Denes Turei
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:07 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (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 1473/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.17.4 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | TIMEOUT | |||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the OmnipathR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| 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: 2025-08-15 06:01:45 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 06:19:48 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 1083.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 4 |
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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
###
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* 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
[2025-08-15 06:02:31] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:02:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:31] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:02:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-15 06:02:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-15 06:02:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-15 06:02:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-15 06:02:31] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpUbU0Sk/filec046b1428f". 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/RtmpUbU0Sk/filec046b1428f -V' had status 1
[2025-08-15 06:02:32] [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=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-15 06:02:33] [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]
[2025-08-15 06:02:33] [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 2.3.2(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(2025-08-14); 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)
[2025-08-15 06:02:33] [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
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:33] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-15 06:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-15 06:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-15 06:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:33] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-15 06:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:33] [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
[2025-08-15 06:02:46] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:02:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:46] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:02:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-15 06:02:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-15 06:02:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-15 06:02:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-15 06:02:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpcNgUu0/file6e1c7f8a162b". Did you mean command "update"?
[2025-08-15 06:02:48] [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=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-15 06:02:48] [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]
[2025-08-15 06:02:48] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(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(2025-08-14); 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)
[2025-08-15 06:02:48] [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
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:02:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:48] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-15 06:02:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-15 06:02:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-15 06:02:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:48] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-15 06:02:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:02:48] [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/Rtmpu49nXJ/filed5e07f7a7272". Did you mean command "update"?
* checking S3 generic/method consistency ... WARNING
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp6FfjfQ/file182183a515332". 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/RtmpkvNlsa/file1148486e31ec". Did you mean command "preview"?
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/RtmpU55G3L/file1eab02db71eea". Did you mean command "create"?
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
[2025-08-15 06:03:15] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:03:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:03:15] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:03:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-15 06:03:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-15 06:03:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-15 06:03:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-15 06:03:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpyKOEdx/file21f1074f036ec". Did you mean command "update"?
[2025-08-15 06:03:16] [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=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-15 06:03:16] [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]
[2025-08-15 06:03:17] [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(2025-08-14); 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)
[2025-08-15 06:03:17] [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
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:03:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:03:17] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-15 06:03:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-15 06:03:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-15 06:03:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:03:17] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-15 06:03:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:03:17] [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/RtmpEFA8ER/file16a81490623d". 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/RtmpKO5RzK/file169f05bd86141". Did you mean command "update"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpcvVuRK/file21be44e946e52". Did you mean command "preview"?
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpSuqdva/file80bc1a4d2800". Did you mean command "preview"?
* checking Rd \usage sections ... NOTE
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpyACipO/file798458577a0". 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 87.07 0.08 87.89
curated_ligrec_stats 42.48 1.86 99.27
omnipath-interactions 35.28 1.30 52.25
all_uniprots 27.56 2.06 44.53
uniprot_organisms 24.32 2.24 27.50
filter_extra_attrs 25.60 0.57 48.00
nichenet_gr_network_omnipath 21.69 1.73 38.13
go_annot_download 16.85 1.42 17.41
extra_attrs_to_cols 15.68 0.42 16.12
with_extra_attrs 15.55 0.50 16.81
giant_component 14.50 0.38 24.13
nichenet_signaling_network_omnipath 14.26 0.43 25.35
extra_attr_values 13.00 0.29 14.00
pivot_annotations 12.16 0.84 15.17
omnipath_for_cosmos 10.83 0.41 19.14
translate_ids_multi 9.72 0.22 17.60
filter_by_resource 9.11 0.42 10.13
filter_intercell 8.92 0.50 9.39
has_extra_attrs 8.99 0.23 22.91
find_all_paths 7.97 0.20 8.83
curated_ligand_receptor_interactions 7.35 0.36 14.83
extra_attrs 7.55 0.16 7.70
print_interactions 7.37 0.25 9.56
static_table 7.13 0.38 7.89
signed_ptms 6.07 0.06 6.68
pubmed_open 5.08 0.32 6.10
ensembl_id_mapping_table 2.11 0.15 10.43
kegg_conv 1.61 0.08 9.25
translate_ids 1.34 0.20 14.48
uniprot_full_id_mapping_table 1.15 0.28 15.60
* 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.
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
[2025-08-14 15:30:26] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-14 15:30:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:26] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-14 15:30:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-14 15:30:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-14 15:30:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-14 15:30:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-14 15:30:26] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpYpeN5s/file1553c48b839e6". Did you mean command "preview"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", :
running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpYpeN5s/file1553c48b839e6 -V' had status 1
[2025-08-14 15:30:30] [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=2025-08-14; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-14 15:30:35] [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]
[2025-08-14 15:30:35] [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(2025-08-14); 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)
[2025-08-14 15:30:35] [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
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-14 15:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:35] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-14 15:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-14 15:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-14 15:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-14 15:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:35] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-08-14 15:30:38] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-14 15:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:38] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-14 15:30:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-14 15:30:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-14 15:30:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-14 15:30:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-14 15:30:38] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpclydMB/file17c74598d4b85". 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/RtmpclydMB/file17c74598d4b85 -V' had status 1
[2025-08-14 15:30:39] [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=2025-08-14; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-14 15:30:39] [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]
[2025-08-14 15:30:40] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(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(2025-08-14); 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)
[2025-08-14 15:30:40] [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
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-14 15:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:40] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-14 15:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-14 15:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-14 15:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-14 15:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-14 15:30:40] [TRACE] [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)
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
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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)
[2025-08-15 06:17:58] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:17:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:17:58] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:17:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-15 06:17:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14
[2025-08-15 06:17:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:27:25 UTC; windows
[2025-08-15 06:17:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-15 06:17:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp0aguWZ/file1e3cc8d37db". Did you mean command "update"?
[2025-08-15 06:17:59] [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=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-08-15 06:17:59] [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]
[2025-08-15 06:18:00] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(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(2025-08-14); 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)
[2025-08-15 06:18:00] [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
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Contains 22 files.
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-15 06:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:18:00] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-15 06:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-15 06:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-15 06:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:18:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-15 06:18:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-15 06:18:00] [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/Rtmp0aguWZ/file1e3cc8d37db -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
56.56 4.50 83.57
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.04 | 0.00 | 0.03 | |
| all_uniprots | 27.56 | 2.06 | 44.53 | |
| ancestors | 0.02 | 0.00 | 0.02 | |
| annotated_network | 1.55 | 0.11 | 3.96 | |
| annotation_categories | 87.07 | 0.08 | 87.89 | |
| annotation_resources | 0.08 | 0.00 | 0.58 | |
| annotations | 0.72 | 0.09 | 1.66 | |
| biomart_query | 1.72 | 0.03 | 2.69 | |
| bioplex1 | 0.02 | 0.00 | 0.01 | |
| bioplex2 | 0.01 | 0.00 | 0.02 | |
| bioplex3 | 0 | 0 | 0 | |
| bioplex_all | 0.02 | 0.00 | 0.01 | |
| bioplex_hct116_1 | 0.01 | 0.00 | 0.02 | |
| bma_motif_es | 0.80 | 0.05 | 1.72 | |
| bma_motif_vs | 0.20 | 0.00 | 0.72 | |
| chalmers_gem | 0.02 | 0.00 | 0.01 | |
| chalmers_gem_id_mapping_table | 0.01 | 0.00 | 0.02 | |
| chalmers_gem_id_type | 0 | 0 | 0 | |
| chalmers_gem_metabolites | 0 | 0 | 0 | |
| chalmers_gem_network | 0.03 | 0.00 | 0.03 | |
| chalmers_gem_raw | 0 | 0 | 0 | |
| chalmers_gem_reactions | 0.02 | 0.00 | 0.02 | |
| common_name | 0.18 | 0.00 | 0.19 | |
| complex_genes | 0.88 | 0.02 | 2.23 | |
| complex_resources | 0.05 | 0.00 | 0.55 | |
| complexes | 0.24 | 0.00 | 0.74 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0.04 | 0.00 | 0.05 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 7.35 | 0.36 | 14.83 | |
| curated_ligrec_stats | 42.48 | 1.86 | 99.27 | |
| database_summary | 1.67 | 0.03 | 2.43 | |
| descendants | 0.02 | 0.00 | 0.02 | |
| ensembl_dataset | 0.06 | 0.02 | 0.08 | |
| ensembl_id_mapping_table | 2.11 | 0.15 | 10.43 | |
| ensembl_id_type | 0.02 | 0.00 | 0.02 | |
| ensembl_name | 0.48 | 0.00 | 0.48 | |
| ensembl_organisms | 0.14 | 0.02 | 0.16 | |
| ensembl_organisms_raw | 0.13 | 0.00 | 0.13 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.50 | 0.11 | 3.98 | |
| enzsub_resources | 0.06 | 0.02 | 0.58 | |
| enzyme_substrate | 1.23 | 0.04 | 1.79 | |
| evex_download | 0.00 | 0.02 | 0.02 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 13.00 | 0.29 | 14.00 | |
| extra_attrs | 7.55 | 0.16 | 7.70 | |
| extra_attrs_to_cols | 15.68 | 0.42 | 16.12 | |
| filter_by_resource | 9.11 | 0.42 | 10.13 | |
| filter_extra_attrs | 25.60 | 0.57 | 48.00 | |
| filter_intercell | 8.92 | 0.50 | 9.39 | |
| filter_intercell_network | 0.03 | 0.00 | 0.03 | |
| find_all_paths | 7.97 | 0.20 | 8.83 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.01 | 0.00 | 0.01 | |
| giant_component | 14.50 | 0.38 | 24.13 | |
| go_annot_download | 16.85 | 1.42 | 17.41 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.14 | 0.00 | 0.14 | |
| guide2pharma_download | 0.02 | 0.00 | 0.02 | |
| harmonizome_download | 0.01 | 0.00 | 0.01 | |
| has_extra_attrs | 8.99 | 0.23 | 22.91 | |
| hmdb_id_mapping_table | 0.01 | 0.00 | 0.02 | |
| hmdb_id_type | 0 | 0 | 0 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.02 | 0.00 | 0.01 | |
| homologene_download | 0.02 | 0.00 | 0.02 | |
| homologene_raw | 0.15 | 0.00 | 0.15 | |
| homologene_uniprot_orthology | 0.02 | 0.00 | 0.02 | |
| hpo_download | 3.28 | 0.35 | 3.69 | |
| htridb_download | 0 | 0 | 0 | |
| id_translation_resources | 0.00 | 0.01 | 0.00 | |
| id_types | 0.05 | 0.00 | 0.05 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.86 | 0.02 | 1.25 | |
| interaction_graph | 0.51 | 0.00 | 1.03 | |
| interaction_resources | 0.05 | 0.00 | 0.56 | |
| interaction_types | 0.09 | 0.01 | 0.11 | |
| intercell | 1.02 | 0.11 | 1.88 | |
| intercell_categories | 0.68 | 0.08 | 1.15 | |
| intercell_consensus_filter | 1.68 | 0.12 | 2.53 | |
| intercell_generic_categories | 0.09 | 0.04 | 0.13 | |
| intercell_network | 0.02 | 0.00 | 0.01 | |
| intercell_resources | 0.03 | 0.01 | 0.57 | |
| intercell_summary | 0.11 | 0.02 | 0.12 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.07 | 0.01 | 0.10 | |
| is_trembl | 0.08 | 0.02 | 0.09 | |
| is_uniprot | 0.00 | 0.01 | 0.02 | |
| kegg_api_templates | 0.00 | 0.02 | 0.01 | |
| kegg_conv | 1.61 | 0.08 | 9.25 | |
| kegg_databases | 0 | 0 | 0 | |
| kegg_ddi | 0.80 | 0.03 | 2.28 | |
| kegg_find | 0.83 | 0.00 | 2.71 | |
| kegg_info | 0.01 | 0.00 | 0.01 | |
| kegg_link | 0.89 | 0.03 | 4.75 | |
| kegg_list | 0.85 | 0.00 | 1.84 | |
| kegg_open | 0 | 0 | 0 | |
| kegg_operations | 0 | 0 | 0 | |
| kegg_organism_codes | 0.05 | 0.03 | 0.09 | |
| kegg_organisms | 0.02 | 0.02 | 0.05 | |
| kegg_pathway_annotations | 0.01 | 0.00 | 0.02 | |
| kegg_pathway_download | 0.02 | 0.00 | 0.01 | |
| kegg_pathway_list | 0.01 | 0.00 | 0.02 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 1.21 | 0.00 | 2.92 | |
| kegg_process | 0.03 | 0.00 | 0.41 | |
| kegg_query | 0.01 | 0.00 | 0.01 | |
| kegg_request | 0.08 | 0.01 | 0.10 | |
| kegg_rm_prefix | 0.91 | 0.02 | 4.40 | |
| latin_name | 0.32 | 0.01 | 0.35 | |
| load_db | 0.10 | 0.00 | 0.09 | |
| metalinksdb_sqlite | 1.19 | 0.05 | 2.72 | |
| metalinksdb_table | 0.18 | 0.09 | 0.49 | |
| metalinksdb_tables | 0.02 | 0.00 | 0.01 | |
| ncbi_taxid | 0.39 | 0.00 | 0.41 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.02 | 0.00 | 0.02 | |
| nichenet_gr_network | 0.03 | 0.00 | 0.03 | |
| nichenet_gr_network_evex | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_harmonizome | 0.02 | 0.00 | 0.02 | |
| nichenet_gr_network_htridb | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_omnipath | 21.69 | 1.73 | 38.13 | |
| nichenet_gr_network_pathwaycommons | 0.02 | 0.00 | 0.01 | |
| nichenet_gr_network_regnetwork | 0.01 | 0.00 | 0.02 | |
| nichenet_gr_network_remap | 0.02 | 0.00 | 0.01 | |
| nichenet_gr_network_trrust | 0.01 | 0.00 | 0.02 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.05 | 0.00 | 0.04 | |
| nichenet_lr_network_guide2pharma | 0.02 | 0.00 | 0.02 | |
| nichenet_lr_network_omnipath | 0.12 | 0.00 | 0.12 | |
| nichenet_lr_network_ramilowski | 0.02 | 0.00 | 0.02 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.07 | 0.00 | 0.08 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.07 | 0.00 | 0.09 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.03 | 0.02 | 0.05 | |
| nichenet_signaling_network_cpdb | 0.01 | 0.00 | 0.01 | |
| nichenet_signaling_network_evex | 0.02 | 0.00 | 0.02 | |
| nichenet_signaling_network_harmonizome | 0.02 | 0.00 | 0.02 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 14.26 | 0.43 | 25.35 | |
| nichenet_signaling_network_pathwaycommons | 0.02 | 0.00 | 0.02 | |
| nichenet_signaling_network_vinayagam | 0.01 | 0.00 | 0.02 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.11 | 0.00 | 0.36 | |
| oma_code | 0.22 | 0.00 | 0.21 | |
| oma_organisms | 0.16 | 0.00 | 0.16 | |
| oma_pairwise | 0.01 | 0.00 | 0.02 | |
| oma_pairwise_genesymbols | 0.02 | 0.00 | 0.01 | |
| oma_pairwise_translated | 0.01 | 0.00 | 0.02 | |
| omnipath-interactions | 35.28 | 1.30 | 52.25 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0 | 0 | 0 | |
| omnipath_cache_clean_db | 0.13 | 0.02 | 0.14 | |
| omnipath_cache_download_ready | 0.64 | 0.03 | 0.73 | |
| omnipath_cache_filter_versions | 0.14 | 0.04 | 0.22 | |
| omnipath_cache_get | 0.09 | 0.04 | 0.13 | |
| omnipath_cache_key | 0 | 0 | 0 | |
| omnipath_cache_latest_or_new | 0.10 | 0.00 | 0.09 | |
| omnipath_cache_load | 0.56 | 0.03 | 1.50 | |
| omnipath_cache_move_in | 0.25 | 0.04 | 0.34 | |
| omnipath_cache_remove | 0.09 | 0.03 | 0.16 | |
| omnipath_cache_save | 0.13 | 0.05 | 0.23 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.12 | 0.02 | 0.18 | |
| omnipath_cache_update_status | 0.07 | 0.04 | 0.11 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 10.83 | 0.41 | 19.14 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0 | 0 | 0 | |
| omnipath_msg | 0.01 | 0.00 | 0.01 | |
| omnipath_query | 3.92 | 0.02 | 3.94 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.05 | 0.00 | 0.05 | |
| omnipath_set_console_loglevel | 0 | 0 | 0 | |
| omnipath_set_logfile_loglevel | 0.02 | 0.00 | 0.01 | |
| omnipath_set_loglevel | 0 | 0 | 0 | |
| omnipath_show_db | 0.14 | 0.00 | 0.14 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.00 | 0.01 | 0.02 | |
| ontology_ensure_name | 0 | 0 | 0 | |
| ontology_name_id | 0 | 0 | 0 | |
| organism_for | 0.21 | 0.02 | 0.23 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 12.16 | 0.84 | 15.17 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.63 | 0.06 | 1.61 | |
| print_bma_motif_vs | 0.18 | 0.00 | 0.71 | |
| print_interactions | 7.37 | 0.25 | 9.56 | |
| print_path_es | 1.07 | 0.03 | 2.15 | |
| print_path_vs | 3.04 | 0.04 | 4.85 | |
| pubmed_open | 5.08 | 0.32 | 6.10 | |
| query_info | 0.61 | 0.02 | 1.00 | |
| ramilowski_download | 0 | 0 | 0 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0 | 0 | 0 | |
| ramp_sqlite | 0 | 0 | 0 | |
| ramp_table | 0.02 | 0.00 | 0.02 | |
| ramp_tables | 0 | 0 | 0 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0 | 0 | 0 | |
| relations_list_to_table | 0.04 | 0.03 | 0.19 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.08 | 0.00 | 0.11 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.61 | 0.03 | 1.04 | |
| resources | 0.03 | 0.03 | 0.57 | |
| resources_colname | 1.19 | 0.03 | 2.06 | |
| resources_in | 4.30 | 0.11 | 4.40 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 6.07 | 0.06 | 6.68 | |
| simplify_intercell_network | 0 | 0 | 0 | |
| static_table | 7.13 | 0.38 | 7.89 | |
| static_tables | 0.06 | 0.00 | 0.14 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0 | 0 | 0 | |
| stitch_remove_prefixes | 0 | 0 | 0 | |
| swap_relations | 0.11 | 0.00 | 0.12 | |
| swissprots_only | 0.19 | 0.00 | 0.19 | |
| tfcensus_download | 0.64 | 0.04 | 0.75 | |
| translate_ids | 1.34 | 0.20 | 14.48 | |
| translate_ids_multi | 9.72 | 0.22 | 17.60 | |
| trembls_only | 0.21 | 0.02 | 0.21 | |
| trrust_download | 0 | 0 | 0 | |
| uniprot_full_id_mapping_table | 1.15 | 0.28 | 15.60 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0 | 0 | 0 | |
| uniprot_id_type | 0.00 | 0.01 | 0.01 | |
| uniprot_idmapping_id_types | 0.50 | 0.05 | 0.86 | |
| uniprot_organisms | 24.32 | 2.24 | 27.50 | |
| unique_intercell_network | 0 | 0 | 0 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0 | 0 | 0 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0 | 0 | 0 | |
| with_extra_attrs | 15.55 | 0.50 | 16.81 | |
| with_references | 0.97 | 0.12 | 2.27 | |
| zenodo_download | 0 | 0 | 0 | |