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This page was generated on 2025-08-12 12:08 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1473/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.17.4  (landing page)
Denes Turei
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 Aug 2025)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: a7f3b9d
git_last_commit_date: 2025-07-16 10:03:35 -0400 (Wed, 16 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for OmnipathR on palomino8

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.

raw results


Summary

Package: OmnipathR
Version: 3.17.4
Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings OmnipathR_3.17.4.tar.gz
StartedAt: 2025-08-12 05:03:53 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 05:21:18 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 1044.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: OmnipathR.Rcheck
Warnings: 4

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings OmnipathR_3.17.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.17.4'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 ... NOTE
[2025-08-12 05:04:37] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:04:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:37] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:04:37] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-12 05:04:37] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-12 05:04:37] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-11 19:28:03 UTC; windows
[2025-08-12 05:04:37] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-12 05:04:37] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpGQUHYB/file19f7c40b64153". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpGQUHYB/file19f7c40b64153 -V' had status 1
[2025-08-12 05:04:38] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-12; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-12 05:04:38] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-12 05:04:39] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-11); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-12 05:04:39] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:39] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:39] [TRACE]   [OmnipathR] Cache locked: FALSE

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-08-12 05:04:52] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:04:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:52] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:04:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-12 05:04:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-12 05:04:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-11 19:28:03 UTC; windows
[2025-08-12 05:04:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-12 05:04:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpuKblHO/file1ccc828b0b8c". Did you mean command "update"?
[2025-08-12 05:04:53] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-12; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-12 05:04:53] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-12 05:04:54] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-11); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-12 05:04:54] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:54] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-12 05:04:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:04:54] [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 ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmpquv8jJ/file202cc1c943a2e". Did you mean command "preview"?
* checking S3 generic/method consistency ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpIV9aMb/file37b84d77213a". Did you mean command "update"?
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpMPkq5S/file13acc626e1366". Did you mean command "create"?
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpYXOoJ9/file2001017f330c". Did you mean command "update"?
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
[2025-08-12 05:05:21] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:05:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:05:21] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:05:21] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-12 05:05:21] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-12 05:05:21] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-11 19:28:03 UTC; windows
[2025-08-12 05:05:21] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-12 05:05:21] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpUvzJax/file7e30544031cf". Did you mean command "preview"?
[2025-08-12 05:05:22] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-12; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-12 05:05:22] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-12 05:05:23] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-11); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-12 05:05:23] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:05:23] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:05:23] [TRACE]   [OmnipathR] Cache locked: FALSE
taxon_names_table: no visible binding for global variable
  'latin_name_uniprot'
taxon_names_table: no visible binding for global variable
  'latin_name_ensembl'
taxon_names_table: no visible binding for global variable
  'latin_name_oma'
taxon_names_table: no visible binding for global variable
  'common_name_ensembl'
taxon_names_table: no visible binding for global variable
  'common_name_uniprot'
Undefined global functions or variables:
  common_name_ensembl common_name_uniprot latin_name_ensembl
  latin_name_oma latin_name_uniprot
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmpyi6y1A/file3b40102f1e6d". Did you mean command "update"?
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpYLKxSq/file105c07d986f0e". Did you mean command "update"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpINfHqC/file22c6042527e25". Did you mean command "update"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpuqWkMK/file20ac46a223f8e". Did you mean command "create"?
* checking Rd \usage sections ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpOy2RV9/file10248374e3953". Did you mean command "update"?
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
annotation_categories                76.70   0.05   77.61
curated_ligrec_stats                 41.05   1.85   96.69
omnipath-interactions                37.07   1.72   86.08
all_uniprots                         26.91   2.34   40.75
uniprot_organisms                    23.83   2.06   26.94
filter_extra_attrs                   21.25   0.60   22.45
go_annot_download                    18.63   1.39   18.01
nichenet_gr_network_omnipath         18.31   0.97   20.03
extra_attrs_to_cols                  14.77   0.36   15.15
with_extra_attrs                     14.13   0.52   15.28
nichenet_signaling_network_omnipath  13.01   0.70   14.42
giant_component                      12.76   0.56   36.50
extra_attr_values                    12.52   0.28   13.36
pivot_annotations                    11.45   0.80   13.95
omnipath_for_cosmos                  10.37   0.20   20.09
has_extra_attrs                       9.61   0.21   18.64
filter_by_resource                    9.48   0.29   10.53
translate_ids_multi                   8.62   0.18   16.72
static_table                          7.68   0.40    8.56
filter_intercell                      7.27   0.58    7.64
curated_ligand_receptor_interactions  6.55   0.39   14.52
print_interactions                    6.55   0.30    8.77
find_all_paths                        6.67   0.13    7.05
extra_attrs                           6.40   0.11    6.52
signed_ptms                           5.72   0.03    6.28
pubmed_open                           4.52   0.46    7.95
ensembl_id_mapping_table              2.25   0.10    9.57
intercell_consensus_filter            2.12   0.16    9.13
kegg_conv                             1.81   0.08   10.52
translate_ids                         1.53   0.20   11.64
uniprot_full_id_mapping_table         1.17   0.12   12.37
kegg_link                             0.80   0.02    5.19
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 6 NOTEs
See
  'F:/biocbuild/bbs-3.22-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.


Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'OmnipathR' ...
** this is package 'OmnipathR' version '3.17.4'
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-08-11 15:31:39] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 15:31:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:39] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-11 15:31:39] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-11 15:31:39] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-11 15:31:39] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-11 19:28:03 UTC; windows
[2025-08-11 15:31:39] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-11 15:31:39] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp0C3wnf/file158585d392f1c". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp0C3wnf/file158585d392f1c -V' had status 1
[2025-08-11 15:31:42] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-11; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-11 15:31:43] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-11 15:31:43] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-11); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-11 15:31:43] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:43] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:43] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-08-11 15:31:46] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 15:31:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:46] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-11 15:31:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-11 15:31:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-11 15:31:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-11 19:28:03 UTC; windows
[2025-08-11 15:31:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-11 15:31:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp8w8OoF/file3cc013a42e98". Did you mean command "create"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp8w8OoF/file3cc013a42e98 -V' had status 1
[2025-08-11 15:31:47] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-11; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-11 15:31:47] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-11 15:31:47] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-11); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-11 15:31:47] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-11 15:31:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-11 15:31:47] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-11 15:31:47] [TRACE]   [OmnipathR] Contains 1 files.
[2025-08-11 15:31:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-11 15:31:47] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-11 15:31:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:47] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-11 15:31:48] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> #!/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)
[2025-08-12 05:19:27] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:19:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:19:27] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:19:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-12 05:19:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-08-11
[2025-08-12 05:19:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-11 19:28:03 UTC; windows
[2025-08-12 05:19:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-12 05:19:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpGIihjp/file215b416d73649". Did you mean command "update"?
[2025-08-12 05:19:28] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=C; collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-12; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-12 05:19:29] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-08-12 05:19:29] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-11); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); testthat 3.2.3(2025-01-13); tibble 3.3.0(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 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-12 05:19:29] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Contains 22 files.
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:19:29] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-12 05:19:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:19:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-12 05:19:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:19:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-12 05:19:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-08-12 05:19:30] [TRACE]   [OmnipathR] Cache locked: FALSE
Warning message:
In system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpGIihjp/file215b416d73649 -V' had status 1
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]

[ FAIL 0 | WARN 12 | SKIP 0 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
  51.90    5.28   80.03 

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR000
all_uniprot_acs0.010.000.01
all_uniprots26.91 2.3440.75
ancestors000
annotated_network1.500.083.75
annotation_categories76.70 0.0577.61
annotation_resources0.030.000.55
annotations0.620.011.97
biomart_query1.330.063.34
bioplex10.020.000.02
bioplex2000
bioplex30.010.000.01
bioplex_all000
bioplex_hct116_1000
bma_motif_es0.810.071.83
bma_motif_vs0.220.000.72
chalmers_gem000
chalmers_gem_id_mapping_table0.020.000.02
chalmers_gem_id_type000
chalmers_gem_metabolites0.010.000.01
chalmers_gem_network000
chalmers_gem_raw000
chalmers_gem_reactions0.020.000.01
common_name0.170.000.17
complex_genes0.800.031.97
complex_resources0.060.000.57
complexes0.220.000.76
consensuspathdb_download000
consensuspathdb_raw_table0.030.000.03
cosmos_pkn000
curated_ligand_receptor_interactions 6.55 0.3914.52
curated_ligrec_stats41.05 1.8596.69
database_summary1.590.042.35
descendants000
ensembl_dataset0.080.000.07
ensembl_id_mapping_table2.250.109.57
ensembl_id_type000
ensembl_name0.350.000.34
ensembl_organisms0.120.000.56
ensembl_organisms_raw0.110.010.13
ensembl_orthology000
enzsub_graph2.110.103.39
enzsub_resources0.050.000.56
enzyme_substrate1.000.001.48
evex_download0.010.000.02
evidences000
extra_attr_values12.52 0.2813.36
extra_attrs6.400.116.52
extra_attrs_to_cols14.77 0.3615.15
filter_by_resource 9.48 0.2910.53
filter_extra_attrs21.25 0.6022.45
filter_intercell7.270.587.64
filter_intercell_network0.010.000.01
find_all_paths6.670.137.05
from_evidences000
get_db000
get_ontology_db0.020.000.02
giant_component12.76 0.5636.50
go_annot_download18.63 1.3918.01
go_annot_slim000
go_ontology_download0.020.000.02
guide2pharma_download0.010.000.01
harmonizome_download0.000.020.02
has_extra_attrs 9.61 0.2118.64
hmdb_id_mapping_table0.020.000.01
hmdb_id_type000
hmdb_metabolite_fields000
hmdb_protein_fields000
hmdb_table0.010.000.02
homologene_download0.020.000.01
homologene_raw0.090.000.10
homologene_uniprot_orthology0.020.000.01
hpo_download3.640.234.03
htridb_download0.010.000.02
id_translation_resources000
id_types0.050.000.04
inbiomap_download000
inbiomap_raw000
interaction_datasets0.720.081.16
interaction_graph0.470.021.00
interaction_resources0.060.000.56
interaction_types0.120.000.13
intercell1.050.061.92
intercell_categories0.850.001.56
intercell_consensus_filter2.120.169.13
intercell_generic_categories0.140.000.20
intercell_network0.020.000.02
intercell_resources0.060.000.73
intercell_summary0.120.010.27
is_ontology_id000
is_swissprot0.090.000.10
is_trembl0.100.020.11
is_uniprot0.060.000.06
kegg_api_templates0.020.000.01
kegg_conv 1.81 0.0810.52
kegg_databases000
kegg_ddi0.760.063.47
kegg_find0.770.032.60
kegg_info0.010.000.01
kegg_link0.800.025.19
kegg_list0.660.011.64
kegg_open000
kegg_operations000
kegg_organism_codes0.040.020.06
kegg_organisms0.020.000.02
kegg_pathway_annotations000
kegg_pathway_download000
kegg_pathway_list0.020.000.02
kegg_pathways_download000
kegg_picture1.200.022.92
kegg_process0.010.000.02
kegg_query0.020.000.01
kegg_request0.060.000.07
kegg_rm_prefix0.740.083.92
latin_name0.390.030.42
load_db0.090.000.09
metalinksdb_sqlite1.110.062.41
metalinksdb_table0.170.020.19
metalinksdb_tables0.030.000.03
ncbi_taxid0.360.030.39
nichenet_build_model000
nichenet_expression_data0.020.000.01
nichenet_gr_network0.030.000.05
nichenet_gr_network_evex0.020.000.02
nichenet_gr_network_harmonizome0.000.010.01
nichenet_gr_network_htridb0.010.000.02
nichenet_gr_network_omnipath18.31 0.9720.03
nichenet_gr_network_pathwaycommons0.020.000.01
nichenet_gr_network_regnetwork0.060.000.06
nichenet_gr_network_remap0.010.000.02
nichenet_gr_network_trrust0.020.000.01
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network0.020.020.03
nichenet_lr_network_guide2pharma0.000.000.02
nichenet_lr_network_omnipath0.030.000.03
nichenet_lr_network_ramilowski000
nichenet_main000
nichenet_networks0.030.020.05
nichenet_optimization000
nichenet_remove_orphan_ligands0.030.010.05
nichenet_results_dir000
nichenet_signaling_network0.050.000.04
nichenet_signaling_network_cpdb000
nichenet_signaling_network_evex0.020.000.02
nichenet_signaling_network_harmonizome0.000.020.02
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath13.01 0.7014.42
nichenet_signaling_network_pathwaycommons0.020.000.01
nichenet_signaling_network_vinayagam0.000.000.02
nichenet_test000
nichenet_workarounds000
obo_parser0.120.030.34
oma_code0.170.050.30
oma_organisms0.110.000.14
oma_pairwise0.020.000.02
oma_pairwise_genesymbols0.020.000.01
oma_pairwise_translated000
omnipath-interactions37.07 1.7286.08
omnipath_cache_autoclean000
omnipath_cache_clean0.020.000.02
omnipath_cache_clean_db0.090.000.09
omnipath_cache_download_ready0.530.050.75
omnipath_cache_filter_versions0.110.010.16
omnipath_cache_get0.110.020.12
omnipath_cache_key000
omnipath_cache_latest_or_new0.070.020.07
omnipath_cache_load0.540.011.58
omnipath_cache_move_in0.170.050.36
omnipath_cache_remove0.130.050.19
omnipath_cache_save0.230.000.48
omnipath_cache_search000
omnipath_cache_set_ext0.140.000.14
omnipath_cache_update_status0.130.030.18
omnipath_cache_wipe000
omnipath_config_path000
omnipath_for_cosmos10.37 0.2020.09
omnipath_load_config000
omnipath_log000
omnipath_logfile000
omnipath_msg0.000.000.02
omnipath_query4.090.034.12
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir0.020.020.03
omnipath_set_console_loglevel000
omnipath_set_logfile_loglevel000
omnipath_set_loglevel0.000.010.02
omnipath_show_db0.060.000.06
omnipath_unlock_cache_db000
only_from000
ontology_ensure_id000
ontology_ensure_name000
ontology_name_id000
organism_for0.230.020.25
pathwaycommons_download000
pivot_annotations11.45 0.8013.95
preppi_download000
preppi_filter000
print_bma_motif_es0.690.061.78
print_bma_motif_vs0.170.000.67
print_interactions6.550.308.77
print_path_es0.990.042.08
print_path_vs2.680.144.48
pubmed_open4.520.467.95
query_info0.510.030.94
ramilowski_download000
ramp_id_mapping_table000
ramp_id_type000
ramp_sqlite000
ramp_table000
ramp_tables000
regnetwork_directions000
regnetwork_download0.020.000.01
relations_list_to_table0.110.020.28
relations_table_to_graph000
relations_table_to_list0.060.000.10
remap_dorothea_download000
remap_filtered000
remap_tf_target_download000
resource_info0.550.050.97
resources0.050.000.56
resources_colname1.020.091.91
resources_in4.390.024.41
show_network000
signed_ptms5.720.036.28
simplify_intercell_network000
static_table7.680.408.56
static_tables0.080.000.16
stitch_actions000
stitch_links000
stitch_network000
stitch_remove_prefixes0.020.000.01
swap_relations0.060.000.11
swissprots_only0.170.000.17
tfcensus_download0.610.050.72
translate_ids 1.53 0.2011.64
translate_ids_multi 8.62 0.1816.72
trembls_only0.570.000.56
trrust_download000
uniprot_full_id_mapping_table 1.17 0.1212.37
uniprot_genesymbol_cleanup000
uniprot_id_mapping_table000
uniprot_id_type000
uniprot_idmapping_id_types0.500.030.85
uniprot_organisms23.83 2.0626.94
unique_intercell_network000
unnest_evidences000
uploadlists_id_type000
vinayagam_download000
walk_ontology_tree000
with_extra_attrs14.13 0.5215.28
with_references1.010.032.08
zenodo_download000