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This page was generated on 2025-10-23 12:06 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 885/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.5.2  (landing page)
Angelo Velle
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: devel
git_last_commit: 7d7f668
git_last_commit_date: 2025-10-10 16:28:01 -0400 (Fri, 10 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.6 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

BUILD results for gINTomics on kjohnson3

To the developers/maintainers of the gINTomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gINTomics
Version: 1.5.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics
StartedAt: 2025-10-22 16:34:10 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 16:39:44 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 334.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics
###
##############################################################################
##############################################################################


* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* preparing ‘gINTomics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gINTomics.Rmd’ using rmarkdown
[2025-10-22 16:34:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-22
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-22 19:05:20 UTC; unix
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-22; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-22 16:34:51] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-22 16:34:51] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.2(2025-10-22); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-10-22); BiocBaseUtils 1.11.2(2025-10-22); BiocGenerics 0.55.4(2025-10-22); BiocIO 1.19.0(2025-10-22); BiocManager 1.30.26(2025-06-05); BiocParallel 1.43.4(2025-10-22); BiocStyle 2.37.1(2025-10-22); Biostrings 2.77.2(2025-10-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); bookdown 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.25.2(2025-10-22); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.35.3(2025-10-22); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.4(2025-10-22); GenomicFeatures 1.61.7(2025-10-22); GenomicRanges 1.61.6(2025-10-22); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.5.2(2025-10-22); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); InteractiveComplexHeatmap 1.17.0(2025-10-22); IRanges 2.43.5(2025-10-22); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.2(2025-10-22); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.21.0(2025-10-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-10-22); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-10-22); OmnipathR 3.17.6(2025-10-22); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); 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); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); Rsamtools 2.25.3(2025-10-22); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-10-22); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-10-22); S4Vectors 0.47.4(2025-10-22); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 0.99.3(2025-10-22); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-10-22); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-10-22); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); 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); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-10-22); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-22 16:34:51] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:34:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:34:51] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-10-22 16:35:00] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:35:00] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-22 16:35:00] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-10-22 16:35:00] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-22 16:35:00] [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]
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-22 16:35:00] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-22 16:36:31] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-22 16:36:36] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-22 16:36:36] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-22 16:36:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-22 16:36:36] [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]
[2025-10-22 16:36:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-22 16:36:36] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-22 16:38:06] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-22 16:38:11] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-22 16:38:11] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-22 16:38:11] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-22 16:38:11] [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]
[2025-10-22 16:38:11] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-10-22 16:38:11] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-22 16:39:42] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-22 16:39:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-22 16:39:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-22
[2025-10-22 16:39:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-22 19:05:20 UTC; unix
[2025-10-22 16:39:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.6
[2025-10-22 16:39:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-10-22 16:39:43] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); os=macOS Ventura 13.7.7; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-10-22; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-10-22 16:39:43] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-10-22 16:39:43] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.2(2025-10-22); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-10-22); BiocBaseUtils 1.11.2(2025-10-22); BiocFileCache 2.99.6(2025-10-22); BiocGenerics 0.55.4(2025-10-22); BiocIO 1.19.0(2025-10-22); BiocManager 1.30.26(2025-06-05); BiocParallel 1.43.4(2025-10-22); BiocStyle 2.37.1(2025-10-22); biomaRt 2.65.16(2025-10-22); Biostrings 2.77.2(2025-10-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); bookdown 0.45(2025-10-03); bslib 0.9.0(2025-01-30); cachem 1.1.0(2024-05-16); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); clusterProfiler 4.17.0(2025-10-22); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.25.2(2025-10-22); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dbplyr 2.5.1(2025-09-10); DelayedArray 0.35.3(2025-10-22); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.3.0(2025-10-22); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.7.6(2025-10-22); enrichplot 1.29.3(2025-10-22); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.35.8(2025-10-22); filelock 1.0.3(2023-12-11); fontawesome 0.5.3(2024-11-16); fontBitstreamVera 0.1.1(2017-02-01); fontLiberation 0.1.0(2016-10-15); fontquiver 0.2.1(2017-02-01); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); gdtools 0.4.4(2025-10-06); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.4(2025-10-22); GenomicFeatures 1.61.7(2025-10-22); GenomicRanges 1.61.6(2025-10-22); GetoptLong 1.0.5(2020-12-15); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.2(2025-10-07); ggplot2 4.0.0(2025-09-11); ggplotify 0.1.3(2025-09-20); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); ggtangle 0.0.7(2025-06-30); ggtree 3.99.2(2025-10-22); ggvenn 0.1.19(2025-10-08); gINTomics 1.5.2(2025-10-22); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-10-08); GOSemSim 2.35.2(2025-10-22); graph 1.87.0(2025-10-22); graphite 1.55.0(2025-10-22); graphlayouts 1.2.2(2025-01-23); gridExtra 2.3(2017-09-09); gridGraphics 0.5-1(2020-12-13); gson 0.1.0(2023-03-07); gtable 0.3.6(2024-10-25); gtools 3.9.5(2023-11-20); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.0(2025-10-13); InteractiveComplexHeatmap 1.17.0(2025-10-22); IRanges 2.43.5(2025-10-22); iterators 1.0.14(2022-02-05); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.2(2025-10-22); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); limma 3.65.7(2025-10-22); locfit 1.5-9.12(2025-03-05); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.21.0(2025-10-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-10-22); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-10-22); nlme 3.1-168(2025-03-31); OmnipathR 3.17.6(2025-10-22); org.Hs.eg.db 3.22.0(2025-10-08); org.Mm.eg.db 3.22.0(2025-10-08); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); plyr 1.8.9(2023-10-02); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.4.0(2025-10-22); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); qvalue 2.41.0(2025-10-22); 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); randomForest 4.7-1.2(2024-09-22); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); reactome.db 1.94.0(2025-10-08); ReactomePA 1.53.0(2025-10-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reshape2 1.4.4(2020-04-09); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); Rsamtools 2.25.3(2025-10-22); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-10-22); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-10-22); S4Vectors 0.47.4(2025-10-22); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 0.99.3(2025-10-22); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.5.0(2025-10-22); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.9.1(2025-10-22); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-10-22); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); tidytree 0.4.6(2023-12-12); timechange 0.3.0(2024-01-18); treeio 1.33.0(2025-10-22); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-10-08); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-09-10); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); visNetwork 2.1.4(2025-09-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-10-22); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-10-22 16:39:43] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE

Quitting from gINTomics.Rmd:138-142 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
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Error: processing vignette 'gINTomics.Rmd' failed with diagnostics:
ℹ In index: 1.
ℹ With name: hsa.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform()`:
! HTTP 504 Gateway Timeout.
--- failed re-building ‘gINTomics.Rmd’

SUMMARY: processing the following file failed:
  ‘gINTomics.Rmd’

Error: Vignette re-building failed.
Execution halted