Denes Turei
| Snapshot Date: 2025-04-24 15:01 -0400 (Thu, 24 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_21 |
| git_last_commit: 08e98a0 |
| git_last_commit_date: 2025-04-15 11:51:33 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-28 13:43 -0400 (Mon, 28 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4832 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4574 |
| 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 1484/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.16.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | 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: 3.16.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OmnipathR_3.16.0.tar.gz |
| StartedAt: 2025-04-25 06:00:07 -0400 (Fri, 25 Apr 2025) |
| EndedAt: 2025-04-25 06:07:21 -0400 (Fri, 25 Apr 2025) |
| EllapsedTime: 433.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OmnipathR_3.16.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 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 '3.16.0'
* 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 ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... NOTE
[2025-04-25 06:01:19] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:01:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:01:19] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:01:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-25 06:01:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-24
[2025-04-25 06:01:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-24 20:31:17 UTC; windows
[2025-04-25 06:01:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-25 06:01:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-25 06:01:20] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-25; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-04-25 06:01:20] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-04-25 06:01:21] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(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 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 1.1.2(2025-03-26); 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 3.16.0(2025-04-24); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 2.3.2(2025-02-01)
[2025-04-25 06:01:21] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:01:21] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-25 06:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-25 06:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-25 06:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-25 06:01:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:01:21] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-04-25 06:02:05] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:02:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:02:05] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:02:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-25 06:02:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-24
[2025-04-25 06:02:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-24 20:31:17 UTC; windows
[2025-04-25 06:02:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-25 06:02:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-25 06:02:06] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-25; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-04-25 06:02:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-04-25 06:02:07] [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 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 1.1.2(2025-03-26); 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 3.16.0(2025-04-24); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 2.3.2(2025-02-01)
[2025-04-25 06:02:07] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:02:07] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-25 06:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-25 06:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-25 06:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:02:07] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-25 06:02:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:02:08] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'OmnipathR-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: complex_genes
> ### Title: Get all the molecular complexes for a given gene(s)
> ### Aliases: complex_genes get_complex_genes
>
> ### ** Examples
>
> complexes <- complexes(resources = c("CORUM", "hu.MAP"))
[2025-04-25 06:05:52] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-25 06:05:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=[CORUM,hu.MAP],query_type=complexes]
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Orthology targets:
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-25 06:05:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:53] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-25 06:05:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-25 06:05:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-25 06:05:54] [TRACE] [OmnipathR] Downloaded 31.7 Kb in 0.484666s from omnipathdb.org (65.3 Kb/s); Redirect: 0s, DNS look up: 0.002224s, Connection: 0.083267s, Pretransfer: 0.182338s, First byte at: 0.48387s
[2025-04-25 06:05:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 25 Apr 2025 10:05:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 25 Apr 2025 11:05:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-25 06:05:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/complexes?resources=CORUM,hu.MAP&license=academic`
[2025-04-25 06:05:54] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:05:54] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:05:55] [INFO] [OmnipathR] Cache item `d9d7d22ab08109542a41373aee9f37f4a6e4f1a5` version 1: status changed from `unknown` to `started`.
[2025-04-25 06:05:55] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/d9d7d22ab08109542a41373aee9f37f4a6e4f1a5-1.rds`.
Error in saveRDS(data, target_path) : error writing to connection
Calls: complexes ... do.call -> <Anonymous> -> omnipath_cache_save -> saveRDS
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 81.17 0.03 82.74
all_uniprots 1.67 0.12 27.80
biomart_query 1.39 0.08 17.14
annotated_network 1.35 0.04 5.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
10. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
11. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
12. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
13. │ └─tidyselect:::as_indices_sel_impl(...)
14. │ └─tidyselect:::as_indices_impl(...)
15. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
16. │ └─vctrs::vec_as_location(...)
17. └─vctrs (local) `<fn>`()
18. └─vctrs:::stop_subscript_oob(...)
19. └─vctrs:::stop_subscript(...)
20. └─rlang::abort(...)
[ FAIL 4 | WARN 9 | SKIP 0 | PASS 15 ]
Error: Test failures
Execution halted
* 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: 2 ERRORs, 2 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'OmnipathR' ... ** this is package 'OmnipathR' version '3.16.0' ** 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 [2025-04-24 16:33:53] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-24 16:33:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:33:53] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-24 16:33:53] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-24 16:33:53] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-24 [2025-04-24 16:33:53] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-24 20:31:17 UTC; windows [2025-04-24 16:33:53] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-24 16:33:53] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-24 16:33:55] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-24; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-04-24 16:33:56] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-04-24 16:33:56] [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 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 1.1.2(2025-03-26); 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 3.16.0(2025-04-24); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 2.3.2(2025-02-01) [2025-04-24 16:33:56] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-24 16:33:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-24 16:33:56] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-24 16:33:56] [TRACE] [OmnipathR] Contains 1 files. [2025-04-24 16:33:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-24 16:33:57] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-24 16:33:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:33:57] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-24 16:33:57] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-24 16:33:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-24 16:33:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:33:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-24 16:33:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:33:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-24 16:33:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:33:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-24 16:33:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:33:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-04-24 16:34:00] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-24 16:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:34:01] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-24 16:34:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-24 16:34:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-24 [2025-04-24 16:34:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-24 20:31:17 UTC; windows [2025-04-24 16:34:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-24 16:34:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-24 16:34:01] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-24; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-04-24 16:34:01] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-04-24 16:34:02] [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 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 1.1.2(2025-03-26); 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 3.16.0(2025-04-24); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 2.3.2(2025-02-01) [2025-04-24 16:34:02] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-24 16:34:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-24 16:34:02] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-24 16:34:02] [TRACE] [OmnipathR] Contains 1 files. [2025-04-24 16:34:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-24 16:34:02] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-24 16:34:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:34:02] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-24 16:34:02] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-24 16:34:02] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-24 16:34:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:34:03] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-24 16:34:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:34:03] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-24 16:34:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:34:03] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-24 16:34:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-24 16:34:03] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
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)
[2025-04-25 06:05:58] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:05:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:05:58] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:05:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-25 06:05:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-24
[2025-04-25 06:05:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-24 20:31:17 UTC; windows
[2025-04-25 06:05:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-25 06:05:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-25 06:05:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-25; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-04-25 06:05:59] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-04-25 06:05:59] [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 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 1.1.2(2025-03-26); 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 3.16.0(2025-04-24); pillar 1.10.2(2025-04-05); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 2.3.2(2025-02-01)
[2025-04-25 06:05:59] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Contains 11 files.
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-25 06:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:06:00] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-25 06:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-25 06:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-25 06:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-25 06:06:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-25 06:06:00] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 4 | WARN 9 | SKIP 0 | PASS 15 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_import.R:169:9'): Testing `annotations` ──────────────────────
`assign("response", method(resources = resources), envir = top_env)` threw an error.
Message: bad 'file' argument
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...)
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::assign("response", method(resources = resources), envir = top_env)
7. ├─OmnipathR (local) method(resources = resources)
8. │ ├─rlang::exec(omnipath_query, proteins = proteins, !!!args)
9. │ └─OmnipathR (local) `<fn>`(proteins = NULL, resources = `<chr>`, query_type = "annotations")
10. │ ├─do.call(omnipath_download, download_args) %>% ...
11. │ ├─base::do.call(omnipath_download, download_args)
12. │ └─OmnipathR (local) `<fn>`(...)
13. │ └─OmnipathR::omnipath_cache_save(data = result, url = the_url)
14. │ └─base::saveRDS(data, target_path)
15. └─OmnipathR:::omnipath_post_download(...)
16. └─OmnipathR:::omnipath_check_result(result, url)
── Failure ('test_import.R:195:9'): annotations: resources ─────────────────────
all(resources %in% resources_in_response) is not TRUE
`actual`: FALSE
`expected`: TRUE
── Failure ('test_import.R:169:9'): Testing `omnipath` ─────────────────────────
`assign("response", method(resources = resources), envir = top_env)` threw an error.
Message: bad 'file' argument
Class: simpleError/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...)
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. ├─base::assign("response", method(resources = resources), envir = top_env)
7. ├─OmnipathR (local) method(resources = resources)
8. │ ├─rlang::exec(omnipath_interactions, !!!args)
9. │ └─OmnipathR (local) `<fn>`(resources = `<chr>`, datasets = "omnipath")
10. │ ├─rlang::exec(omnipath_query, !!!args)
11. │ └─OmnipathR (local) `<fn>`(datasets = "omnipath", resources = `<chr>`, query_type = "interactions")
12. │ ├─do.call(omnipath_download, download_args) %>% ...
13. │ ├─base::do.call(omnipath_download, download_args)
14. │ └─OmnipathR (local) `<fn>`(...)
15. │ └─OmnipathR::omnipath_cache_save(data = result, url = the_url)
16. │ └─base::saveRDS(data, target_path)
17. └─OmnipathR:::omnipath_post_download(...)
18. └─OmnipathR:::omnipath_check_result(result, url)
── Error ('test_import.R:182:13'): (code run outside of `test_that()`) ─────────
<vctrs_error_subscript_oob/vctrs_error_subscript/rlang_error/error/condition>
Error in `separate_rows(., sources, sep = ";")`: Can't select columns that don't exist.
✖ Column `sources` doesn't exist.
Backtrace:
▆
1. ├─response %<>% separate_rows(sources, sep = ";") at test_import.R:182:13
2. ├─tidyr::separate_rows(., sources, sep = ";")
3. ├─tidyr:::separate_rows.data.frame(., sources, sep = ";")
4. │ └─tidyselect::eval_select(expr(c(...)), data, allow_rename = FALSE)
5. │ └─tidyselect:::eval_select_impl(...)
6. │ ├─tidyselect:::with_subscript_errors(...)
7. │ │ └─base::withCallingHandlers(...)
8. │ └─tidyselect:::vars_select_eval(...)
9. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
10. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
11. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
12. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
13. │ └─tidyselect:::as_indices_sel_impl(...)
14. │ └─tidyselect:::as_indices_impl(...)
15. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
16. │ └─vctrs::vec_as_location(...)
17. └─vctrs (local) `<fn>`()
18. └─vctrs:::stop_subscript_oob(...)
19. └─vctrs:::stop_subscript(...)
20. └─rlang::abort(...)
[ FAIL 4 | WARN 9 | SKIP 0 | PASS 15 ]
Error: Test failures
Execution halted
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.00 | 0.02 | 0.11 | |
| all_uniprots | 1.67 | 0.12 | 27.80 | |
| ancestors | 0.01 | 0.00 | 0.05 | |
| annotated_network | 1.35 | 0.04 | 5.21 | |
| annotation_categories | 81.17 | 0.03 | 82.74 | |
| annotation_resources | 0.06 | 0.00 | 0.52 | |
| annotations | 0.61 | 0.03 | 2.18 | |
| biomart_query | 1.39 | 0.08 | 17.14 | |
| bioplex1 | 0.02 | 0.00 | 0.05 | |
| bioplex2 | 0.00 | 0.00 | 0.06 | |
| bioplex3 | 0.01 | 0.00 | 0.05 | |
| bioplex_all | 0.03 | 0.00 | 0.06 | |
| bioplex_hct116_1 | 0.04 | 0.00 | 0.06 | |
| bma_motif_es | 0.64 | 0.05 | 2.22 | |
| bma_motif_vs | 0.18 | 0.01 | 0.87 | |
| chalmers_gem | 0.02 | 0.00 | 0.06 | |
| chalmers_gem_id_mapping_table | 0.03 | 0.00 | 0.06 | |
| chalmers_gem_id_type | 0 | 0 | 0 | |
| chalmers_gem_metabolites | 0.02 | 0.00 | 0.05 | |
| chalmers_gem_network | 0.00 | 0.00 | 0.05 | |
| chalmers_gem_raw | 0.00 | 0.00 | 0.04 | |
| chalmers_gem_reactions | 0.03 | 0.00 | 0.06 | |
| common_name | 0.04 | 0.00 | 0.04 | |