Denes Turei
| Snapshot Date: 2025-09-02 13:45 -0400 (Tue, 02 Sep 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: a7f3b9d |
| git_last_commit_date: 2025-07-16 10:03:35 -0400 (Wed, 16 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-09-03 12:07 -0400 (Wed, 03 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4826 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4616 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4563 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1476/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.17.4 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 3.17.4 |
| 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_3.17.4.tar.gz |
| StartedAt: 2025-09-02 09:19:05 -0000 (Tue, 02 Sep 2025) |
| EndedAt: 2025-09-02 09:51:51 -0000 (Tue, 02 Sep 2025) |
| EllapsedTime: 1966.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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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_3.17.4.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.17.4’
* 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
[2025-09-02 09:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-02 09:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:19:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:19:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-02 09:19:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-01
[2025-09-02 09:19:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-01 20:24:28 UTC; unix
[2025-09-02 09:19:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-02 09:19:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-02 09:19:43] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-02; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-02 09:19:43] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-02 09:19:43] [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 0.6.37(2024-08-19); 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 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); 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 0.4.0(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 3.17.4(2025-09-01); pillar 1.11.0(2025-07-04); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-02 09:19:43] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Contains 1 files.
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-02 09:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:19:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-02 09:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-02 09:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-02 09:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-02 09:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:19:43] [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
[2025-09-02 09:20:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-02 09:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:20:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:20:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-02 09:20:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-01
[2025-09-02 09:20:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-01 20:24:28 UTC; unix
[2025-09-02 09:20:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-02 09:20:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-02 09:20:05] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-02; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-02 09:20:05] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-02 09:20:06] [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 0.6.37(2024-08-19); 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 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); 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 0.4.0(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 3.17.4(2025-09-01); pillar 1.11.0(2025-07-04); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-02 09:20:06] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Contains 1 files.
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-02 09:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:20:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-02 09:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-02 09:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-02 09:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-02 09:20:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:20:06] [TRACE] [OmnipathR] Cache locked: FALSE
taxon_names_table: no visible binding for global variable
‘latin_name_uniprot’
taxon_names_table: no visible binding for global variable
‘latin_name_ensembl’
taxon_names_table: no visible binding for global variable
‘latin_name_oma’
taxon_names_table: no visible binding for global variable
‘common_name_ensembl’
taxon_names_table: no visible binding for global variable
‘common_name_uniprot’
Undefined global functions or variables:
common_name_ensembl common_name_uniprot latin_name_ensembl
latin_name_oma latin_name_uniprot
* 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 108.655 0.106 110.354
curated_ligrec_stats 44.018 4.122 154.087
filter_extra_attrs 35.259 5.443 46.752
omnipath-interactions 35.527 3.323 68.646
all_uniprots 34.648 2.532 56.394
uniprot_organisms 25.988 1.908 33.407
extra_attrs_to_cols 21.360 1.516 27.393
nichenet_gr_network_omnipath 20.022 0.929 22.504
extra_attr_values 18.624 1.751 27.693
with_extra_attrs 16.621 1.724 21.493
nichenet_signaling_network_omnipath 14.061 0.871 16.747
go_annot_download 13.621 0.623 32.539
giant_component 12.821 0.785 17.154
omnipath_for_cosmos 12.321 0.862 37.393
extra_attrs 10.813 1.394 16.351
filter_by_resource 11.232 0.530 18.934
has_extra_attrs 9.954 1.363 13.601
translate_ids_multi 9.976 0.391 36.934
pivot_annotations 9.826 0.511 20.730
curated_ligand_receptor_interactions 7.736 0.962 21.416
print_interactions 7.627 0.353 13.273
find_all_paths 7.356 0.223 7.596
filter_intercell 6.744 0.356 12.191
static_table 5.965 0.692 16.109
signed_ptms 6.278 0.285 8.414
pubmed_open 5.305 0.247 5.585
omnipath_query 4.929 0.210 5.162
hpo_download 3.435 0.274 25.363
print_path_vs 2.817 0.222 6.539
enzsub_graph 2.706 0.162 7.454
ensembl_id_mapping_table 2.621 0.224 21.655
annotated_network 1.458 0.382 5.522
metalinksdb_sqlite 1.081 0.135 12.892
translate_ids 1.123 0.071 11.821
uniprot_full_id_mapping_table 1.064 0.048 14.203
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
57. │ └─rlang:::signal_abort(cnd, .file)
58. │ └─base::signalCondition(cnd)
59. └─purrr (local) `<fn>`(`<prrr_rr_>`)
60. └─cli::cli_abort(...)
61. └─rlang::abort(...)
── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ─────────
Error in `eval(code, test_env)`: object 'response' not found
Backtrace:
▆
1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13
2. └─tidyr::separate_rows(., sources, sep = ";")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-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-4.5.0/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.17.4’ ** 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 [2025-09-01 20:24:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-01 20:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:47] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-09-01 20:24:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-09-01 20:24:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-01 [2025-09-01 20:24:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-01 20:24:28 UTC; unix [2025-09-01 20:24:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-09-01 20:24:47] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-09-01 20:24:47] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-01; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-09-01 20:24:48] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-09-01 20:24:48] [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 0.6.37(2024-08-19); 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 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); 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 0.4.0(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 3.17.4(2025-09-01); pillar 1.11.0(2025-07-04); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-09-01 20:24:48] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2025-09-01 20:24:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-09-01 20:24:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-09-01 20:24:48] [TRACE] [OmnipathR] Contains 7 files. [2025-09-01 20:24:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-09-01 20:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-01 20:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-09-01 20:24:48] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-09-01 20:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-09-01 20:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-09-01 20:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-09-01 20:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-09-01 20:24:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:48] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-09-01 20:24:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-01 20:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:51] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-09-01 20:24:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-09-01 20:24:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-01 [2025-09-01 20:24:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-01 20:24:28 UTC; unix [2025-09-01 20:24:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-09-01 20:24:51] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-09-01 20:24:51] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-01; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-09-01 20:24:51] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-09-01 20:24:51] [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 0.6.37(2024-08-19); 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 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); 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 0.4.0(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 3.17.4(2025-09-01); pillar 1.11.0(2025-07-04); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-09-01 20:24:51] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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 [2025-09-01 20:24:51] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-09-01 20:24:51] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-09-01 20:24:51] [TRACE] [OmnipathR] Contains 1 files. [2025-09-01 20:24:51] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-09-01 20:24:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-09-01 20:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-09-01 20:24:51] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-09-01 20:24:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-09-01 20:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-09-01 20:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-09-01 20:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-09-01 20:24:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-09-01 20:24:52] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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)
[2025-09-02 09:38:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-02 09:38:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:38:52] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:38:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-02 09:38:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-09-01
[2025-09-02 09:38:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-09-01 20:24:28 UTC; unix
[2025-09-02 09:38:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-02 09:38:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-02 09:38:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-09-02; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto]
[2025-09-02 09:38:53] [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=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; 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=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0]
[2025-09-02 09:38:53] [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 0.6.37(2024-08-19); 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 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); 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 0.4.0(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 3.17.4(2025-09-01); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); 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 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); 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 3.3.0(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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-02 09:38:53] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; 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
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Contains 22 files.
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-02 09:38:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:38:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-02 09:38:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-02 09:38:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-02 09:38:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-02 09:38:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-09-02 09:38:53] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_import.R:169:9'): Testing `complexes` ────────────────────────
`assign("response", method(resources = resources), envir = top_env)` threw an error.
Message: ℹ In index: 1.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform()`:
! HTTP 404 Not Found.
Class: purrr_error_indexed/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...)
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::assign("response", method(resources = resources), envir = top_env)
7. ├─OmnipathR (local) method(resources = resources)
8. │ ├─rlang::exec(omnipath_query, !!!args)
9. │ └─OmnipathR (local) `<fn>`(resources = `<chr>`, query_type = "complexes")
10. │ └─environment() %>% as.list %>% c(list(...)) %>% ...
11. ├─OmnipathR:::omnipath_check_param(.)
12. │ └─param$organisms %<>% map_int(ncbi_taxid)
13. ├─purrr::map_int(., ncbi_taxid)
14. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
15. │ ├─purrr:::with_indexed_errors(...)
16. │ │ └─base::withCallingHandlers(...)
17. │ ├─purrr:::call_with_cleanup(...)
18. │ └─OmnipathR (local) .f(.x[[i]], ...)
19. │ └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
20. ├─purrr::map_int(., taxon_name, "ncbi")
21. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
22. │ ├─purrr:::with_indexed_errors(...)
23. │ │ └─base::withCallingHandlers(...)
24. │ ├─purrr:::call_with_cleanup(...)
25. │ └─OmnipathR (local) .f(.x[[i]], ...)
26. │ ├─... %>% if_null_len0(NA)
27. │ └─OmnipathR::get_db("organisms")
28. │ └─OmnipathR::load_db(key, param = param)
29. │ ├─rlang::exec(loader, !!!param)
30. │ └─OmnipathR (local) `<fn>`()
31. │ ├─... %>% ...
32. │ └─OmnipathR::ensembl_organisms()
33. │ ├─... %>% ...
34. │ └─OmnipathR::ensembl_organisms_raw()
35. │ └─... %>% html_table()
36. ├─OmnipathR:::if_null_len0(., NA)
37. │ └─value1 %>% is_empty_2 %>% if (value2) value1
38. ├─OmnipathR:::is_empty_2(.)
39. │ └─value %>% ...
40. ├─dplyr::pull(., name_type)
41. ├─dplyr::filter(...)
42. ├─dplyr::mutate(...)
43. ├─dplyr::full_join(...)
44. ├─dplyr::full_join(...)
45. ├─dplyr::rename(., common_name_ensembl = common_name)
46. ├─dplyr::mutate(...)
47. ├─dplyr::select(...)
48. ├─rvest::html_table(.)
49. ├─rvest::html_element(., "table")
50. ├─xml2::read_html(.)
51. ├─OmnipathR:::download_to_cache(., http_headers = user_agent())
52. │ └─OmnipathR:::download_base(...)
53. │ └─base::stop(result)
54. ├─purrr (local) `<fn>`(`<ht2__404>`)
55. │ └─cli::cli_abort(...)
56. │ └─rlang::abort(...)
57. │ └─rlang:::signal_abort(cnd, .file)
58. │ └─base::signalCondition(cnd)
59. └─purrr (local) `<fn>`(`<prrr_rr_>`)
60. └─cli::cli_abort(...)
61. └─rlang::abort(...)
── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ─────────
Error in `eval(code, test_env)`: object 'response' not found
Backtrace:
▆
1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13
2. └─tidyr::separate_rows(., sources, sep = ";")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
Error: Test failures
Execution halted
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.025 | 0.000 | 0.025 | |
| all_uniprots | 34.648 | 2.532 | 56.394 | |
| ancestors | 0.014 | 0.000 | 0.014 | |
| annotated_network | 1.458 | 0.382 | 5.522 | |
| annotation_categories | 108.655 | 0.106 | 110.354 | |
| annotation_resources | 0.079 | 0.016 | 1.099 | |
| annotations | 0.661 | 0.139 | 2.289 | |
| biomart_query | 1.330 | 0.126 | 2.970 | |
| bioplex1 | 0.015 | 0.000 | 0.015 | |
| bioplex2 | 0.013 | 0.000 | 0.014 | |
| bioplex3 | 0.009 | 0.004 | 0.013 | |
| bioplex_all | 0.014 | 0.000 | 0.015 | |
| bioplex_hct116_1 | 0.014 | 0.000 | 0.015 | |
| bma_motif_es | 0.763 | 0.093 | 2.357 | |
| bma_motif_vs | 0.271 | 0.028 | 2.649 | |
| chalmers_gem | 0.014 | 0.000 | 0.013 | |
| chalmers_gem_id_mapping_table | 0.010 | 0.004 | 0.013 | |
| chalmers_gem_id_type | 0.003 | 0.000 | 0.003 | |
| chalmers_gem_metabolites | 0.013 | 0.000 | 0.013 | |
| chalmers_gem_network | 0.013 | 0.000 | 0.013 | |
| chalmers_gem_raw | 0.013 | 0.000 | 0.013 | |
| chalmers_gem_reactions | 0.013 | 0.000 | 0.012 | |
| common_name | 0.179 | 0.016 | 0.196 | |
| complex_genes | 0.786 | 0.071 | 4.938 | |
| complex_resources | 0.077 | 0.016 | 1.091 | |
| complexes | 0.222 | 0.012 | 1.051 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.046 | 0.008 | 0.054 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.736 | 0.962 | 21.416 | |
| curated_ligrec_stats | 44.018 | 4.122 | 154.087 | |
| database_summary | 1.946 | 0.121 | 3.350 | |
| descendants | 0.013 | 0.000 | 0.013 | |
| ensembl_dataset | 0.057 | 0.000 | 0.056 | |
| ensembl_id_mapping_table | 2.621 | 0.224 | 21.655 | |
| ensembl_id_type | 0.002 | 0.000 | 0.002 | |
| ensembl_name | 0.353 | 0.028 | 0.383 | |
| ensembl_organisms | 0.162 | 0.020 | 0.182 | |
| ensembl_organisms_raw | 0.133 | 0.040 | 0.173 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.706 | 0.162 | 7.454 | |
| enzsub_resources | 0.083 | 0.004 | 1.079 | |
| enzyme_substrate | 1.478 | 0.084 | 2.406 | |
| evex_download | 0.008 | 0.004 | 0.013 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 18.624 | 1.751 | 27.693 | |
| extra_attrs | 10.813 | 1.394 | 16.351 | |
| extra_attrs_to_cols | 21.360 | 1.516 | 27.393 | |
| filter_by_resource | 11.232 | 0.530 | 18.934 | |
| filter_extra_attrs | 35.259 | 5.443 | 46.752 | |
| filter_intercell | 6.744 | 0.356 | 12.191 | |
| filter_intercell_network | 0.023 | 0.004 | 0.027 | |
| find_all_paths | 7.356 | 0.223 | 7.596 | |
| from_evidences | 0.001 | 0.000 | 0.001 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.015 | 0.000 | 0.015 | |
| giant_component | 12.821 | 0.785 | 17.154 | |
| go_annot_download | 13.621 | 0.623 | 32.539 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.012 | 0.000 | 0.014 | |
| guide2pharma_download | 0.009 | 0.004 | 0.013 | |
| harmonizome_download | 0.013 | 0.000 | 0.013 | |
| has_extra_attrs | 9.954 | 1.363 | 13.601 | |
| hmdb_id_mapping_table | 0.013 | 0.000 | 0.013 | |
| hmdb_id_type | 0.003 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_protein_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_table | 0.014 | 0.000 | 0.014 | |
| homologene_download | 0.006 | 0.008 | 0.015 | |
| homologene_raw | 0.071 | 0.000 | 0.071 | |
| homologene_uniprot_orthology | 0.010 | 0.004 | 0.013 | |
| hpo_download | 3.435 | 0.274 | 25.363 | |
| htridb_download | 0.013 | 0.000 | 0.013 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.062 | 0.000 | 0.061 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.766 | 0.085 | 1.945 | |
| interaction_graph | 0.501 | 0.023 | 1.770 | |
| interaction_resources | 0.091 | 0.009 | 1.161 | |
| interaction_types | 0.096 | 0.000 | 0.142 | |
| intercell | 0.855 | 0.124 | 2.323 | |
| intercell_categories | 0.741 | 0.061 | 1.324 | |
| intercell_consensus_filter | 1.456 | 0.102 | 3.062 | |
| intercell_generic_categories | 0.085 | 0.024 | 0.110 | |
| intercell_network | 0.014 | 0.000 | 0.014 | |
| intercell_resources | 0.082 | 0.008 | 1.126 | |
| intercell_summary | 0.088 | 0.012 | 0.100 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.064 | 0.009 | 0.072 | |
| is_trembl | 0.068 | 0.003 | 0.072 | |
| is_uniprot | 0.013 | 0.000 | 0.014 | |
| kegg_api_templates | 0.001 | 0.000 | 0.002 | |
| kegg_conv | 1.433 | 0.140 | 4.600 | |
| kegg_databases | 0.001 | 0.000 | 0.000 | |
| kegg_ddi | 0.620 | 0.101 | 1.753 | |
| kegg_find | 0.608 | 0.056 | 1.907 | |
| kegg_info | 0.012 | 0.000 | 0.013 | |
| kegg_link | 0.710 | 0.068 | 2.538 | |
| kegg_list | 0.603 | 0.048 | 1.083 | |
| kegg_open | 0.012 | 0.000 | 0.012 | |
| kegg_operations | 0.001 | 0.000 | 0.000 | |
| kegg_organism_codes | 0.012 | 0.012 | 0.024 | |
| kegg_organisms | 0.023 | 0.004 | 0.028 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.011 | 0.000 | 0.012 | |
| kegg_pathway_list | 0.012 | 0.000 | 0.011 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.940 | 0.059 | 1.914 | |
| kegg_process | 0.019 | 0.004 | 0.023 | |
| kegg_query | 0.009 | 0.000 | 0.010 | |
| kegg_request | 0.070 | 0.008 | 0.079 | |
| kegg_rm_prefix | 0.757 | 0.069 | 2.198 | |
| latin_name | 0.299 | 0.004 | 0.304 | |
| load_db | 0.109 | 0.025 | 0.135 | |
| metalinksdb_sqlite | 1.081 | 0.135 | 12.892 | |
| metalinksdb_table | 0.264 | 0.020 | 0.284 | |
| metalinksdb_tables | 0.023 | 0.000 | 0.023 | |
| ncbi_taxid | 0.295 | 0.012 | 0.308 | |
| nichenet_build_model | 0.000 | 0.000 | 0.001 | |
| nichenet_expression_data | 0.012 | 0.000 | 0.012 | |
| nichenet_gr_network | 0.031 | 0.004 | 0.035 | |
| nichenet_gr_network_evex | 0.012 | 0.000 | 0.012 | |
| nichenet_gr_network_harmonizome | 0.013 | 0.000 | 0.013 | |
| nichenet_gr_network_htridb | 0.012 | 0.000 | 0.011 | |
| nichenet_gr_network_omnipath | 20.022 | 0.929 | 22.504 | |
| nichenet_gr_network_pathwaycommons | 0.015 | 0.000 | 0.015 | |
| nichenet_gr_network_regnetwork | 0.010 | 0.004 | 0.015 | |
| nichenet_gr_network_remap | 0.013 | 0.000 | 0.013 | |
| nichenet_gr_network_trrust | 0.013 | 0.000 | 0.012 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.030 | 0.008 | 0.037 | |
| nichenet_lr_network_guide2pharma | 0.013 | 0.000 | 0.013 | |
| nichenet_lr_network_omnipath | 0.035 | 0.004 | 0.039 | |
| nichenet_lr_network_ramilowski | 0.009 | 0.004 | 0.013 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.059 | 0.004 | 0.062 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.038 | 0.000 | 0.038 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.041 | 0.000 | 0.040 | |
| nichenet_signaling_network_cpdb | 0.013 | 0.000 | 0.012 | |
| nichenet_signaling_network_evex | 0.012 | 0.000 | 0.013 | |
| nichenet_signaling_network_harmonizome | 0.009 | 0.004 | 0.013 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 14.061 | 0.871 | 16.747 | |
| nichenet_signaling_network_pathwaycommons | 0.367 | 0.032 | 0.400 | |
| nichenet_signaling_network_vinayagam | 0.012 | 0.000 | 0.013 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.100 | 0.024 | 0.757 | |
| oma_code | 0.153 | 0.000 | 0.154 | |
| oma_organisms | 0.078 | 0.008 | 0.086 | |
| oma_pairwise | 0.013 | 0.000 | 0.013 | |
| oma_pairwise_genesymbols | 0.009 | 0.004 | 0.013 | |
| oma_pairwise_translated | 0.013 | 0.000 | 0.013 | |
| omnipath-interactions | 35.527 | 3.323 | 68.646 | |
| omnipath_cache_autoclean | 0.000 | 0.000 | 0.001 | |
| omnipath_cache_clean | 0.013 | 0.000 | 0.013 | |
| omnipath_cache_clean_db | 0.122 | 0.016 | 0.138 | |
| omnipath_cache_download_ready | 0.618 | 0.130 | 0.831 | |
| omnipath_cache_filter_versions | 0.109 | 0.021 | 0.183 | |
| omnipath_cache_get | 0.109 | 0.010 | 0.195 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.003 | |
| omnipath_cache_latest_or_new | 0.078 | 0.005 | 0.105 | |
| omnipath_cache_load | 0.581 | 0.042 | 4.349 | |
| omnipath_cache_move_in | 0.199 | 0.015 | 0.351 | |
| omnipath_cache_remove | 0.113 | 0.016 | 0.135 | |
| omnipath_cache_save | 0.182 | 0.028 | 0.358 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.000 | |
| omnipath_cache_set_ext | 0.102 | 0.008 | 0.122 | |
| omnipath_cache_update_status | 0.217 | 0.146 | 0.512 | |
| omnipath_cache_wipe | 0.001 | 0.000 | 0.000 | |
| omnipath_config_path | 0.001 | 0.000 | 0.005 | |
| omnipath_for_cosmos | 12.321 | 0.862 | 37.393 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.002 | 0.000 | 0.003 | |
| omnipath_msg | 0.008 | 0.000 | 0.007 | |
| omnipath_query | 4.929 | 0.210 | 5.162 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.036 | 0.000 | 0.036 | |
| omnipath_set_console_loglevel | 0.005 | 0.000 | 0.005 | |
| omnipath_set_logfile_loglevel | 0.005 | 0.000 | 0.005 | |
| omnipath_set_loglevel | 0.003 | 0.000 | 0.003 | |
| omnipath_show_db | 0.079 | 0.012 | 0.091 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.000 | |
| only_from | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_id | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_name | 0.000 | 0.000 | 0.001 | |
| ontology_name_id | 0.001 | 0.000 | 0.002 | |
| organism_for | 0.204 | 0.004 | 0.209 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 9.826 | 0.511 | 20.730 | |
| preppi_download | 0.001 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.000 | 0.001 | |
| print_bma_motif_es | 0.561 | 0.024 | 2.609 | |
| print_bma_motif_vs | 0.203 | 0.007 | 1.151 | |
| print_interactions | 7.627 | 0.353 | 13.273 | |
| print_path_es | 0.895 | 0.051 | 3.053 | |
| print_path_vs | 2.817 | 0.222 | 6.539 | |
| pubmed_open | 5.305 | 0.247 | 5.585 | |
| query_info | 0.441 | 0.025 | 0.984 | |
| ramilowski_download | 0.000 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.000 | 0.000 | 0.001 | |
| ramp_id_type | 0.002 | 0.000 | 0.003 | |
| ramp_sqlite | 0.000 | 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 | 0.106 | 0.008 | 0.749 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.092 | 0.012 | 0.325 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.000 | 0.000 | 0.001 | |
| resource_info | 0.452 | 0.077 | 1.096 | |
| resources | 0.076 | 0.000 | 0.912 | |
| resources_colname | 1.089 | 0.095 | 4.298 | |
| resources_in | 4.706 | 0.210 | 4.931 | |
| show_network | 0.001 | 0.000 | 0.000 | |
| signed_ptms | 6.278 | 0.285 | 8.414 | |
| simplify_intercell_network | 0.002 | 0.000 | 0.001 | |
| static_table | 5.965 | 0.692 | 16.109 | |
| static_tables | 0.186 | 0.001 | 0.430 | |
| stitch_actions | 0.000 | 0.000 | 0.001 | |
| stitch_links | 0.001 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.010 | 0.000 | 0.011 | |
| swap_relations | 0.105 | 0.003 | 0.596 | |
| swissprots_only | 0.156 | 0.004 | 0.238 | |
| tfcensus_download | 0.521 | 0.070 | 0.795 | |
| translate_ids | 1.123 | 0.071 | 11.821 | |
| translate_ids_multi | 9.976 | 0.391 | 36.934 | |
| trembls_only | 0.158 | 0.000 | 0.158 | |
| trrust_download | 0.001 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.064 | 0.048 | 14.203 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.003 | 0.000 | 0.002 | |
| uniprot_idmapping_id_types | 0.471 | 0.020 | 1.640 | |
| uniprot_organisms | 25.988 | 1.908 | 33.407 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0.000 | 0.000 | 0.001 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.002 | |
| vinayagam_download | 0.001 | 0.000 | 0.001 | |
| walk_ontology_tree | 0.001 | 0.000 | 0.002 | |
| with_extra_attrs | 16.621 | 1.724 | 21.493 | |
| with_references | 0.871 | 0.072 | 3.469 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |