Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 2025-08-15 05:01:07 -0400 (Fri, 15 Aug 2025) |
EndedAt: 2025-08-15 05:12:38 -0400 (Fri, 15 Aug 2025) |
EllapsedTime: 691.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OmnipathR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-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 '3.16.0' * 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 [2025-08-15 05:02:04] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:02:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:04] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:02:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-15 05:02:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14 [2025-08-15 05:02:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:29:05 UTC; windows [2025-08-15 05:02:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-15 05:02:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-15 05:02:05] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-08-15 05:02:05] [INFO] [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-08-15 05:02:06] [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 3.16.0(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-15 05:02:06] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-15 05:02:06] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-15 05:02:06] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:02:06] [TRACE] [OmnipathR] Contains 1 files. [2025-08-15 05:02:06] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-15 05:02:06] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:02:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:06] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:02:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-15 05:02:06] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-15 05:02:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:06] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-15 05:02:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:06] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-15 05:02:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:06] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-15 05:02:06] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:06] [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 [2025-08-15 05:02:31] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:02:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:31] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:02:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-15 05:02:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14 [2025-08-15 05:02:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:29:05 UTC; windows [2025-08-15 05:02:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-15 05:02:31] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-15 05:02:32] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-08-15 05:02:32] [INFO] [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-08-15 05:02:33] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-15 05:02:33] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-15 05:02:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-15 05:02:33] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:02:33] [TRACE] [OmnipathR] Contains 1 files. [2025-08-15 05:02:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-15 05:02:33] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:33] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:02:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-15 05:02:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-15 05:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-15 05:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-15 05:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-15 05:02:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:02:33] [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: metalinksdb_sqlite > ### Title: Open MetalinksDB as an SQLite3 connection > ### Aliases: metalinksdb_sqlite > > ### ** Examples > > con <- metalinksdb_sqlite() [2025-08-15 05:10:50] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:10:50] [INFO] [OmnipathR] Looking up in cache `metalinksdb.sqlite`: key=e2682a205032a8eff5e0533edafd2730b9eb450c, no version available. [2025-08-15 05:10:50] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:10:50] [INFO] [OmnipathR] Created new version for cache record e2682a205032a8eff5e0533edafd2730b9eb450c: version 1. [2025-08-15 05:10:50] [TRACE] [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/e2682a205032a8eff5e0533edafd2730b9eb450c-1 [2025-08-15 05:10:51] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:10:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:10:51] [INFO] [OmnipathR] Looking up in cache `https://figshare.com/ndownloader/files/47567597`: key=7b250a38d14fd754d28d2b7803ee3069659251ec, no version available. [2025-08-15 05:10:51] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:10:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:10:51] [INFO] [OmnipathR] Created new version for cache record 7b250a38d14fd754d28d2b7803ee3069659251ec: version 1. [2025-08-15 05:10:51] [TRACE] [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7b250a38d14fd754d28d2b7803ee3069659251ec-1 [2025-08-15 05:10:51] [INFO] [OmnipathR] Retrieving URL: `https://figshare.com/ndownloader/files/47567597` [2025-08-15 05:10:51] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-08-15 05:10:51] [TRACE] [OmnipathR] Attempt 1/3: `https://figshare.com/ndownloader/files/47567597` [2025-08-15 05:10:51] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://figshare.com/ndownloader/files/47567597`. [2025-08-15 05:10:51] [TRACE] [OmnipathR] HTTP headers: <NULL> [2025-08-15 05:10:51] [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] [2025-08-15 05:10:51] [TRACE] [OmnipathR] HTTP headers: [] [2025-08-15 05:10:51] [TRACE] [OmnipathR] Sending HTTP request. [2025-08-15 05:10:51] [WARN] [OmnipathR] Failed to download `https://figshare.com/ndownloader/files/47567597` (attempt 1/3); error: HTTP 403 Forbidden. [2025-08-15 05:10:57] [TRACE] [OmnipathR] Attempt 2/3: `https://figshare.com/ndownloader/files/47567597` [2025-08-15 05:10:57] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://figshare.com/ndownloader/files/47567597`. [2025-08-15 05:10:57] [TRACE] [OmnipathR] HTTP headers: <NULL> [2025-08-15 05:10:57] [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] [2025-08-15 05:10:57] [TRACE] [OmnipathR] HTTP headers: [] [2025-08-15 05:10:57] [TRACE] [OmnipathR] Sending HTTP request. [2025-08-15 05:10:57] [WARN] [OmnipathR] Failed to download `https://figshare.com/ndownloader/files/47567597` (attempt 2/3); error: HTTP 403 Forbidden. [2025-08-15 05:11:02] [TRACE] [OmnipathR] Attempt 3/3: `https://figshare.com/ndownloader/files/47567597` [2025-08-15 05:11:02] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://figshare.com/ndownloader/files/47567597`. [2025-08-15 05:11:02] [TRACE] [OmnipathR] HTTP headers: <NULL> [2025-08-15 05:11:02] [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] [2025-08-15 05:11:02] [TRACE] [OmnipathR] HTTP headers: [] [2025-08-15 05:11:02] [TRACE] [OmnipathR] Sending HTTP request. [2025-08-15 05:11:02] [ERROR] [OmnipathR] Failed to download `https://figshare.com/ndownloader/files/47567597` (attempt 3/3); error: HTTP 403 Forbidden. [2025-08-15 05:11:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-15 05:11:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14 [2025-08-15 05:11:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:29:05 UTC; windows [2025-08-15 05:11:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-15 05:11:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-15 05:11:06] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=en; collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-08-15 05:11:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-08-15 05:11:07] [INFO] [OmnipathR] Loaded packages: archive 1.1.12(2025-03-20); 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 3.16.0(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); selectr 0.4-2(2019-11-20); 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); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); vroom 1.6.5(2023-12-05); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-15 05:11:07] [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 Error in req_perform(., path = path) : HTTP 403 Forbidden. Calls: metalinksdb_sqlite ... sqlite_downloader -> %>% -> download_to_cache -> download_base Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed annotation_categories 90.14 0.06 90.95 curated_ligrec_stats 37.96 1.85 94.03 filter_extra_attrs 21.81 0.53 22.99 go_annot_download 15.74 1.25 15.28 extra_attrs_to_cols 14.06 0.33 14.54 extra_attr_values 12.81 0.39 13.80 giant_component 11.79 0.38 12.59 filter_by_resource 9.61 0.25 10.39 has_extra_attrs 9.26 0.09 26.58 filter_intercell 8.02 0.63 8.78 curated_ligand_receptor_interactions 6.75 0.40 14.64 extra_attrs 6.91 0.09 7.02 find_all_paths 6.34 0.12 6.47 ensembl_id_mapping_table 2.11 0.03 10.14 all_uniprots 1.87 0.07 13.42 kegg_conv 1.70 0.13 9.67 * 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: 1 ERROR, 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 [2025-08-14 15:32:35] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-14 15:32:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:35] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-14 15:32:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-14 15:32:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14 [2025-08-14 15:32:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:29:05 UTC; windows [2025-08-14 15:32:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-14 15:32:35] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-14 15:32:38] [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=2025-08-14; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-08-14 15:32:38] [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] [2025-08-14 15:32:39] [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 3.16.0(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-14 15:32:39] [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 [2025-08-14 15:32:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-14 15:32:39] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-14 15:32:39] [TRACE] [OmnipathR] Contains 1 files. [2025-08-14 15:32:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-14 15:32:39] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-14 15:32:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:39] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-14 15:32:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-14 15:32:39] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-14 15:32:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:39] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-14 15:32:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:39] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-14 15:32:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:39] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-14 15:32:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:39] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-14 15:32:41] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-14 15:32:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:41] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-14 15:32:41] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-14 15:32:41] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14 [2025-08-14 15:32:41] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:29:05 UTC; windows [2025-08-14 15:32:41] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-14 15:32:41] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-14 15:32:42] [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=2025-08-14; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-08-14 15:32:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-08-14 15:32:42] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); 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 3.16.0(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-14 15:32:42] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-14 15:32:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-14 15:32:42] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-14 15:32:42] [TRACE] [OmnipathR] Contains 1 files. [2025-08-14 15:32:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-14 15:32:42] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-14 15:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:42] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-14 15:32:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-14 15:32:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-14 15:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-14 15:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-14 15:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-14 15:32:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-14 15:32:42] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > #!/usr/bin/env Rscript > > # > # This file is part of the `OmnipathR` R package > # > # Copyright > # 2018-2024 > # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University > # > # File author(s): Alberto Valdeolivas > # Dénes Türei (turei.denes@gmail.com) > # Attila Gábor > # > # Distributed under the MIT (Expat) License. > # See accompanying file `LICENSE` or find a copy at > # https://directory.fsf.org/wiki/License:Expat > # > # Website: https://r.omnipathdb.org/ > # Git repo: https://github.com/saezlab/OmnipathR > # > > > library(testthat) > library(OmnipathR) [2025-08-15 05:11:27] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:11:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:11:27] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:11:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-15 05:11:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-14 [2025-08-15 05:11:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-14 19:29:05 UTC; windows [2025-08-15 05:11:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-08-15 05:11:27] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-08-15 05:11:29] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=C; collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-08-15; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-08-15 05:11:29] [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] [2025-08-15 05:11:30] [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 3.16.0(2025-08-14); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-15 05:11:30] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-15 05:11:30] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-15 05:11:30] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:11:30] [TRACE] [OmnipathR] Contains 57 files. [2025-08-15 05:11:30] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-15 05:11:30] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-08-15 05:11:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:11:30] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-08-15 05:11:30] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-15 05:11:31] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-15 05:11:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:11:31] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-15 05:11:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:11:31] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-15 05:11:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:11:31] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-15 05:11:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-15 05:11:31] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check('OmnipathR') [ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ] [ FAIL 0 | WARN 11 | SKIP 0 | PASS 38 ] > > proc.time() user system elapsed 17.31 2.10 57.95
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprot_acs | 0.00 | 0.01 | 0.02 | |
all_uniprots | 1.87 | 0.07 | 13.42 | |
ancestors | 0.02 | 0.00 | 0.02 | |
annotated_network | 1.30 | 0.09 | 3.56 | |
annotation_categories | 90.14 | 0.06 | 90.95 | |
annotation_resources | 0.06 | 0.00 | 0.67 | |
annotations | 0.56 | 0.06 | 1.61 | |
biomart_query | 1.35 | 0.07 | 2.64 | |
bioplex1 | 0.01 | 0.00 | 0.02 | |
bioplex2 | 0.02 | 0.00 | 0.02 | |
bioplex3 | 0 | 0 | 0 | |
bioplex_all | 0.01 | 0.00 | 0.01 | |
bioplex_hct116_1 | 0.02 | 0.00 | 0.02 | |
bma_motif_es | 0.70 | 0.00 | 1.78 | |
bma_motif_vs | 0.19 | 0.00 | 0.92 | |
chalmers_gem | 0.01 | 0.00 | 0.02 | |
chalmers_gem_id_mapping_table | 0.02 | 0.00 | 0.01 | |
chalmers_gem_id_type | 0 | 0 | 0 | |
chalmers_gem_metabolites | 0 | 0 | 0 | |
chalmers_gem_network | 0.02 | 0.00 | 0.02 | |
chalmers_gem_raw | 0.01 | 0.00 | 0.01 | |
chalmers_gem_reactions | 0 | 0 | 0 | |
common_name | 0.05 | 0.00 | 0.05 | |
complex_genes | 0.67 | 0.07 | 2.12 | |
complex_resources | 0.08 | 0.00 | 0.58 | |
complexes | 0.17 | 0.00 | 0.69 | |
consensuspathdb_download | 0 | 0 | 0 | |
consensuspathdb_raw_table | 0.02 | 0.00 | 0.02 | |
cosmos_pkn | 0 | 0 | 0 | |
curated_ligand_receptor_interactions | 6.75 | 0.40 | 14.64 | |
curated_ligrec_stats | 37.96 | 1.85 | 94.03 | |
database_summary | 1.55 | 0.02 | 2.33 | |
descendants | 0.00 | 0.02 | 0.01 | |
ensembl_dataset | 0.02 | 0.00 | 0.01 | |
ensembl_id_mapping_table | 2.11 | 0.03 | 10.14 | |
ensembl_id_type | 0 | 0 | 0 | |
ensembl_name | 0.12 | 0.00 | 0.12 | |
ensembl_organisms | 0.14 | 0.00 | 0.14 | |
ensembl_organisms_raw | 0.17 | 0.00 | 0.18 | |
ensembl_orthology | 0 | 0 | 0 | |
enzsub_graph | 2.64 | 0.14 | 3.99 | |
enzsub_resources | 0.06 | 0.00 | 0.57 | |
enzyme_substrate | 1.17 | 0.00 | 1.80 | |
evex_download | 0.03 | 0.00 | 0.03 | |
evidences | 0 | 0 | 0 | |
extra_attr_values | 12.81 | 0.39 | 13.80 | |
extra_attrs | 6.91 | 0.09 | 7.02 | |
extra_attrs_to_cols | 14.06 | 0.33 | 14.54 | |
filter_by_resource | 9.61 | 0.25 | 10.39 | |
filter_extra_attrs | 21.81 | 0.53 | 22.99 | |
filter_intercell | 8.02 | 0.63 | 8.78 | |
filter_intercell_network | 0.03 | 0.00 | 0.03 | |
find_all_paths | 6.34 | 0.12 | 6.47 | |
from_evidences | 0 | 0 | 0 | |
get_db | 0 | 0 | 0 | |
get_ontology_db | 0.02 | 0.00 | 0.02 | |
giant_component | 11.79 | 0.38 | 12.59 | |
go_annot_download | 15.74 | 1.25 | 15.28 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0 | 0 | 0 | |
guide2pharma_download | 0 | 0 | 0 | |
harmonizome_download | 0.02 | 0.00 | 0.01 | |
has_extra_attrs | 9.26 | 0.09 | 26.58 | |
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 | 0.02 | 0.00 | 0.03 | |
homologene_download | 0.01 | 0.00 | 0.02 | |
homologene_raw | 0.02 | 0.01 | 0.04 | |
homologene_uniprot_orthology | 0.06 | 0.00 | 0.06 | |
hpo_download | 3.75 | 0.28 | 4.53 | |
htridb_download | 0.02 | 0.00 | 0.02 | |
id_translation_resources | 0 | 0 | 0 | |
id_types | 0.05 | 0.00 | 0.05 | |
inbiomap_download | 0 | 0 | 0 | |
inbiomap_raw | 0 | 0 | 0 | |
interaction_datasets | 0.78 | 0.04 | 1.34 | |
interaction_graph | 0.51 | 0.00 | 1.16 | |
interaction_resources | 0.08 | 0.00 | 0.64 | |
interaction_types | 0.07 | 0.00 | 0.06 | |
intercell | 1.00 | 0.18 | 3.03 | |
intercell_categories | 0.77 | 0.03 | 1.19 | |
intercell_consensus_filter | 1.82 | 0.19 | 2.59 | |
intercell_generic_categories | 0.08 | 0.00 | 0.08 | |
intercell_network | 0.01 | 0.00 | 0.02 | |
intercell_resources | 0.10 | 0.00 | 0.59 | |
intercell_summary | 0.06 | 0.02 | 0.08 | |
is_ontology_id | 0 | 0 | 0 | |
is_swissprot | 0.04 | 0.00 | 0.04 | |
is_trembl | 0.05 | 0.01 | 0.07 | |
is_uniprot | 0.02 | 0.00 | 0.01 | |
kegg_api_templates | 0 | 0 | 0 | |
kegg_conv | 1.70 | 0.13 | 9.67 | |
kegg_databases | 0 | 0 | 0 | |
kegg_ddi | 0.76 | 0.03 | 2.41 | |
kegg_find | 0.83 | 0.00 | 2.58 | |
kegg_info | 0.03 | 0.00 | 0.04 | |
kegg_link | 0.88 | 0.09 | 4.96 | |
kegg_list | 0.86 | 0.00 | 1.83 | |
kegg_open | 0 | 0 | 0 | |
kegg_operations | 0 | 0 | 0 | |
kegg_organism_codes | 0.04 | 0.05 | 0.09 | |
kegg_organisms | 0.04 | 0.00 | 0.03 | |
kegg_pathway_annotations | 0 | 0 | 0 | |
kegg_pathway_download | 0.01 | 0.00 | 0.02 | |
kegg_pathway_list | 0.02 | 0.00 | 0.01 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 1.22 | 0.02 | 2.97 | |
kegg_process | 0.03 | 0.01 | 0.09 | |
kegg_query | 0.01 | 0.00 | 0.02 | |
kegg_request | 0.10 | 0.02 | 0.17 | |
kegg_rm_prefix | 1.01 | 0.03 | 4.17 | |
latin_name | 0.11 | 0.00 | 0.14 | |
load_db | 0.13 | 0.00 | 0.24 | |