Denes Turei
| Snapshot Date: 2025-12-12 13:40 -0500 (Fri, 12 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: f5182b3 |
| git_last_commit_date: 2025-12-10 07:50:10 -0500 (Wed, 10 Dec 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-13 11:46 -0500 (Sat, 13 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4874 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4582 |
| 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 1491/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.19.5 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: OmnipathR |
| Version: 3.19.5 |
| 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_3.19.5.tar.gz |
| StartedAt: 2025-12-13 02:06:34 -0500 (Sat, 13 Dec 2025) |
| EndedAt: 2025-12-13 02:40:37 -0500 (Sat, 13 Dec 2025) |
| EllapsedTime: 2043.3 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_3.19.5.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.19.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-12-13 02:07:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:07:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:07:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-13 02:07:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-12
[2025-12-13 02:07:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-12 20:08:54 UTC; unix
[2025-12-13 02:07:10] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-13 02:07:10] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-13 02:07:15] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-13; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-13 02:07:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-13 02:07:15] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-12); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-13 02:07:15] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-13 02:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-13 02:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-13 02:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-13 02:07:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:15] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-12-13 02:07:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:07:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:40] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:07:40] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-13 02:07:40] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-12
[2025-12-13 02:07:40] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-12 20:08:54 UTC; unix
[2025-12-13 02:07:40] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-13 02:07:40] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-13 02:07:45] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-13; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-13 02:07:45] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-13 02:07:46] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-12); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-13 02:07:46] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Contains 1 files.
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:07:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-13 02:07:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-13 02:07:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-13 02:07:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-13 02:07:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:07:46] [TRACE] [OmnipathR] Cache locked: FALSE
cosmos_ksn: no visible binding for global variable ‘enzyme_genesymbol’
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 handle
* 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 ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hpo_download
> ### Title: Downloads protein annotations from Human Phenotype Ontology
> ### Aliases: hpo_download
>
> ### ** Examples
>
> hpo_data <- hpo_download()
[2025-12-13 02:19:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-12-13 02:19:08] [TRACE] [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-12-13 02:19:08] [INFO] [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-13 02:19:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-12-13 02:19:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:09] [INFO] [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-12-13 02:19:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-12-13 02:19:09] [INFO] [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-13 02:19:09] [TRACE] [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-13 02:19:09] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-12-13 02:19:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-13 02:19:09] [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]
[2025-12-13 02:19:20] [TRACE] [OmnipathR] HTTP v2 GET: status 504.
[2025-12-13 02:19:20] [TRACE] [OmnipathR] Downloaded 0 bytes in 11.514542s from purl.obolibrary.org (0 bytes/s); Redirect: 0.248374s, DNS look up: 0.141999s, Connection: 0.233379s, Pretransfer: 0.398353s, First byte at: 11.514168s
[2025-12-13 02:19:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sat, 13 Dec 2025 07:19:09 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Server: cloudflare; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; set-cookie: __cf_bm=eWvSELLcxP_hxpwVbaryynLZo3Xty2phKvpmr1tZ0hw-1765610349.434904-1.0.1.1-_AbIgSuVVd2BPzGItqdqOocbAGJXeRmaP2TK35TLrNUUmM0M2a1Vz3HfycwM1_e15rXYq5EtS3aAXJyzCLIje2oJiQUgCTY7VcuouH9OpoxTgHRnZzzhzFBm0lDDYMyY; HttpOnly; Path=/; Domain=obolibrary.org; Expires=Sat, 13 Dec 2025 07:49:09 GMT; cf-cache-status: DYNAMIC; CF-RAY: 9ad3b10bf94ab560-IAD; HTTP/2 504 ; content-length: 92; cache-control: no-cache; content-type: text/html; date: Sat, 13 Dec 2025 07:19:20 GMT; set-cookie: _gh_sess=omkifSYcp%2BX6QLnLlixsF32KGMOt8bGFpMQ3W93lnz5TlmZY7y7w1ngrlik9H6j2eXayE1mumXjPSE4X59oTYAK%2B0n3RGqqQa7i4PRo96yVhCKNDyeb%2FreucxQ%2FRVXpW6%2Ft2Sougf7rJ3mOqVN2Gyhmoy6ZeoprKCA8zqUnmrWspda5B9XQo3OM9Nrin0KJvdxqxcjwWUHw2iuDLsulu2bAUoazJRzFmkSYoDkNVn9JeyKe4d%2BrjEWFsL9wYKWsh7%2BmHySLKKWxfz8ZTz1I75A%3D%3D--%2Br25lm0EzNTq8Y3b--sijguge345ti4InJ5HwwaQ%3D%3D; Path=/; HttpOnly; Secure; SameSite=Lax; set-cookie: _octo=GH1.1.833650730.1765610349; Path=/; Domain=github.com; Expires=Sun, 13 Dec 2026 07:19:09 GMT; Secure; SameSite=Lax; set-cookie: logged_in=no; Path=/; Domain=github.com; Expires=Sun, 13 Dec 2026 07:19:09 GMT; HttpOnly; Secure; SameSite=Lax; x-github-request-id: D2DE:21C2A5:F195AC:14F53C6:693D136D; x-frame-options: DENY; strict-transport-security: max-age=31536000; includeSubDomains; preload
[2025-12-13 02:19:20] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 504
[2025-12-13 02:19:20] [WARN] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 1/3); error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 504
[2025-12-13 02:19:25] [TRACE] [OmnipathR] Attempt 2/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-13 02:19:25] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-12-13 02:19:25] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-13 02:19:25] [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]
[2025-12-13 02:19:26] [TRACE] [OmnipathR] HTTP v2 GET: status 504.
[2025-12-13 02:19:26] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.256371s from purl.obolibrary.org (0 bytes/s); Redirect: 0.108918s, DNS look up: 0.003726s, Connection: 0.09153s, Pretransfer: 0.149168s, First byte at: 0.256098s
[2025-12-13 02:19:26] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sat, 13 Dec 2025 07:19:26 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Server: cloudflare; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; set-cookie: __cf_bm=uVUaCtqB.8YuyYuW78zfw7ZAdcQQvQU5m1dI9E28cNY-1765610366.0062766-1.0.1.1-IiiYC0cz1SVFZOJDQP34XlXpa0ggy.uA4sa2.hOt_odbNGKVs9XKolTm9M5n79rx1vm.4OWCPMQqpsP.XlQbnETvL4VbgghPjSq5EgmZMYZAtos.G9k4KaGO7zmgucw2; HttpOnly; Path=/; Domain=obolibrary.org; Expires=Sat, 13 Dec 2025 07:49:26 GMT; cf-cache-status: DYNAMIC; CF-RAY: 9ad3b1738bf05ceb-IAD; HTTP/2 504 ; content-length: 92; cache-control: no-cache; content-type: text/html; date: Sat, 13 Dec 2025 07:19:20 GMT; set-cookie: _gh_sess=KY6xicox5oBJ4qh%2F9pKwOzZmugTF%2F6Cxsnlp%2B3HLtbi5JbgVM1TzQsYyMGFQfi%2BXJWiv7ZQ4vk%2B0%2F0hAzgn0WUzwxON4HqHnb1MTvswJbmGYlrixVeAjQMagohnCpO55WOsCP9yjpNHMxhlJ%2F1Qe57pEmkxzeabitivtNP9yvh7Lpoa9NoNKnQuU4ZQ4xA%2Brk5DrlB1hBqIp7236kvgyHiF5wzrrLZ9rF6rPJ7tEWzbmuDixoJ5fQlhbTnrRO%2BEl4%2FWM9h3CP0mDiQqDhaM3rA%3D%3D--wOS2b3MAAnZkwQqI--mghNPj6x98GLU4WCqdqq%2FQ%3D%3D; Path=/; HttpOnly; Secure; SameSite=Lax; set-cookie: _octo=GH1.1.321104278.1765610366; Path=/; Domain=github.com; Expires=Sun, 13 Dec 2026 07:19:26 GMT; Secure; SameSite=Lax; set-cookie: logged_in=no; Path=/; Domain=github.com; Expires=Sun, 13 Dec 2026 07:19:26 GMT; HttpOnly; Secure; SameSite=Lax; x-github-request-id: 830C:3157B1:E00A4F:132F9FA:693D137E; x-frame-options: DENY; strict-transport-security: max-age=31536000; includeSubDomains; preload
[2025-12-13 02:19:26] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 504
[2025-12-13 02:19:26] [WARN] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 2/3); error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 504
[2025-12-13 02:19:31] [TRACE] [OmnipathR] Attempt 3/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-12-13 02:19:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-12-13 02:19:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-13 02:19:31] [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]
[2025-12-13 02:19:31] [TRACE] [OmnipathR] HTTP v2 GET: status 504.
[2025-12-13 02:19:31] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.195942s from purl.obolibrary.org (0 bytes/s); Redirect: 0.113038s, DNS look up: 0.003212s, Connection: 0.060852s, Pretransfer: 0.11504s, First byte at: 0.195706s
[2025-12-13 02:19:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sat, 13 Dec 2025 07:19:31 GMT; Content-Type: text/html; charset=iso-8859-1; Transfer-Encoding: chunked; Connection: keep-alive; Server: cloudflare; Location: https://github.com/obophenotype/human-phenotype-ontology/releases/latest/download/genes_to_phenotype.txt; set-cookie: __cf_bm=HFiUd8pm.QcFcC8RPXrs2VsbE7p25iPnqx7zaXC6RJ8-1765610371.4843664-1.0.1.1-3sQ11sPi4I7O.VB3LpS3UZ_SUbC8I2Th7uSPTIlCYiKmTqwLbqtYQGdhwWij1ftgWPsMUK1T8S8O7Mxpbjh24eZe7ABbzUuNvZdwGaJMnO_pejGHKn.iuquCK.4PJaf6; HttpOnly; Path=/; Domain=obolibrary.org; Expires=Sat, 13 Dec 2025 07:49:31 GMT; cf-cache-status: DYNAMIC; CF-RAY: 9ad3b195cd631281-IAD; HTTP/2 504 ; content-length: 92; cache-control: no-cache; content-type: text/html; date: Sat, 13 Dec 2025 07:19:20 GMT; set-cookie: _gh_sess=3gZdXgbcMBVx2gngnm3CpZh3lamSgis9SfKWChM43RPoRN93FRIhg2%2B1sQhQdb5oP1oNDjUxalzXKDMTqyWjLirO2xuVlyEJ5g4hmXBYKwVa7vLOIYKYP44e3nbgLTKh5DKfmQsdhYBy6o85lZy%2FeMSWMD0q3biv7%2F5hFmQLLKg6B8iml4AkqdZUj%2FwUxHyXJ3CTmmV%2BCS6BeKKilMnbhSmPLCzVEgGPpYdl11yKJ%2FHJUEjBr7VmrvIAI8IVNcSdeUjIiAM8j53yf3YPoPQpAA%3D%3D--DsfJl0y0x76XOnCf--jamJqIpr3MwRocnst7HHpg%3D%3D; Path=/; HttpOnly; Secure; SameSite=Lax; set-cookie: _octo=GH1.1.561537567.1765610371; Path=/; Domain=github.com; Expires=Sun, 13 Dec 2026 07:19:31 GMT; Secure; SameSite=Lax; set-cookie: logged_in=no; Path=/; Domain=github.com; Expires=Sun, 13 Dec 2026 07:19:31 GMT; HttpOnly; Secure; SameSite=Lax; x-github-request-id: 8310:AC718:E18988:1384834:693D1383; x-frame-options: DENY; strict-transport-security: max-age=31536000; includeSubDomains; preload
[2025-12-13 02:19:31] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 504
[2025-12-13 02:19:31] [ERROR] [OmnipathR] Failed to download `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt` (attempt 3/3); error: Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 504
[2025-12-13 02:19:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-13 02:19:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-12
[2025-12-13 02:19:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-12 20:08:54 UTC; unix
[2025-12-13 02:19:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-13 02:19:31] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-13 02:19:33] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-13; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-13 02:19:33] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-13 02:19:33] [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); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-12); 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 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); selectr 0.5-0(2025-11-21); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); vroom 1.6.6(2025-09-19); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-13 02:19:33] [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
Error in (function (url, curlopt = list(), callback = NULL, compr = NULL, :
Failed to open 'http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt': The requested URL returned error: 504
Calls: hpo_download ... omnipath_cache_save -> saveRDS -> exec -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 79.344 0.161 81.946
curated_ligrec_stats 42.699 3.225 146.878
filter_extra_attrs 38.117 6.005 52.295
extra_attrs_to_cols 28.035 2.013 33.565
extra_attr_values 25.402 2.084 37.707
all_uniprots 23.376 1.856 41.443
giant_component 20.342 1.615 27.781
go_annot_download 18.779 1.229 23.131
has_extra_attrs 15.121 1.664 17.327
extra_attrs 12.440 1.543 14.795
find_all_paths 12.431 0.278 14.809
filter_intercell 12.087 0.570 22.180
filter_by_resource 10.601 0.383 14.888
curated_ligand_receptor_interactions 7.514 0.939 23.486
enzsub_graph 4.595 0.278 8.943
ensembl_id_mapping_table 3.887 0.285 43.564
annotated_network 1.615 0.255 6.367
* 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 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 ‘3.19.5’ ** 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 [2025-12-12 15:09:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-12 15:09:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-12 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-12 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-12 [2025-12-12 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-12 20:08:54 UTC; unix [2025-12-12 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5 [2025-12-12 15:09:08] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-12 15:09:08] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-12; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-12 15:09:08] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-12 15:09:09] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-12); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2025-12-12 15:09:09] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-12-12 15:09:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-12 15:09:09] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-12 15:09:09] [TRACE] [OmnipathR] Contains 9 files. [2025-12-12 15:09:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-12 15:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-12 15:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-12 15:09:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-12-12 15:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-12 15:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-12 15:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-12 15:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-12 15:09:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:09] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-12-12 15:09:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-12 15:09:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:11] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-12 15:09:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-12 15:09:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-12 [2025-12-12 15:09:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-12 20:08:54 UTC; unix [2025-12-12 15:09:11] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5 [2025-12-12 15:09:11] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-12 15:09:11] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-12; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-12 15:09:11] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-12 15:09:12] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-12); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2025-12-12 15:09:12] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-12-12 15:09:12] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-12 15:09:12] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-12 15:09:12] [TRACE] [OmnipathR] Contains 1 files. [2025-12-12 15:09:12] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-12 15:09:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-12 15:09:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-12 15:09:12] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-12-12 15:09:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-12 15:09:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-12 15:09:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-12 15:09:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-12 15:09:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-12 15:09:12] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
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> #!/usr/bin/env Rscript
>
> #
> # This file is part of the `OmnipathR` R package
> #
> # Copyright
> # 2018-2024
> # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> # File author(s): Alberto Valdeolivas
> # Dénes Türei (turei.denes@gmail.com)
> # Attila Gábor
> #
> # Distributed under the MIT (Expat) License.
> # See accompanying file `LICENSE` or find a copy at
> # https://directory.fsf.org/wiki/License:Expat
> #
> # Website: https://r.omnipathdb.org/
> # Git repo: https://github.com/saezlab/OmnipathR
> #
>
>
> library(testthat)
> library(OmnipathR)
[2025-12-13 02:19:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:19:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:38] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:19:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-12-13 02:19:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-12
[2025-12-13 02:19:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-12 20:08:54 UTC; unix
[2025-12-13 02:19:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.5
[2025-12-13 02:19:38] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-12-13 02:19:42] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-13; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-12-13 02:19:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-12-13 02:19:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); digest 0.6.39(2025-11-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(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 1.50(2025-03-16); later 1.4.4(2025-08-27); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); memoise 2.0.1(2021-11-26); OmnipathR 3.19.5(2025-12-12); 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 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); testthat 3.3.1(2025-11-25); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2025-12-13 02:19:42] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-12-13 02:19:42] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-12-13 02:19:42] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:19:42] [TRACE] [OmnipathR] Contains 45 files.
[2025-12-13 02:19:42] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-12-13 02:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-13 02:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-12-13 02:19:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-12-13 02:19:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-12-13 02:19:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-12-13 02:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-12-13 02:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-12-13 02:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-13 02:19:43] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
[ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ]
>
> proc.time()
user system elapsed
63.950 4.292 125.261
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.017 | 0.000 | 0.018 | |
| all_uniprots | 23.376 | 1.856 | 41.443 | |
| ancestors | 0.007 | 0.002 | 0.008 | |
| annotated_network | 1.615 | 0.255 | 6.367 | |
| annotation_categories | 79.344 | 0.161 | 81.946 | |
| annotation_resources | 0.129 | 0.019 | 1.083 | |
| annotations | 0.736 | 0.248 | 2.104 | |
| biomart_query | 1.369 | 0.088 | 2.504 | |
| bioplex1 | 0.009 | 0.002 | 0.011 | |
| bioplex2 | 0.008 | 0.002 | 0.010 | |
| bioplex3 | 0.008 | 0.001 | 0.009 | |
| bioplex_all | 0.008 | 0.002 | 0.009 | |
| bioplex_hct116_1 | 0.009 | 0.000 | 0.009 | |
| bma_motif_es | 0.917 | 0.208 | 2.385 | |
| bma_motif_vs | 0.350 | 0.021 | 1.334 | |
| chalmers_gem | 0.010 | 0.001 | 0.012 | |
| chalmers_gem_id_mapping_table | 0.009 | 0.000 | 0.010 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.003 | |
| chalmers_gem_metabolites | 0.008 | 0.000 | 0.009 | |
| chalmers_gem_network | 0.008 | 0.001 | 0.009 | |
| chalmers_gem_raw | 0.030 | 0.002 | 0.032 | |
| chalmers_gem_reactions | 0.006 | 0.002 | 0.008 | |
| common_name | 0.124 | 0.009 | 0.133 | |
| complex_genes | 0.843 | 0.088 | 3.611 | |
| complex_resources | 0.169 | 0.006 | 1.030 | |
| complexes | 0.351 | 0.024 | 1.400 | |
| consensuspathdb_download | 0.001 | 0.000 | 0.000 | |
| consensuspathdb_raw_table | 0.008 | 0.000 | 0.009 | |
| cosmos_pkn | 0.000 | 0.000 | 0.001 | |
| curated_ligand_receptor_interactions | 7.514 | 0.939 | 23.486 | |
| curated_ligrec_stats | 42.699 | 3.225 | 146.878 | |
| database_summary | 1.736 | 0.113 | 4.073 | |
| descendants | 0.007 | 0.002 | 0.009 | |
| ensembl_dataset | 0.047 | 0.002 | 0.050 | |
| ensembl_id_mapping_table | 3.887 | 0.285 | 43.564 | |
| ensembl_id_type | 0.003 | 0.002 | 0.005 | |
| ensembl_name | 0.769 | 0.013 | 0.906 | |
| ensembl_organisms | 0.261 | 0.024 | 0.287 | |
| ensembl_organisms_raw | 0.250 | 0.016 | 0.266 | |
| ensembl_orthology | 0.001 | 0.001 | 0.001 | |
| enzsub_graph | 4.595 | 0.278 | 8.943 | |
| enzsub_resources | 0.175 | 0.006 | 1.089 | |
| enzyme_substrate | 2.190 | 0.057 | 4.227 | |
| evex_download | 0.019 | 0.001 | 0.020 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 25.402 | 2.084 | 37.707 | |
| extra_attrs | 12.440 | 1.543 | 14.795 | |
| extra_attrs_to_cols | 28.035 | 2.013 | 33.565 | |
| filter_by_resource | 10.601 | 0.383 | 14.888 | |
| filter_extra_attrs | 38.117 | 6.005 | 52.295 | |
| filter_intercell | 12.087 | 0.570 | 22.180 | |
| filter_intercell_network | 0.049 | 0.002 | 0.052 | |
| find_all_paths | 12.431 | 0.278 | 14.809 | |
| from_evidences | 0.000 | 0.001 | 0.000 | |
| get_db | 0.000 | 0.001 | 0.000 | |
| get_ontology_db | 0.015 | 0.002 | 0.018 | |
| giant_component | 20.342 | 1.615 | 27.781 | |
| go_annot_download | 18.779 | 1.229 | 23.131 | |
| go_annot_slim | 0.000 | 0.000 | 0.001 | |
| go_ontology_download | 0.016 | 0.001 | 0.017 | |
| guide2pharma_download | 0.013 | 0.003 | 0.016 | |
| harmonizome_download | 0.015 | 0.001 | 0.016 | |
| has_extra_attrs | 15.121 | 1.664 | 17.327 | |
| hmdb_id_mapping_table | 0.022 | 0.001 | 0.022 | |
| hmdb_id_type | 0.005 | 0.000 | 0.005 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_table | 0.022 | 0.001 | 0.023 | |
| homologene_download | 0.020 | 0.001 | 0.022 | |
| homologene_raw | 0.122 | 0.004 | 0.125 | |
| homologene_uniprot_orthology | 0.022 | 0.001 | 0.022 | |