| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-06 11:32 -0500 (Fri, 06 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4857 |
| 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 1500/2347 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.6 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for OmnipathR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.19.6 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_3.19.6.tar.gz |
| StartedAt: 2026-02-06 02:11:40 -0500 (Fri, 06 Feb 2026) |
| EndedAt: 2026-02-06 02:45:44 -0500 (Fri, 06 Feb 2026) |
| EllapsedTime: 2044.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings OmnipathR_3.19.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.6’
* 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
[2026-02-06 02:12:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:12:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:20] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:12:20] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-06 02:12:20] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-05
[2026-02-06 02:12:20] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-05 20:08:25 UTC; unix
[2026-02-06 02:12:20] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-06 02:12:20] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-06 02:12:21] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-06 02:12:21] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-06 02:12:21] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-06 02:12:21] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Contains 1 files.
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:12:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-06 02:12:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-06 02:12:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-06 02:12:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-06 02:12:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:21] [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 ... WARNING
'::' or ':::' import not declared from: ‘SBMLR’
'loadNamespace' or 'requireNamespace' call not declared from: ‘SBMLR’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-02-06 02:12:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:12:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:45] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:12:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-06 02:12:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-05
[2026-02-06 02:12:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-05 20:08:25 UTC; unix
[2026-02-06 02:12:45] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-06 02:12:45] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-06 02:12:48] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-06 02:12:48] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-06 02:12:48] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-06 02:12:48] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Contains 1 files.
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-06 02:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-06 02:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-06 02:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-06 02:12:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:12:48] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
metabolic_atlas_list_gems: no visible binding for global variable
‘git_repo’
metabolic_atlas_list_gems: no visible binding for global variable
‘git_host’
metabolic_atlas_list_gems: no visible binding for global variable
‘gem_info’
metabolic_atlas_list_gems: no visible binding for global variable
‘latest_version’
metabolic_atlas_model: no visible binding for global variable ‘path’
metabolic_atlas_model : silent_sbml: no visible binding for global
variable ‘result’
metabolic_atlas_models: no visible binding for global variable ‘id’
patch_httr2_keep_handle: no visible binding for global variable
‘handle’
patch_httr2_keep_handle: no visible global function definition for
‘ORIGINAL’
Undefined global functions or variables:
ORIGINAL enzyme_genesymbol gem_info git_host git_repo handle id
latest_version path result
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'load_db.Rd':
load_db
Code: function(key, param = list(), reload = FALSE)
Docs: function(key, param = list())
Argument names in code not in docs:
reload
* 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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: metabolic_atlas_list_models
> ### Title: List of original GEMs in Metabolic Atlas
> ### Aliases: metabolic_atlas_list_models
>
> ### ** Examples
>
> metabolic_atlas_models()
[2026-02-06 02:26:47] [WARN] [OmnipathR] SBMLR package not available, install with: BiocManager::install('SBMLR')
[2026-02-06 02:26:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:48] [INFO] [OmnipathR] Looking up in cache `https://metabolicatlas.org/api/v2/repository/models/`: key=035dd3150b56361f57dd12fb4ecb7f1416d31ddf, no version available.
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:48] [INFO] [OmnipathR] Created new version for cache record 035dd3150b56361f57dd12fb4ecb7f1416d31ddf: version 1.
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/035dd3150b56361f57dd12fb4ecb7f1416d31ddf-1
[2026-02-06 02:26:48] [INFO] [OmnipathR] Retrieving URL: `https://metabolicatlas.org/api/v2/repository/models/`
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Attempt 1/3: `https://metabolicatlas.org/api/v2/repository/models/`
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://metabolicatlas.org/api/v2/repository/models/`.
[2026-02-06 02:26:48] [TRACE] [OmnipathR] HTTP headers: <NULL>
[2026-02-06 02:26:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-06 02:26:48] [TRACE] [OmnipathR] HTTP headers: []
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-06 02:26:48] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-06 02:26:48] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-06 02:26:48] [TRACE] [OmnipathR] Downloaded 32.8 Kb in 0.513174s from metabolicatlas.org (63.8 Kb/s); Redirect: 0s, DNS look up: 0.185145s, Connection: 0.198824s, Pretransfer: 0.258387s, First byte at: 0.509799s
[2026-02-06 02:26:48] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 06 Feb 2026 07:26:48 GMT; content-type: application/json; charset=utf-8; server: cloudflare; x-powered-by: Express; etag: W/"7b9e6-L2oww6jQElU58qCfhBAtYNT1rHA"; strict-transport-security: max-age=63072000; includeSubdomains;; x-frame-options: DENY; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=A2uLKhP3tgrkcYJq6Rx8gY4c29Q90ObePUBXqpabbhgvqkqOQAqc%2Bhqn1CbouWc3iGdHEnw9Dai58oYWRGfz%2B%2BSzC68qj9dyeVOpjv2NhimRSw%3D%3D"}]}; cf-ray: 9c98ebe19b97f274-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-06 02:26:49] [TRACE] [OmnipathR] Response headers: [date=Fri, 06 Feb 2026 07:26:48 GMT,content-type=application/json; charset=utf-8,server=cloudflare,x-powered-by=Express,etag=W/"7b9e6-L2oww6jQElU58qCfhBAtYNT1rHA",strict-transport-security=max-age=63072000; includeSubdomains;,x-frame-options=DENY,content-encoding=gzip,cf-cache-status=DYNAMIC,vary=accept-encoding,nel={"report_to":"cf-nel","success_fraction":0.0,"max_age":604800},report-to={"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=A2uLKhP3tgrkcYJq6Rx8gY4c29Q90ObePUBXqpabbhgvqkqOQAqc%2Bhqn1CbouWc3iGdHEnw9Dai58oYWRGfz%2B%2BSzC68qj9dyeVOpjv2NhimRSw%3D%3D"}]},cf-ray=9c98ebe19b97f274-IAD,alt-svc=h3=":443"; ma=86400]
[2026-02-06 02:26:49] [INFO] [OmnipathR] Download ready [key=035dd3150b56361f57dd12fb4ecb7f1416d31ddf, version=1]
[2026-02-06 02:26:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:49] [INFO] [OmnipathR] Cache item `035dd3150b56361f57dd12fb4ecb7f1416d31ddf` version 1: status changed from `unknown` to `ready`.
[2026-02-06 02:26:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/035dd3150b56361f57dd12fb4ecb7f1416d31ddf-1` (encoding: UTF-8).
[2026-02-06 02:26:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:50] [INFO] [OmnipathR] Downloading model: INIT normal models [id=1,organism=Homo sapiens,tissue=Breast,cell_type=Myoepithelial cells,condition=Healthy,reaction_count=4772,metabolite_count=4046,gene_count=1776,year=2014]
[2026-02-06 02:26:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:50] [INFO] [OmnipathR] Looking up in cache `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`: key=7852b38b808236483c3516bf8c7cc803b60135ff, no version available.
[2026-02-06 02:26:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:51] [INFO] [OmnipathR] Created new version for cache record 7852b38b808236483c3516bf8c7cc803b60135ff: version 1.
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7852b38b808236483c3516bf8c7cc803b60135ff-1
[2026-02-06 02:26:51] [INFO] [OmnipathR] Downloading `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-06 02:26:51] [INFO] [OmnipathR] Retrieving URL: `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Attempt 1/3: `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`.
[2026-02-06 02:26:51] [TRACE] [OmnipathR] HTTP headers: <NULL>
[2026-02-06 02:26:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-06 02:26:51] [TRACE] [OmnipathR] HTTP headers: []
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-06 02:26:51] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-06 02:26:51] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Downloaded 351.5 Kb in 0.398305s from metabolicatlas.org (882.4 Kb/s); Redirect: 0s, DNS look up: 0.002001s, Connection: 0s, Pretransfer: 0.002656s, First byte at: 0.362237s
[2026-02-06 02:26:51] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 06 Feb 2026 07:26:51 GMT; content-type: application/zip; server: cloudflare; x-powered-by: Express; cache-control: public, max-age=1382400; last-modified: Sat, 06 Sep 2025 22:47:44 GMT; etag: W/"5a69b-1992136d0d2"; strict-transport-security: max-age=63072000; includeSubdomains;; x-frame-options: DENY; content-encoding: gzip; cf-cache-status: REVALIDATED; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=zNoNxh1XsBtWkhpVKnQi50xmirsUL4sjsZL7Eo2UYoazhdFPW9h%2FkdE%2F2zXoH2ccsIT4Ai%2FHXJVRHcyzAezRZXBltobAVkx1u7oIl%2BezF2eoXg%3D%3D"}]}; cf-ray: 9c98ebf1b84cf274-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-06 02:26:51] [TRACE] [OmnipathR] Response headers: [date=Fri, 06 Feb 2026 07:26:51 GMT,content-type=application/zip,server=cloudflare,x-powered-by=Express,cache-control=public, max-age=1382400,last-modified=Sat, 06 Sep 2025 22:47:44 GMT,etag=W/"5a69b-1992136d0d2",strict-transport-security=max-age=63072000; includeSubdomains;,x-frame-options=DENY,content-encoding=gzip,cf-cache-status=REVALIDATED,vary=accept-encoding,nel={"report_to":"cf-nel","success_fraction":0.0,"max_age":604800},report-to={"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=zNoNxh1XsBtWkhpVKnQi50xmirsUL4sjsZL7Eo2UYoazhdFPW9h%2FkdE%2F2zXoH2ccsIT4Ai%2FHXJVRHcyzAezRZXBltobAVkx1u7oIl%2BezF2eoXg%3D%3D"}]},cf-ray=9c98ebf1b84cf274-IAD,alt-svc=h3=":443"; ma=86400]
[2026-02-06 02:26:52] [INFO] [OmnipathR] Download ready [key=7852b38b808236483c3516bf8c7cc803b60135ff, version=1]
[2026-02-06 02:26:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:52] [INFO] [OmnipathR] Cache item `7852b38b808236483c3516bf8c7cc803b60135ff` version 1: status changed from `unknown` to `ready`.
[2026-02-06 02:26:52] [TRACE] [OmnipathR] Archive type `zip`: `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`
[2026-02-06 02:26:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:52] [INFO] [OmnipathR] Looking up in cache `https://metabolicatlas.org/api/v2/repository/models/homo_sapiens/init_normal_models/breast_and_female_reproductive_system/breast/breast_-_myoepithelial_cells_2.xml-9a7735edecc2890e0c68120259a97a48.zip`: key=7852b38b808236483c3516bf8c7cc803b60135ff, latest version=1.
[2026-02-06 02:26:52] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7852b38b808236483c3516bf8c7cc803b60135ff-1.zip
[2026-02-06 02:26:52] [TRACE] [OmnipathR] Path in archive: `breast_-_myoepithelial_cells_2.xml`
[2026-02-06 02:26:53] [INFO] [OmnipathR] Downloading model: Bacteria models [id=2,organism=Streptomyces coelicolor,tissue=NA,cell_type=NA,condition=Evaluating metabolic capabilities,reaction_count=971,metabolite_count=500,gene_count=711,year=2005]
Error in `map()`:
ℹ In index: 2.
Caused by error in `pmap()`:
! Can't recycle `.l[[1]]` (size 0) to match `.l[[2]]` (size 2).
Backtrace:
▆
1. ├─OmnipathR::metabolic_atlas_models()
2. │ └─... %>% ...
3. ├─purrr::map(...)
4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
5. │ ├─purrr:::with_indexed_errors(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ ├─purrr:::call_with_cleanup(...)
8. │ └─OmnipathR (local) .f(.x[[i]], ...)
9. │ └─OmnipathR:::metabolic_atlas_model(slice(models, .x), return_xml = return_xml)
10. │ ├─rlang::exec(method, !!!dl_args)
11. │ └─OmnipathR (local) `<fn>`(...)
12. │ └─OmnipathR:::archive_downloader(...)
13. │ └─OmnipathR::omnipath_cache_latest_or_new(url = cache_url, post = cache_post)
14. │ └─OmnipathR::omnipath_cache_get(...)
15. │ └─OmnipathR:::omnipath_cache_ensure_key(...)
16. │ └─OmnipathR::omnipath_cache_key(url = url, post = post, payload = payload)
17. │ └─... %>% map_chr(digest::sha1_digest)
18. ├─purrr::map_chr(., digest::sha1_digest)
19. │ └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
20. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
21. ├─purrr::pmap(., list)
22. │ └─purrr:::pmap_("list", .l, .f, ..., .progress = .progress)
23. │ └─vctrs::vec_size_common(!!!.l, .arg = ".l", .call = .purrr_error_call)
24. └─vctrs::stop_incompatible_size(...)
25. └─vctrs:::stop_incompatible(...)
26. └─vctrs:::stop_vctrs(...)
27. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 80.772 0.082 82.185
metabolic_atlas_list_gems 54.188 7.516 142.037
curated_ligrec_stats 43.593 4.074 112.447
filter_extra_attrs 35.707 6.598 48.911
all_uniprots 26.273 1.637 40.939
extra_attrs_to_cols 25.316 2.006 33.908
extra_attr_values 24.968 2.245 37.262
giant_component 19.787 1.053 27.447
go_annot_download 16.391 1.538 18.070
filter_by_resource 15.869 0.488 29.233
has_extra_attrs 14.255 1.680 16.123
filter_intercell 11.694 0.999 18.046
extra_attrs 10.709 1.356 12.856
curated_ligand_receptor_interactions 7.812 1.230 17.588
hpo_download 5.667 0.583 7.065
find_all_paths 5.595 0.234 6.135
kegg_conv 3.948 0.863 17.058
ensembl_id_mapping_table 2.353 0.214 27.770
kinasephos 1.768 0.296 18.761
kegg_link 1.266 0.182 7.021
kegg_picture 1.234 0.109 5.594
kegg_rm_prefix 1.150 0.110 5.701
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.19.6’ ** 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 [2026-02-05 15:08:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-05 15:08:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:39] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-02-05 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-05 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-05 [2026-02-05 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-05 20:08:25 UTC; unix [2026-02-05 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6 [2026-02-05 15:08:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-02-05 15:08:39] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-05; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-02-05 15:08:40] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-02-05 15:08:40] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-02-05 15:08:40] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-02-05 15:08:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-05 15:08:40] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-02-05 15:08:40] [TRACE] [OmnipathR] Contains 8 files. [2026-02-05 15:08:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-05 15:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-05 15:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-02-05 15:08:40] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-02-05 15:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-02-05 15:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-02-05 15:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-05 15:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-02-05 15:08:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:40] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-02-05 15:08:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-05 15:08:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2026-02-05 15:08:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-05 15:08:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-05 [2026-02-05 15:08:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-05 20:08:25 UTC; unix [2026-02-05 15:08:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6 [2026-02-05 15:08:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-02-05 15:08:42] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-05; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2026-02-05 15:08:43] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2026-02-05 15:08:43] [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 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-02-05 15:08:43] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2026-02-05 15:08:43] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-05 15:08:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2026-02-05 15:08:43] [TRACE] [OmnipathR] Contains 1 files. [2026-02-05 15:08:43] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-05 15:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-05 15:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2026-02-05 15:08:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2026-02-05 15:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-02-05 15:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-02-05 15:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-05 15:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-02-05 15:08:43] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-05 15:08:43] [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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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)
[2026-02-06 02:26:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:26:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:26:59] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:26:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-06 02:26:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-05
[2026-02-06 02:26:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-05 20:08:25 UTC; unix
[2026-02-06 02:26:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-06 02:26:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-06 02:26:59] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-02-06 02:26:59] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-06 02:27:00] [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 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.5(2026-01-08); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.6(2026-02-05); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.20(2025-11-08); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-06 02:27:00] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Contains 105 files.
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-06 02:27:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:27:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-06 02:27:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-06 02:27:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-06 02:27:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-06 02:27:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-06 02:27:00] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
61.042 4.115 97.261
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.015 | 0.001 | 0.016 | |
| all_uniprots | 26.273 | 1.637 | 40.939 | |
| ancestors | 0.008 | 0.002 | 0.010 | |
| annotated_network | 1.853 | 0.105 | 4.843 | |
| annotation_categories | 80.772 | 0.082 | 82.185 | |
| annotation_resources | 0.165 | 0.030 | 0.785 | |
| annotations | 0.798 | 0.127 | 1.632 | |
| biomart_query | 1.347 | 0.340 | 4.722 | |
| bioplex1 | 0.010 | 0.001 | 0.010 | |
| bioplex2 | 0.009 | 0.000 | 0.010 | |
| bioplex3 | 0.007 | 0.002 | 0.009 | |
| bioplex_all | 0.009 | 0.000 | 0.008 | |
| bioplex_hct116_1 | 0.006 | 0.003 | 0.009 | |
| bma_motif_es | 0.843 | 0.088 | 1.643 | |
| bma_motif_vs | 0.322 | 0.093 | 0.929 | |
| chalmers_gem | 0.009 | 0.005 | 0.014 | |
| chalmers_gem_id_mapping_table | 0.012 | 0.000 | 0.012 | |
| chalmers_gem_id_type | 0.000 | 0.001 | 0.001 | |
| chalmers_gem_metabolites | 0.005 | 0.006 | 0.012 | |
| chalmers_gem_network | 0.006 | 0.007 | 0.013 | |
| chalmers_gem_raw | 0.008 | 0.005 | 0.012 | |
| chalmers_gem_reactions | 0.009 | 0.004 | 0.012 | |
| common_name | 0.123 | 0.016 | 0.139 | |
| complex_genes | 0.998 | 0.166 | 2.733 | |
| complex_resources | 0.177 | 0.008 | 0.770 | |
| complexes | 0.320 | 0.027 | 0.830 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.009 | 0.001 | 0.011 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.812 | 1.230 | 17.588 | |
| curated_ligrec_stats | 43.593 | 4.074 | 112.447 | |
| database_summary | 1.605 | 0.094 | 2.851 | |
| descendants | 0.008 | 0.001 | 0.009 | |
| ensembl_dataset | 0.123 | 0.006 | 0.130 | |
| ensembl_id_mapping_table | 2.353 | 0.214 | 27.770 | |
| ensembl_id_type | 0.000 | 0.000 | 0.001 | |
| ensembl_name | 0.293 | 0.001 | 0.294 | |
| ensembl_organisms | 0.103 | 0.012 | 0.116 | |
| ensembl_organisms_raw | 0.104 | 0.007 | 0.111 | |
| ensembl_orthology | 0.001 | 0.000 | 0.000 | |
| enzsub_graph | 2.261 | 0.107 | 4.307 | |
| enzsub_resources | 0.177 | 0.005 | 0.886 | |
| enzyme_substrate | 1.091 | 0.028 | 1.731 | |
| evex_download | 0.008 | 0.001 | 0.009 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 24.968 | 2.245 | 37.262 | |
| extra_attrs | 10.709 | 1.356 | 12.856 | |
| extra_attrs_to_cols | 25.316 | 2.006 | 33.908 | |
| filter_by_resource | 15.869 | 0.488 | 29.233 | |
| filter_extra_attrs | 35.707 | 6.598 | 48.911 | |
| filter_intercell | 11.694 | 0.999 | 18.046 | |
| filter_intercell_network | 0.019 | 0.001 | 0.019 | |
| find_all_paths | 5.595 | 0.234 | 6.135 | |
| from_evidences | 0.001 | 0.000 | 0.001 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.01 | 0.00 | 0.01 | |
| giant_component | 19.787 | 1.053 | 27.447 | |
| go_annot_download | 16.391 | 1.538 | 18.070 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.018 | 0.001 | 0.019 | |
| guide2pharma_download | 0.016 | 0.000 | 0.015 | |
| harmonizome_download | 0.015 | 0.001 | 0.016 | |
| has_extra_attrs | 14.255 | 1.680 | 16.123 | |
| hmdb_id_mapping_table | 0.021 | 0.002 | 0.023 | |
| hmdb_id_type | 0.002 | 0.000 | 0.002 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.000 | |
| hmdb_table | 0.022 | 0.001 | 0.023 | |
| homologene_download | 0.022 | 0.000 | 0.021 | |
| homologene_raw | 0.124 | 0.003 | 0.126 | |
| homologene_uniprot_orthology | 0.027 | 0.001 | 0.029 | |
| hpo_download | 5.667 | 0.583 | 7.065 | |
| htridb_download | 0.013 | 0.002 | 0.015 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.062 | 0.012 | 0.075 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 1.068 | 0.121 | 1.380 | |
| interaction_graph | 0.656 | 0.039 | 1.441 | |
| interaction_resources | 0.154 | 0.024 | 0.731 | |
| interaction_types | 0.125 | 0.003 | 0.128 | |
| intercell | 1.487 | 0.261 | 2.553 | |
| intercell_categories | 1.260 | 0.165 | 1.568 | |
| intercell_consensus_filter | 2.222 | 0.242 | 3.794 | |
| intercell_generic_categories | 0.094 | 0.007 | 0.100 | |
| intercell_network | 0.009 | 0.001 | 0.011 | |
| intercell_resources | 0.147 | 0.009 | 0.778 | |
| intercell_summary | 0.078 | 0.024 | 0.102 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.301 | 0.026 | 0.327 | |
| is_trembl | 0.559 | 0.092 | 1.153 | |
| is_uniprot | 0.027 | 0.002 | 0.058 | |
| kegg_api_templates | 0.004 | 0.004 | 0.014 | |
| kegg_conv | 3.948 | 0.863 | 17.058 | |
| kegg_databases | 0.001 | 0.000 | 0.000 | |
| kegg_ddi | 1.508 | 0.180 | 4.021 | |
| kegg_find | 1.739 | 0.201 | 4.350 | |
| kegg_info | 0.029 | 0.002 | 0.059 | |
| kegg_link | 1.266 | 0.182 | 7.021 | |
| kegg_list | 0.968 | 0.114 | 1.950 | |
| kegg_open | 0.013 | 0.001 | 0.014 | |
| kegg_operations | 0.000 | 0.000 | 0.001 | |
| kegg_organism_codes | 0.033 | 0.108 | 0.141 | |
| kegg_organisms | 0.027 | 0.008 | 0.035 | |
| kegg_pathway_annotations | 0.000 | 0.001 | 0.001 | |
| kegg_pathway_download | 0.012 | 0.003 | 0.015 | |
| kegg_pathway_list | 0.011 | 0.003 | 0.014 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 1.234 | 0.109 | 5.594 | |
| kegg_process | 0.020 | 0.000 | 0.021 | |
| kegg_query | 0.01 | 0.00 | 0.01 | |
| kegg_request | 0.102 | 0.005 | 0.106 | |
| kegg_rm_prefix | 1.150 | 0.110 | 5.701 | |
| kinasephos | 1.768 | 0.296 | 18.761 | |
| latin_name | 0.313 | 0.015 | 0.327 | |
| load_db | 0.433 | 0.077 | 0.512 | |
| metabolic_atlas_list_gems | 54.188 | 7.516 | 142.037 | |