Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-12 12:08 -0400 (Tue, 12 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 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" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 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 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 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: 2025-08-12 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 |
############################################################################## ############################################################################## ### ### 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.
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)
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) [2025-08-12 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
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.01 | 0.00 | 0.01 | |
all_uniprots | 26.91 | 2.34 | 40.75 | |
ancestors | 0 | 0 | 0 | |
annotated_network | 1.50 | 0.08 | 3.75 | |
annotation_categories | 76.70 | 0.05 | 77.61 | |
annotation_resources | 0.03 | 0.00 | 0.55 | |
annotations | 0.62 | 0.01 | 1.97 | |
biomart_query | 1.33 | 0.06 | 3.34 | |
bioplex1 | 0.02 | 0.00 | 0.02 | |
bioplex2 | 0 | 0 | 0 | |
bioplex3 | 0.01 | 0.00 | 0.01 | |
bioplex_all | 0 | 0 | 0 | |
bioplex_hct116_1 | 0 | 0 | 0 | |
bma_motif_es | 0.81 | 0.07 | 1.83 | |
bma_motif_vs | 0.22 | 0.00 | 0.72 | |
chalmers_gem | 0 | 0 | 0 | |
chalmers_gem_id_mapping_table | 0.02 | 0.00 | 0.02 | |
chalmers_gem_id_type | 0 | 0 | 0 | |
chalmers_gem_metabolites | 0.01 | 0.00 | 0.01 | |
chalmers_gem_network | 0 | 0 | 0 | |
chalmers_gem_raw | 0 | 0 | 0 | |
chalmers_gem_reactions | 0.02 | 0.00 | 0.01 | |
common_name | 0.17 | 0.00 | 0.17 | |
complex_genes | 0.80 | 0.03 | 1.97 | |
complex_resources | 0.06 | 0.00 | 0.57 | |
complexes | 0.22 | 0.00 | 0.76 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.03 | 0.00 | 0.03 | |
cosmos_pkn | 0 | 0 | 0 | |
curated_ligand_receptor_interactions | 6.55 | 0.39 | 14.52 | |
curated_ligrec_stats | 41.05 | 1.85 | 96.69 | |
database_summary | 1.59 | 0.04 | 2.35 | |
descendants | 0 | 0 | 0 | |
ensembl_dataset | 0.08 | 0.00 | 0.07 | |
ensembl_id_mapping_table | 2.25 | 0.10 | 9.57 | |
ensembl_id_type | 0 | 0 | 0 | |
ensembl_name | 0.35 | 0.00 | 0.34 | |
ensembl_organisms | 0.12 | 0.00 | 0.56 | |
ensembl_organisms_raw | 0.11 | 0.01 | 0.13 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 2.11 | 0.10 | 3.39 | |
enzsub_resources | 0.05 | 0.00 | 0.56 | |
enzyme_substrate | 1.00 | 0.00 | 1.48 | |
evex_download | 0.01 | 0.00 | 0.02 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 12.52 | 0.28 | 13.36 | |
extra_attrs | 6.40 | 0.11 | 6.52 | |
extra_attrs_to_cols | 14.77 | 0.36 | 15.15 | |
filter_by_resource | 9.48 | 0.29 | 10.53 | |
filter_extra_attrs | 21.25 | 0.60 | 22.45 | |
filter_intercell | 7.27 | 0.58 | 7.64 | |
filter_intercell_network | 0.01 | 0.00 | 0.01 | |
find_all_paths | 6.67 | 0.13 | 7.05 | |
from_evidences | 0 | 0 | 0 | |
get_db | 0 | 0 | 0 | |
get_ontology_db | 0.02 | 0.00 | 0.02 | |
giant_component | 12.76 | 0.56 | 36.50 | |
go_annot_download | 18.63 | 1.39 | 18.01 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.02 | 0.00 | 0.02 | |
guide2pharma_download | 0.01 | 0.00 | 0.01 | |
harmonizome_download | 0.00 | 0.02 | 0.02 | |
has_extra_attrs | 9.61 | 0.21 | 18.64 | |
hmdb_id_mapping_table | 0.02 | 0.00 | 0.01 | |
hmdb_id_type | 0 | 0 | 0 | |
hmdb_metabolite_fields | 0 | 0 | 0 | |
hmdb_protein_fields | 0 | 0 | 0 | |
hmdb_table | 0.01 | 0.00 | 0.02 | |
homologene_download | 0.02 | 0.00 | 0.01 | |
homologene_raw | 0.09 | 0.00 | 0.10 | |
homologene_uniprot_orthology | 0.02 | 0.00 | 0.01 | |
hpo_download | 3.64 | 0.23 | 4.03 | |
htridb_download | 0.01 | 0.00 | 0.02 | |
id_translation_resources | 0 | 0 | 0 | |
id_types | 0.05 | 0.00 | 0.04 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.72 | 0.08 | 1.16 | |
interaction_graph | 0.47 | 0.02 | 1.00 | |
interaction_resources | 0.06 | 0.00 | 0.56 | |
interaction_types | 0.12 | 0.00 | 0.13 | |
intercell | 1.05 | 0.06 | 1.92 | |
intercell_categories | 0.85 | 0.00 | 1.56 | |
intercell_consensus_filter | 2.12 | 0.16 | 9.13 | |
intercell_generic_categories | 0.14 | 0.00 | 0.20 | |
intercell_network | 0.02 | 0.00 | 0.02 | |
intercell_resources | 0.06 | 0.00 | 0.73 | |
intercell_summary | 0.12 | 0.01 | 0.27 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.09 | 0.00 | 0.10 | |
is_trembl | 0.10 | 0.02 | 0.11 | |
is_uniprot | 0.06 | 0.00 | 0.06 | |
kegg_api_templates | 0.02 | 0.00 | 0.01 | |
kegg_conv | 1.81 | 0.08 | 10.52 | |
kegg_databases | 0 | 0 | 0 | |
kegg_ddi | 0.76 | 0.06 | 3.47 | |
kegg_find | 0.77 | 0.03 | 2.60 | |
kegg_info | 0.01 | 0.00 | 0.01 | |
kegg_link | 0.80 | 0.02 | 5.19 | |
kegg_list | 0.66 | 0.01 | 1.64 | |
kegg_open | 0 | 0 | 0 | |
kegg_operations | 0 | 0 | 0 | |
kegg_organism_codes | 0.04 | 0.02 | 0.06 | |
kegg_organisms | 0.02 | 0.00 | 0.02 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0 | 0 | 0 | |
kegg_pathway_list | 0.02 | 0.00 | 0.02 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 1.20 | 0.02 | 2.92 | |
kegg_process | 0.01 | 0.00 | 0.02 | |
kegg_query | 0.02 | 0.00 | 0.01 | |
kegg_request | 0.06 | 0.00 | 0.07 | |
kegg_rm_prefix | 0.74 | 0.08 | 3.92 | |
latin_name | 0.39 | 0.03 | 0.42 | |
load_db | 0.09 | 0.00 | 0.09 | |
metalinksdb_sqlite | 1.11 | 0.06 | 2.41 | |
metalinksdb_table | 0.17 | 0.02 | 0.19 | |
metalinksdb_tables | 0.03 | 0.00 | 0.03 | |
ncbi_taxid | 0.36 | 0.03 | 0.39 | |
nichenet_build_model | 0 | 0 | 0 | |
nichenet_expression_data | 0.02 | 0.00 | 0.01 | |
nichenet_gr_network | 0.03 | 0.00 | 0.05 | |
nichenet_gr_network_evex | 0.02 | 0.00 | 0.02 | |
nichenet_gr_network_harmonizome | 0.00 | 0.01 | 0.01 | |
nichenet_gr_network_htridb | 0.01 | 0.00 | 0.02 | |
nichenet_gr_network_omnipath | 18.31 | 0.97 | 20.03 | |
nichenet_gr_network_pathwaycommons | 0.02 | 0.00 | 0.01 | |
nichenet_gr_network_regnetwork | 0.06 | 0.00 | 0.06 | |
nichenet_gr_network_remap | 0.01 | 0.00 | 0.02 | |
nichenet_gr_network_trrust | 0.02 | 0.00 | 0.01 | |
nichenet_ligand_activities | 0 | 0 | 0 | |
nichenet_ligand_target_links | 0 | 0 | 0 | |
nichenet_ligand_target_matrix | 0 | 0 | 0 | |
nichenet_lr_network | 0.02 | 0.02 | 0.03 | |
nichenet_lr_network_guide2pharma | 0.00 | 0.00 | 0.02 | |
nichenet_lr_network_omnipath | 0.03 | 0.00 | 0.03 | |
nichenet_lr_network_ramilowski | 0 | 0 | 0 | |
nichenet_main | 0 | 0 | 0 | |
nichenet_networks | 0.03 | 0.02 | 0.05 | |
nichenet_optimization | 0 | 0 | 0 | |
nichenet_remove_orphan_ligands | 0.03 | 0.01 | 0.05 | |
nichenet_results_dir | 0 | 0 | 0 | |
nichenet_signaling_network | 0.05 | 0.00 | 0.04 | |
nichenet_signaling_network_cpdb | 0 | 0 | 0 | |
nichenet_signaling_network_evex | 0.02 | 0.00 | 0.02 | |
nichenet_signaling_network_harmonizome | 0.00 | 0.02 | 0.02 | |
nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
nichenet_signaling_network_omnipath | 13.01 | 0.70 | 14.42 | |
nichenet_signaling_network_pathwaycommons | 0.02 | 0.00 | 0.01 | |
nichenet_signaling_network_vinayagam | 0.00 | 0.00 | 0.02 | |
nichenet_test | 0 | 0 | 0 | |
nichenet_workarounds | 0 | 0 | 0 | |
obo_parser | 0.12 | 0.03 | 0.34 | |
oma_code | 0.17 | 0.05 | 0.30 | |
oma_organisms | 0.11 | 0.00 | 0.14 | |
oma_pairwise | 0.02 | 0.00 | 0.02 | |
oma_pairwise_genesymbols | 0.02 | 0.00 | 0.01 | |
oma_pairwise_translated | 0 | 0 | 0 | |
omnipath-interactions | 37.07 | 1.72 | 86.08 | |
omnipath_cache_autoclean | 0 | 0 | 0 | |
omnipath_cache_clean | 0.02 | 0.00 | 0.02 | |
omnipath_cache_clean_db | 0.09 | 0.00 | 0.09 | |
omnipath_cache_download_ready | 0.53 | 0.05 | 0.75 | |
omnipath_cache_filter_versions | 0.11 | 0.01 | 0.16 | |
omnipath_cache_get | 0.11 | 0.02 | 0.12 | |
omnipath_cache_key | 0 | 0 | 0 | |
omnipath_cache_latest_or_new | 0.07 | 0.02 | 0.07 | |
omnipath_cache_load | 0.54 | 0.01 | 1.58 | |
omnipath_cache_move_in | 0.17 | 0.05 | 0.36 | |
omnipath_cache_remove | 0.13 | 0.05 | 0.19 | |
omnipath_cache_save | 0.23 | 0.00 | 0.48 | |
omnipath_cache_search | 0 | 0 | 0 | |
omnipath_cache_set_ext | 0.14 | 0.00 | 0.14 | |
omnipath_cache_update_status | 0.13 | 0.03 | 0.18 | |
omnipath_cache_wipe | 0 | 0 | 0 | |
omnipath_config_path | 0 | 0 | 0 | |
omnipath_for_cosmos | 10.37 | 0.20 | 20.09 | |
omnipath_load_config | 0 | 0 | 0 | |
omnipath_log | 0 | 0 | 0 | |
omnipath_logfile | 0 | 0 | 0 | |
omnipath_msg | 0.00 | 0.00 | 0.02 | |
omnipath_query | 4.09 | 0.03 | 4.12 | |
omnipath_reset_config | 0 | 0 | 0 | |
omnipath_save_config | 0 | 0 | 0 | |
omnipath_set_cachedir | 0.02 | 0.02 | 0.03 | |
omnipath_set_console_loglevel | 0 | 0 | 0 | |
omnipath_set_logfile_loglevel | 0 | 0 | 0 | |
omnipath_set_loglevel | 0.00 | 0.01 | 0.02 | |
omnipath_show_db | 0.06 | 0.00 | 0.06 | |
omnipath_unlock_cache_db | 0 | 0 | 0 | |
only_from | 0 | 0 | 0 | |
ontology_ensure_id | 0 | 0 | 0 | |
ontology_ensure_name | 0 | 0 | 0 | |
ontology_name_id | 0 | 0 | 0 | |
organism_for | 0.23 | 0.02 | 0.25 | |
pathwaycommons_download | 0 | 0 | 0 | |
pivot_annotations | 11.45 | 0.80 | 13.95 | |
preppi_download | 0 | 0 | 0 | |
preppi_filter | 0 | 0 | 0 | |
print_bma_motif_es | 0.69 | 0.06 | 1.78 | |
print_bma_motif_vs | 0.17 | 0.00 | 0.67 | |
print_interactions | 6.55 | 0.30 | 8.77 | |
print_path_es | 0.99 | 0.04 | 2.08 | |
print_path_vs | 2.68 | 0.14 | 4.48 | |
pubmed_open | 4.52 | 0.46 | 7.95 | |
query_info | 0.51 | 0.03 | 0.94 | |
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 | 0 | 0 | |
ramp_tables | 0 | 0 | 0 | |
regnetwork_directions | 0 | 0 | 0 | |
regnetwork_download | 0.02 | 0.00 | 0.01 | |
relations_list_to_table | 0.11 | 0.02 | 0.28 | |
relations_table_to_graph | 0 | 0 | 0 | |
relations_table_to_list | 0.06 | 0.00 | 0.10 | |
remap_dorothea_download | 0 | 0 | 0 | |
remap_filtered | 0 | 0 | 0 | |
remap_tf_target_download | 0 | 0 | 0 | |
resource_info | 0.55 | 0.05 | 0.97 | |
resources | 0.05 | 0.00 | 0.56 | |
resources_colname | 1.02 | 0.09 | 1.91 | |
resources_in | 4.39 | 0.02 | 4.41 | |
show_network | 0 | 0 | 0 | |
signed_ptms | 5.72 | 0.03 | 6.28 | |
simplify_intercell_network | 0 | 0 | 0 | |
static_table | 7.68 | 0.40 | 8.56 | |
static_tables | 0.08 | 0.00 | 0.16 | |
stitch_actions | 0 | 0 | 0 | |
stitch_links | 0 | 0 | 0 | |
stitch_network | 0 | 0 | 0 | |
stitch_remove_prefixes | 0.02 | 0.00 | 0.01 | |
swap_relations | 0.06 | 0.00 | 0.11 | |
swissprots_only | 0.17 | 0.00 | 0.17 | |
tfcensus_download | 0.61 | 0.05 | 0.72 | |
translate_ids | 1.53 | 0.20 | 11.64 | |
translate_ids_multi | 8.62 | 0.18 | 16.72 | |
trembls_only | 0.57 | 0.00 | 0.56 | |
trrust_download | 0 | 0 | 0 | |
uniprot_full_id_mapping_table | 1.17 | 0.12 | 12.37 | |
uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
uniprot_id_mapping_table | 0 | 0 | 0 | |
uniprot_id_type | 0 | 0 | 0 | |
uniprot_idmapping_id_types | 0.50 | 0.03 | 0.85 | |
uniprot_organisms | 23.83 | 2.06 | 26.94 | |
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 | 14.13 | 0.52 | 15.28 | |
with_references | 1.01 | 0.03 | 2.08 | |
zenodo_download | 0 | 0 | 0 | |