Multiple platform build/check report for BioC 3.21 - BUILD results for decoupleR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4831
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4612
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4584
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 decoupleR on nebbiolo1

To the developers/maintainers of the decoupleR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.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: decoupleR
Version: 2.14.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
StartedAt: 2025-10-01 17:08:52 -0400 (Wed, 01 Oct 2025)
EndedAt: 2025-10-01 17:45:48 -0400 (Wed, 01 Oct 2025)
EllapsedTime: 2215.8 seconds
RetCode: 1
Status: ERROR
PackageFile: None
PackageFileSize: NA
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data decoupleR
###
##############################################################################
##############################################################################


* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* preparing ‘decoupleR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘decoupleR.Rmd’ using rmarkdown
--- finished re-building ‘decoupleR.Rmd’

--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:09:18] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:09:18] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); 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 1.34.2(2025-10-01); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); 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); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plyr 1.8.9(2023-10-02); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-01 17:09:18] [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
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:18] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:19] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:19] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:09:19] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-10-01 17:09:19] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:09:19] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:09:20] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:09:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:09:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:09:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:09:20] [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]
[2025-10-01 17:09:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:09:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:10:51] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:10:56] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:10:56] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:10:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:10:56] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:10:56] [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]
[2025-10-01 17:10:56] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:10:56] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:12:26] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:12:31] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:12:31] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:12:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:12:31] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:12:31] [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]
[2025-10-01 17:12:31] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:12:31] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:13:32] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:13:32] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:13:32] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:13:32] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:13:32] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:13:32] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:13:32] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:13:32] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:13:33] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); 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 1.34.2(2025-10-01); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); 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); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plyr 1.8.9(2023-10-02); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-01 17:13:33] [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
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-10-01 17:13:33] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:13:33] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:13:33] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2025-10-01 17:13:33] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:13:33] [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]
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:13:33] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:15:04] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:15:09] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:15:09] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:15:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:15:09] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:15:09] [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]
[2025-10-01 17:15:09] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:15:09] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:16:40] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:16:45] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:16:45] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:16:45] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:16:45] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:16:45] [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]
[2025-10-01 17:16:45] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:16:45] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:18:16] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:18:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:18:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:18:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:18:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:18:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:18:16] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:18:16] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:18:16] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); 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 1.34.2(2025-10-01); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); 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); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plyr 1.8.9(2023-10-02); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.3(2025-08-20); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.6.5(2023-12-01); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-10-01 17:18:16] [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
[2025-10-01 17:18:16] [WARN]    [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-10-01 17:18:17] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:18:17] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:18:17] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:18:17] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:18:17] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:18:26] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:18:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:18:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:18:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:18:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:18:26] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`.
[2025-10-01 17:18:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2025-10-01 17:18:29] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2025-10-01 17:18:29] [INFO]    [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1]
[2025-10-01 17:18:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:18:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:18:29] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`.
[2025-10-01 17:18:29] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
Warning: ggrepel: 445 unlabeled data points (too many overlaps). Consider increasing max.overlaps
--- finished re-building ‘pw_bk.Rmd’

--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:18:48] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:18:48] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:18:48] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2025-10-01 17:18:48] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:18:48] [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]
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:18:48] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:20:19] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:20:24] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:20:24] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:20:24] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:20:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:20:24] [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]
[2025-10-01 17:20:24] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:20:24] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:21:24] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:21:30] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:21:30] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:21:30] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:21:30] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:21:30] [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]
[2025-10-01 17:21:30] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:21:30] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:22:30] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:22:30] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:22:30] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:22:30] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:22:30] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:22:30] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:22:31] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:22:31] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:22:31] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dotCall64 1.2(2024-10-04); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.2(2025-10-01); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.67.0(2025-07-29); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); globals 0.18.0(2025-05-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); 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); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); labeling 0.4.3(2023-08-29); 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); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); 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); progressr 0.16.0(2025-09-19); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.43.0(2025-07-21); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.3(2025-08-20); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.2(2025-04-30); sessioninfo 1.2.3(2025-02-05); Seurat 5.3.0(2025-04-23); SeuratObject 5.2.0(2025-08-27); shiny 1.11.1(2025-07-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-8(2025-08-18); spatstat.explore 3.5-3(2025-09-22); spatstat.geom 3.6-0(2025-09-20); spatstat.random 3.4-2(2025-09-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-4(2025-07-13); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); survival 3.8-3(2024-12-17); tensor 1.5.1(2025-06-17); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10)
[2025-10-01 17:22:31] [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
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-10-01 17:22:32] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:22:32] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:22:32] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2025-10-01 17:22:32] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:22:32] [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]
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:22:32] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:24:03] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:24:08] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:24:08] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:24:08] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:24:08] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:24:08] [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]
[2025-10-01 17:24:08] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:24:08] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:25:38] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:25:43] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:25:43] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:25:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:25:43] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:25:43] [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]
[2025-10-01 17:25:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:25:43] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:27:14] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:27:14] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:27:14] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:27:14] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:27:14] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:27:14] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:27:14] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:27:14] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:27:15] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dotCall64 1.2(2024-10-04); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.2(2025-10-01); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.67.0(2025-07-29); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); globals 0.18.0(2025-05-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); 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); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); labeling 0.4.3(2023-08-29); 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); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); 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); progressr 0.16.0(2025-09-19); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.43.0(2025-07-21); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.3(2025-08-20); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.2(2025-04-30); sessioninfo 1.2.3(2025-02-05); Seurat 5.3.0(2025-04-23); SeuratObject 5.2.0(2025-08-27); shiny 1.11.1(2025-07-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-8(2025-08-18); spatstat.explore 3.5-3(2025-09-22); spatstat.geom 3.6-0(2025-09-20); spatstat.random 3.4-2(2025-09-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-4(2025-07-13); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); survival 3.8-3(2024-12-17); tensor 1.5.1(2025-06-17); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10)
[2025-10-01 17:27:15] [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
[2025-10-01 17:27:15] [WARN]    [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-10-01 17:27:15] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:27:17] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2025-10-01 17:27:17] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-10-01 17:27:17] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.

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--- finished re-building ‘pw_sc.Rmd’

--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2025-10-01 17:27:25] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:27:25] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:27:25] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2025-10-01 17:27:25] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:27:25] [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]
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:27:25] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:28:56] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:29:01] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:29:01] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:29:01] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:29:01] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:29:01] [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]
[2025-10-01 17:29:01] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:29:01] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:30:01] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:30:06] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:30:06] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:30:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:30:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:30:06] [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]
[2025-10-01 17:30:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:30:06] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:31:37] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:31:37] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:31:37] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:31:37] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:31:37] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:31:37] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:31:37] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:31:37] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:31:37] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dotCall64 1.2(2024-10-04); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.2(2025-10-01); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.67.0(2025-07-29); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); globals 0.18.0(2025-05-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); 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); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); labeling 0.4.3(2023-08-29); 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); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); 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); progressr 0.16.0(2025-09-19); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.43.0(2025-07-21); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.3(2025-08-20); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.2(2025-04-30); sessioninfo 1.2.3(2025-02-05); Seurat 5.3.0(2025-04-23); SeuratObject 5.2.0(2025-08-27); shiny 1.11.1(2025-07-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-8(2025-08-18); spatstat.explore 3.5-3(2025-09-22); spatstat.geom 3.6-0(2025-09-20); spatstat.random 3.4-2(2025-09-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-4(2025-07-13); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); survival 3.8-3(2024-12-17); tensor 1.5.1(2025-06-17); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10)
[2025-10-01 17:31:37] [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
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-10-01 17:31:38] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:31:38] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:31:38] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6.
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html
[2025-10-01 17:31:38] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:31:38] [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]
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:31:38] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:33:09] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:33:14] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:33:14] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:33:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:33:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:33:14] [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]
[2025-10-01 17:33:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:33:14] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:34:44] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:34:49] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:34:50] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:34:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:34:50] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:34:50] [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]
[2025-10-01 17:34:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:34:50] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:36:20] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:36:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:36:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:36:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:36:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:36:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:36:21] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:36:21] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:36:21] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dotCall64 1.2(2024-10-04); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.2(2025-10-01); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.67.0(2025-07-29); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); globals 0.18.0(2025-05-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); 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); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); labeling 0.4.3(2023-08-29); 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); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); 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); progressr 0.16.0(2025-09-19); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.43.0(2025-07-21); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.3(2025-08-20); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.2(2025-04-30); sessioninfo 1.2.3(2025-02-05); Seurat 5.3.0(2025-04-23); SeuratObject 5.2.0(2025-08-27); shiny 1.11.1(2025-07-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-8(2025-08-18); spatstat.explore 3.5-3(2025-09-22); spatstat.geom 3.6-0(2025-09-20); spatstat.random 3.4-2(2025-09-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-4(2025-07-13); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); survival 3.8-3(2024-12-17); tensor 1.5.1(2025-06-17); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10)
[2025-10-01 17:36:21] [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
[2025-10-01 17:36:22] [WARN]    [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-10-01 17:36:22] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:36:22] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:36:22] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:36:22] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:36:22] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:36:26] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:36:26] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2025-10-01 17:36:26] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:36:26] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2025-10-01 17:36:26] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-10-01 17:36:32] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from tf_bk.Rmd:117-120 [collectri]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (.keep) ...`:
! argument is of length zero
---
Backtrace:
     ▆
  1. ├─decoupleR::get_collectri(organism = "human", split_complexes = FALSE)
  2. │ └─base::tryCatch(...)
  3. │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │       └─value[[3L]](cond)
  6. │         └─OmnipathR::static_table(...)
  7. │           └─... %>% ...
  8. ├─OmnipathR:::omnipath_post_download(...)
  9. │ └─result %<>% ...
 10. ├─OmnipathR::only_from(...)
 11. │ └─... %>% ...
 12. ├─dplyr::filter(., if_any(EVIDENCES_KEYS, ~not(map_lgl(.x, is.null))))
 13. ├─OmnipathR::from_evidences(., .keep = .keep)
 14. │ └─OmnipathR:::must_have_evidences(data, wide_ok = TRUE)
 15. │   └─OmnipathR:::has_evidences(data, wide_ok = wide_ok)
 16. │     └─data %>% has_column("evidences") %>% ...
 17. ├─OmnipathR:::has_column(., "evidences")
 18. │ ├─col %in% colnames(data)
 19. │ └─base::colnames(data)
 20. │   └─base::is.data.frame(x)
 21. ├─OmnipathR::filter_evidences(...)
 22. │ └─expr(...) %>% eval_select(data) %>% names %>% ...
 23. ├─OmnipathR:::if_null_len0(...)
 24. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 25. ├─OmnipathR:::is_empty_2(.)
 26. │ └─value %>% ...
 27. ├─tidyselect::eval_select(., data)
 28. │ └─tidyselect::tidyselect_data_has_predicates(data)
 29. └─OmnipathR::unnest_evidences(., .keep = .keep)
 30.   └─... %>% ...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tf_bk.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘tf_bk.Rmd’

--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2025-10-01 17:36:38] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:36:38] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:36:38] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7.
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html
[2025-10-01 17:36:38] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:36:38] [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]
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:36:38] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:37:39] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:37:44] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:37:44] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:37:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:37:44] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:37:44] [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]
[2025-10-01 17:37:44] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:37:44] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:39:15] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:39:20] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:39:20] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:39:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:39:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:39:20] [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]
[2025-10-01 17:39:20] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:39:20] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:40:50] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:40:50] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:40:50] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:40:50] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:40:50] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:40:50] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:40:51] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:40:51] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:40:51] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dotCall64 1.2(2024-10-04); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.2(2025-10-01); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.67.0(2025-07-29); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); globals 0.18.0(2025-05-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); 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); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); labeling 0.4.3(2023-08-29); 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); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); 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); progressr 0.16.0(2025-09-19); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.43.0(2025-07-21); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.3(2025-08-20); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.2(2025-04-30); sessioninfo 1.2.3(2025-02-05); Seurat 5.3.0(2025-04-23); SeuratObject 5.2.0(2025-08-27); shiny 1.11.1(2025-07-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-8(2025-08-18); spatstat.explore 3.5-3(2025-09-22); spatstat.geom 3.6-0(2025-09-20); spatstat.random 3.4-2(2025-09-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-4(2025-07-13); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); survival 3.8-3(2024-12-17); tensor 1.5.1(2025-06-17); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10)
[2025-10-01 17:40:51] [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
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-10-01 17:40:53] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-10-01 17:40:53] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-10-01 17:40:53] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 8.
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-8.html
[2025-10-01 17:40:53] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:40:53] [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]
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:40:53] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:42:23] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:42:28] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:42:28] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:42:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:42:28] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:42:28] [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]
[2025-10-01 17:42:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:42:28] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:43:59] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:44:04] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-10-01 17:44:04] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-10-01 17:44:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:44:04] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-10-01 17:44:04] [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]
[2025-10-01 17:44:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-10-01 17:44:04] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-10-01 17:45:35] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-10-01 17:45:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-10-01 17:45:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-10-01
[2025-10-01 17:45:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-10-01 19:11:32 UTC; unix
[2025-10-01 17:45:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-10-01 17:45:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-10-01 17:45:35] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-10-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-10-01 17:45:35] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; 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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-10-01 17:45:35] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.26(2025-06-05); BiocParallel 1.42.2(2025-10-01); BiocStyle 2.36.0(2025-10-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.44(2025-08-21); 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); cli 3.6.5(2025-04-23); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); 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); decoupleR 2.14.0(2025-10-01); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dotCall64 1.2(2024-10-04); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.2(2025-10-01); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.67.0(2025-07-29); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.0(2025-09-11); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); globals 0.18.0(2025-05-08); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); 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); ica 1.0-3(2022-07-08); igraph 2.1.4(2025-01-23); irlba 2.3.5.1(2022-10-03); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); labeling 0.4.3(2023-08-29); 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); listenv 0.9.1(2024-01-29); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.16.2(2025-10-01); parallelly 1.45.1(2025-07-24); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); 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); progressr 0.16.0(2025-09-19); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.4(2020-04-09); reticulate 1.43.0(2025-07-21); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); ROCR 1.0-11(2020-05-02); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.3(2025-08-20); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.0(2024-11-07); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.2(2025-04-30); sessioninfo 1.2.3(2025-02-05); Seurat 5.3.0(2025-04-23); SeuratObject 5.2.0(2025-08-27); shiny 1.11.1(2025-07-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-8(2025-08-18); spatstat.explore 3.5-3(2025-09-22); spatstat.geom 3.6-0(2025-09-20); spatstat.random 3.4-2(2025-09-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-4(2025-07-13); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); survival 3.8-3(2024-12-17); tensor 1.5.1(2025-06-17); 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); tinytex 0.57(2025-04-15); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.3(2025-02-24); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); 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); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10)
[2025-10-01 17:45:35] [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
[2025-10-01 17:45:36] [WARN]    [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-10-01 17:45:36] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:45:37] [TRACE]   [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2025-10-01 17:45:37] [INFO]    [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-10-01 17:45:37] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-10-01 17:45:42] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any

Quitting from tf_sc.Rmd:85-88 [collectri]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `if (.keep) ...`:
! argument is of length zero
---
Backtrace:
     ▆
  1. ├─decoupleR::get_collectri(organism = "human", split_complexes = FALSE)
  2. │ └─base::tryCatch(...)
  3. │   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  4. │     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5. │       └─value[[3L]](cond)
  6. │         └─OmnipathR::static_table(...)
  7. │           └─... %>% ...
  8. ├─OmnipathR:::omnipath_post_download(...)
  9. │ └─result %<>% ...
 10. ├─OmnipathR::only_from(...)
 11. │ └─... %>% ...
 12. ├─dplyr::filter(., if_any(EVIDENCES_KEYS, ~not(map_lgl(.x, is.null))))
 13. ├─OmnipathR::from_evidences(., .keep = .keep)
 14. │ └─OmnipathR:::must_have_evidences(data, wide_ok = TRUE)
 15. │   └─OmnipathR:::has_evidences(data, wide_ok = wide_ok)
 16. │     └─data %>% has_column("evidences") %>% ...
 17. ├─OmnipathR:::has_column(., "evidences")
 18. │ ├─col %in% colnames(data)
 19. │ └─base::colnames(data)
 20. │   └─base::is.data.frame(x)
 21. ├─OmnipathR::filter_evidences(...)
 22. │ └─expr(...) %>% eval_select(data) %>% names %>% ...
 23. ├─OmnipathR:::if_null_len0(...)
 24. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 25. ├─OmnipathR:::is_empty_2(.)
 26. │ └─value %>% ...
 27. ├─tidyselect::eval_select(., data)
 28. │ └─tidyselect::tidyselect_data_has_predicates(data)
 29. └─OmnipathR::unnest_evidences(., .keep = .keep)
 30.   └─... %>% ...
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tf_sc.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘tf_sc.Rmd’

SUMMARY: processing the following files failed:
  ‘tf_bk.Rmd’ ‘tf_sc.Rmd’

Error: Vignette re-building failed.
Execution halted