Multiple platform build/check report for BioC 3.22 - BUILD results for gINTomics on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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 kjohnson1

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: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data gINTomics
StartedAt: 2025-11-17 21:32:33 -0500 (Mon, 17 Nov 2025)
EndedAt: 2025-11-17 21:33:38 -0500 (Mon, 17 Nov 2025)
EllapsedTime: 64.5 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
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###
### 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
[2025-11-17 21:33:11] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:47 UTC; unix
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-17; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-11-17 21:33:11] [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=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-17 21:33:11] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.72.0(2025-11-17); backports 1.5.0(2024-05-23); Biobase 2.70.0(2025-11-17); BiocBaseUtils 1.12.0(2025-11-17); BiocGenerics 0.56.0(2025-11-17); BiocIO 1.20.0(2025-11-17); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2025-11-17); BiocStyle 2.38.0(2025-11-17); Biostrings 2.78.0(2025-11-17); 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 1.0.0(2025-11-17); 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 2.26.0(2025-11-17); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.36.0(2025-11-17); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); 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 1.46.0(2025-11-17); GenomicFeatures 1.62.0(2025-11-17); GenomicRanges 1.62.0(2025-11-17); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.1(2025-11-14); gINTomics 1.6.0(2025-11-17); 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 1.18.0(2025-11-17); IRanges 2.44.0(2025-11-17); 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 1.50.0(2025-11-17); 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 1.22.0(2025-11-17); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.40.0(2025-11-17); mime 0.13(2025-03-17); MultiAssayExperiment 1.36.1(2025-11-17); OmnipathR 3.18.2(2025-11-17); 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 2.1.6(2025-11-14); 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 2.26.0(2025-11-17); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.70.0(2025-11-17); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-17); S4Vectors 0.48.0(2025-11-17); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); Seqinfo 1.0.0(2025-11-17); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.10.2(2025-11-17); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-17); 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 1.5.0(2025-11-17); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-17 21:33:11] [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
[2025-11-17 21:33:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-17 21:33:11] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Pandoc version: `3.6.4`.
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:12] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-17 21:33:20] [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]
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.095042s from rescued.omnipathdb.org (419.4 Kb/s); Redirect: 0s, DNS look up: 0.034379s, Connection: 0.046746s, Pretransfer: 0.060531s, First byte at: 0.083549s
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 18 Nov 2025 02:33:20 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Tue, 18 Nov 2025 03:33:20 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Tue, 18 Nov 2025 02:33:20 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Tue, 18 Nov 2025 03:33:20 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-17 21:33:20] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-17 21:33:20] [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]
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.131348s from omabrowser.org (66.2 Kb/s); Redirect: 0s, DNS look up: 0.019079s, Connection: 0.054192s, Pretransfer: 0.092229s, First byte at: 0.131177s
[2025-11-17 21:33:20] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 18 Nov 2025 02:33:20 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-17 21:33:21] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:21] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-17 21:33:21] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-17 21:33:21] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-17 21:33:21] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-17 21:33:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-17 21:33:26] [WARN]    [OmnipathR] Failed to download `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` (attempt 1/3); error: cannot open the connection to 'https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt'
[2025-11-17 21:33:31] [TRACE]   [OmnipathR] Attempt 2/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-17 21:33:31] [WARN]    [OmnipathR] Failed to download `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` (attempt 2/3); error: cannot open the connection to 'https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt'
[2025-11-17 21:33:36] [TRACE]   [OmnipathR] Attempt 3/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-17 21:33:36] [ERROR]   [OmnipathR] Failed to download `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` (attempt 3/3); error: cannot open the connection to 'https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt'
[2025-11-17 21:33:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-17 21:33:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-17 21:33:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:47 UTC; unix
[2025-11-17 21:33:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-17 21:33:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-17 21:33:36] [INFO]    [OmnipathR] Session info: [version=R version 4.5.2 Patched (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-17; pandoc=3.6.4 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-11-17 21:33:36] [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=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-11-17 21:33:36] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.72.0(2025-11-17); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.70.0(2025-11-17); BiocBaseUtils 1.12.0(2025-11-17); BiocFileCache 3.0.0(2025-11-17); BiocGenerics 0.56.0(2025-11-17); BiocIO 1.20.0(2025-11-17); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2025-11-17); BiocStyle 2.38.0(2025-11-17); biomaRt 2.66.0(2025-11-17); Biostrings 2.78.0(2025-11-17); 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 1.0.0(2025-11-17); 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 4.18.1(2025-11-17); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.26.0(2025-11-17); 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 0.36.0(2025-11-17); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); DOSE 4.4.0(2025-11-17); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.8.0(2025-11-17); enrichplot 1.30.3(2025-11-17); 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 1.36.0(2025-11-17); 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 1.46.0(2025-11-17); GenomicFeatures 1.62.0(2025-11-17); GenomicRanges 1.62.0(2025-11-17); 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 4.0.1(2025-11-14); 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 4.0.1(2025-11-17); ggvenn 0.1.19(2025-10-08); gINTomics 1.6.0(2025-11-17); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-11-17); GOSemSim 2.36.0(2025-11-17); graph 1.88.0(2025-11-17); graphite 1.56.0(2025-11-17); 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 1.18.0(2025-11-17); IRanges 2.44.0(2025-11-17); 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 1.50.0(2025-11-17); 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 3.66.0(2025-11-17); 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 1.22.0(2025-11-17); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.40.0(2025-11-17); mime 0.13(2025-03-17); MultiAssayExperiment 1.36.1(2025-11-17); nlme 3.1-168(2025-03-31); OmnipathR 3.18.2(2025-11-17); org.Hs.eg.db 3.22.0(2025-11-17); org.Mm.eg.db 3.22.0(2025-11-17); 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 2.42.0(2025-11-17); 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(2025-11-17); ReactomePA 1.54.0(2025-11-17); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); 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 2.26.0(2025-11-17); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.70.0(2025-11-17); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-17); S4Vectors 0.48.0(2025-11-17); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); selectr 0.4-2(2019-11-20); Seqinfo 1.0.0(2025-11-17); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.6.0(2025-11-17); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.10.2(2025-11-17); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-17); 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 1.34.0(2025-11-17); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-11-17); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-11-17); 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); vroom 1.6.6(2025-09-19); 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 1.5.0(2025-11-17); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-17); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-11-17 21:33:37] [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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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 `file()`:
! cannot open the connection to 'https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt'
--- failed re-building ‘gINTomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted