Build/check report for BioC 3.23 - BUILD results for gINTomics on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4823
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*
BUILD results for gINTomics on nebbiolo1

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: 1.7.0
Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics
StartedAt: 2025-11-11 17:53:27 -0500 (Tue, 11 Nov 2025)
EndedAt: 2025-11-11 17:56:59 -0500 (Tue, 11 Nov 2025)
EllapsedTime: 212.2 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/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 (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘gINTomics.Rmd’ using rmarkdown
[2025-11-11 17:55:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-11 17:55:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:00] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-11 17:55:00] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-11 17:55:00] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-11
[2025-11-11 17:55:00] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-11 20:12:50 UTC; unix
[2025-11-11 17:55:00] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-11 17:55:00] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-11 17:55:02] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-11 17:55:02] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-11 17:55:02] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-11); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-11); BiocGenerics 0.57.0(2025-11-11); BiocIO 1.21.0(2025-11-11); BiocManager 1.30.26(2025-06-05); BiocParallel 1.45.0(2025-11-11); BiocStyle 2.39.0(2025-11-11); Biostrings 2.79.2(2025-11-11); 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); cigarillo 1.1.0(2025-11-11); 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 2.27.0(2025-11-11); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-11); 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 1.47.0(2025-11-11); GenomicFeatures 1.63.1(2025-11-11); GenomicRanges 1.63.0(2025-11-11); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-11); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-11); IRanges 2.45.0(2025-11-11); 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 1.51.0(2025-11-11); 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 1.23.0(2025-11-11); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-11); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-11); OmnipathR 3.19.0(2025-11-11); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); 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 2.27.0(2025-11-11); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-11); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-11); S4Vectors 0.49.0(2025-11-11); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-11); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-11); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-11); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-11); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-11 17:55:02] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:02] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-11-11 17:55:26] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:26] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:55:26] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-11-11 17:55:26] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:55:26] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-11 17:55:37] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [www.ensembl.org]:
SSL connection timeout
[2025-11-11 17:55:42] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-11 17:55:42] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-11 17:55:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:55:42] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-11 17:55:42] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-11 17:55:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:55:42] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-11 17:55:52] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [www.ensembl.org]:
SSL connection timeout
[2025-11-11 17:55:57] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-11 17:55:57] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-11 17:55:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:55:57] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-11 17:55:57] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-11 17:55:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:55:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-11 17:56:07] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [www.ensembl.org]:
SSL connection timeout
[2025-11-11 17:56:07] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-11 17:56:07] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-11
[2025-11-11 17:56:07] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-11 20:12:50 UTC; unix
[2025-11-11 17:56:07] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-11 17:56:07] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-11 17:56:08] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-11 17:56:08] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-11 17:56:08] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-11); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-11); BiocFileCache 3.1.0(2025-11-11); BiocGenerics 0.57.0(2025-11-11); BiocIO 1.21.0(2025-11-11); BiocManager 1.30.26(2025-06-05); BiocParallel 1.45.0(2025-11-11); BiocStyle 2.39.0(2025-11-11); biomaRt 2.67.0(2025-11-11); Biostrings 2.79.2(2025-11-11); 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); cigarillo 1.1.0(2025-11-11); 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 4.19.1(2025-11-11); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-11); 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 0.37.0(2025-11-11); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.5.0(2025-11-11); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.9.0(2025-11-11); enrichplot 1.31.0(2025-11-11); 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 1.37.0(2025-11-11); 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 1.47.0(2025-11-11); GenomicFeatures 1.63.1(2025-11-11); GenomicRanges 1.63.0(2025-11-11); 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 0.0.8(2025-11-06); ggtree 4.1.1(2025-11-11); ggvenn 0.1.19(2025-10-08); gINTomics 1.7.0(2025-11-11); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-10-28); GOSemSim 2.37.0(2025-11-11); graph 1.89.0(2025-11-11); graphite 1.57.0(2025-11-11); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-11); IRanges 2.45.0(2025-11-11); 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 1.51.0(2025-11-11); 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 3.67.0(2025-11-11); 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 1.23.0(2025-11-11); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-11); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-11); nlme 3.1-168(2025-03-31); OmnipathR 3.19.0(2025-11-11); org.Hs.eg.db 3.22.0(2025-10-28); org.Mm.eg.db 3.22.0(2025-10-31); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); qvalue 2.43.0(2025-11-11); 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(2025-10-31); ReactomePA 1.55.0(2025-11-11); 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 2.27.0(2025-11-11); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-11); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-11); S4Vectors 0.49.0(2025-11-11); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-11); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.7.0(2025-11-11); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.11.1(2025-11-11); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-11); 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 1.35.0(2025-11-11); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-10-31); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-10-31); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-11); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-11-11 17:56:08] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-11 17:56:09] [ERROR]   [OmnipathR] Failed to download Ensembl organisms table.
[2025-11-11 17:56:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-11 17:56:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-11
[2025-11-11 17:56:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-11 20:12:50 UTC; unix
[2025-11-11 17:56:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-11 17:56:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-11 17:56:10] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-11 17:56:10] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-11 17:56:10] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-11); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-11); BiocFileCache 3.1.0(2025-11-11); BiocGenerics 0.57.0(2025-11-11); BiocIO 1.21.0(2025-11-11); BiocManager 1.30.26(2025-06-05); BiocParallel 1.45.0(2025-11-11); BiocStyle 2.39.0(2025-11-11); biomaRt 2.67.0(2025-11-11); Biostrings 2.79.2(2025-11-11); 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); cigarillo 1.1.0(2025-11-11); 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 4.19.1(2025-11-11); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-11); 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 0.37.0(2025-11-11); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.5.0(2025-11-11); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.9.0(2025-11-11); enrichplot 1.31.0(2025-11-11); 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 1.37.0(2025-11-11); 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 1.47.0(2025-11-11); GenomicFeatures 1.63.1(2025-11-11); GenomicRanges 1.63.0(2025-11-11); 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 0.0.8(2025-11-06); ggtree 4.1.1(2025-11-11); ggvenn 0.1.19(2025-10-08); gINTomics 1.7.0(2025-11-11); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-10-28); GOSemSim 2.37.0(2025-11-11); graph 1.89.0(2025-11-11); graphite 1.57.0(2025-11-11); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-11); IRanges 2.45.0(2025-11-11); 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 1.51.0(2025-11-11); 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 3.67.0(2025-11-11); 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 1.23.0(2025-11-11); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-11); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-11); nlme 3.1-168(2025-03-31); OmnipathR 3.19.0(2025-11-11); org.Hs.eg.db 3.22.0(2025-10-28); org.Mm.eg.db 3.22.0(2025-10-31); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); qvalue 2.43.0(2025-11-11); 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(2025-10-31); ReactomePA 1.55.0(2025-11-11); 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 2.27.0(2025-11-11); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-11); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-11); S4Vectors 0.49.0(2025-11-11); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-11); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.7.0(2025-11-11); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.11.1(2025-11-11); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-11); 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 1.35.0(2025-11-11); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-10-31); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-10-31); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-11); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-11-11 17:56:10] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:56:10] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-11 17:56:10] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-11-11 17:56:10] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:56:10] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-11 17:56:30] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [rescued.omnipathdb.org]:
Resolving timed out after 10000 milliseconds
[2025-11-11 17:56:35] [TRACE]   [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-11 17:56:35] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-11-11 17:56:35] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:56:35] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-11 17:56:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-11 17:56:36] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:56:36] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-11 17:56:40] [WARN]    [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! SSL connect error [rescued.omnipathdb.org]:
OpenSSL SSL_connect: SSL_ERROR_SYSCALL in connection to rescued.omnipathdb.org:443 
[2025-11-11 17:56:45] [TRACE]   [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-11 17:56:45] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-11-11 17:56:45] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:56:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-11 17:56:45] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-11 17:56:45] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-11 17:56:45] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-11 17:56:55] [ERROR]   [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [rescued.omnipathdb.org]:
SSL connection timeout
[2025-11-11 17:56:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-11 17:56:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-11
[2025-11-11 17:56:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-11 20:12:50 UTC; unix
[2025-11-11 17:56:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-11 17:56:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-11 17:56:56] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-11; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-11 17:56:56] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-11 17:56:56] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-11); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-11); BiocFileCache 3.1.0(2025-11-11); BiocGenerics 0.57.0(2025-11-11); BiocIO 1.21.0(2025-11-11); BiocManager 1.30.26(2025-06-05); BiocParallel 1.45.0(2025-11-11); BiocStyle 2.39.0(2025-11-11); biomaRt 2.67.0(2025-11-11); Biostrings 2.79.2(2025-11-11); 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); cigarillo 1.1.0(2025-11-11); 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 4.19.1(2025-11-11); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-11); 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 0.37.0(2025-11-11); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.5.0(2025-11-11); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.9.0(2025-11-11); enrichplot 1.31.0(2025-11-11); 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 1.37.0(2025-11-11); 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 1.47.0(2025-11-11); GenomicFeatures 1.63.1(2025-11-11); GenomicRanges 1.63.0(2025-11-11); 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 0.0.8(2025-11-06); ggtree 4.1.1(2025-11-11); ggvenn 0.1.19(2025-10-08); gINTomics 1.7.0(2025-11-11); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-10-28); GOSemSim 2.37.0(2025-11-11); graph 1.89.0(2025-11-11); graphite 1.57.0(2025-11-11); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-11); IRanges 2.45.0(2025-11-11); 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 1.51.0(2025-11-11); 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 3.67.0(2025-11-11); 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 1.23.0(2025-11-11); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-11); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-11); nlme 3.1-168(2025-03-31); OmnipathR 3.19.0(2025-11-11); org.Hs.eg.db 3.22.0(2025-10-28); org.Mm.eg.db 3.22.0(2025-10-31); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); qvalue 2.43.0(2025-11-11); 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(2025-10-31); ReactomePA 1.55.0(2025-11-11); 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 2.27.0(2025-11-11); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-11); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-11); S4Vectors 0.49.0(2025-11-11); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-11); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.7.0(2025-11-11); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.11.1(2025-11-11); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-11); 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 1.35.0(2025-11-11); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-10-31); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-10-31); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-11); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-11-11 17:56:56] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from gINTomics.Rmd:138-142 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_disk()`:
! Timeout was reached [rescued.omnipathdb.org]:
SSL connection timeout
--- failed re-building ‘gINTomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted