0.003 | 0.000 | 0.003 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.000 | 0.000 | 0.001 | |
| ramp_tables | 0.000 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.000 | |
| relations_list_to_table | 0.110 | 0.012 | 0.713 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.084 | 0.008 | 0.315 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.000 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.000 | 0.000 | 0.001 | |
| resource_info | 0.425 | 0.069 | 0.999 | |
| resources | 0.073 | 0.004 | 1.001 | |
| resources_colname | 1.115 | 0.050 | 3.520 | |
| resources_in | 4.811 | 0.318 | 5.179 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 6.420 | 0.386 | 8.288 | |
| simplify_intercell_network | 0.000 | 0.001 | 0.001 | |
| static_table | 6.783 | 0.552 | 12.650 | |
| static_tables | 0.058 | 0.025 | 0.252 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.001 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.003 | 0.008 | 0.011 | |
| swap_relations | 0.104 | 0.013 | 0.329 | |
| swissprots_only | 0.043 | 0.008 | 0.051 | |
| tfcensus_download | 0.679 | 0.036 | 0.730 | |
| translate_ids | 1.393 | 0.178 | 11.559 | |
| translate_ids_multi | 10.630 | 1.228 | 33.525 | |
| trembls_only | 0.044 | 0.000 | 0.045 | |
| trrust_download | 0.001 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.065 | 0.064 | 15.497 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.003 | 0.000 | 0.003 | |
| uniprot_idmapping_id_types | 0.521 | 0.019 | 1.366 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.003 | |
| vinayagam_download | 0.000 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.002 | |
| with_extra_attrs | 16.119 | 1.826 | 19.734 | |
| with_references | 0.883 | 0.068 | 2.943 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |