############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-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 (it is needed to build vignettes) * creating vignettes ... ERROR --- re-building ‘decoupleR.Rmd’ using rmarkdown --- finished re-building ‘decoupleR.Rmd’ --- re-building ‘pw_bk.Rmd’ using rmarkdown [2025-12-08 17:14:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:14:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-12-08 17:14:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:14:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:14:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:14:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:14:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:14:15] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:14:16] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:14:16] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); 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 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 1.6.0(2025-11-04); 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 0.58(2025-11-19); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-08 17:14:16] [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 [2025-12-08 17:14:16] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-12-08 17:14:16] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-12-08 17:14:16] [TRACE] [OmnipathR] Contains 1 files. [2025-12-08 17:14:16] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-12-08 17:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-12-08 17:14:16] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-12-08 17:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-12-08 17:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-12-08 17:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-12-08 17:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-12-08 17:14:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:16] [TRACE] [OmnipathR] Cache locked: FALSE [2025-12-08 17:14:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-12-08 17:14:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:17] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:14:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:14:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:17] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:14:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:14:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:17] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1. [2025-12-08 17:14:17] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html [2025-12-08 17:14:17] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:17] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:14:17] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:17] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:17] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:17] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:17] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:17] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:22] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:22] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:22] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:23] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:28] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:28] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:28] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:28] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:14:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:14:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:14:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:14:28] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:14:28] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:14:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:14:28] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); 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 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 1.6.0(2025-11-04); 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 0.58(2025-11-19); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-08 17:14:28] [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 [2025-12-08 17:14:29] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:14:29] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:14:29] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:14:29] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:14:29] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:14:29] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:14:29] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:14:29] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:14:30] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); 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 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 1.6.0(2025-11-04); 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 0.58(2025-11-19); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-08 17:14:30] [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 [2025-12-08 17:14:30] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:14:30] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:14:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:14:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:30] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 2. [2025-12-08 17:14:30] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-2.html [2025-12-08 17:14:30] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:30] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:14:30] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:30] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:30] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:30] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:30] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:35] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:35] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:35] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:35] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:35] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:40] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:40] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:40] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:40] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:40] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:14:40] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:14:40] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:14:40] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:14:40] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:14:41] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:14:41] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:14:41] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); 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 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 1.6.0(2025-11-04); 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 0.58(2025-11-19); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-08 17:14:41] [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 [2025-12-08 17:14:41] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-12-08 17:14:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-12-08 17:14:41] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:14:41] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:14:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:14:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:41] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 3. [2025-12-08 17:14:41] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-3.html [2025-12-08 17:14:41] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:41] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:14:41] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:41] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:41] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:41] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:41] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:46] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:46] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:46] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:46] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:46] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:46] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:46] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:51] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:51] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:51] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:51] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:51] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:51] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:14:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:14:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:14:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:14:51] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:14:52] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:14:52] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:14:52] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); 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 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 1.6.0(2025-11-04); 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 0.58(2025-11-19); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-08 17:14:52] [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 [2025-12-08 17:14:52] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:14:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:14:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:14:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:14:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:14:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:14:53] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:14:53] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:14:53] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); 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 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 1.6.0(2025-11-04); 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 0.58(2025-11-19); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-08 17:14:53] [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 [2025-12-08 17:14:53] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:14:53] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:14:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:14:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:14:53] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 4. [2025-12-08 17:14:53] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-4.html [2025-12-08 17:14:53] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:53] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:14:53] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:53] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:53] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:53] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:14:58] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:14:58] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:14:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:14:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:14:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:14:58] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:14:58] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:15:03] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:15:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:15:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:15:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:03] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:15:03] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:15:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:15:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:15:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:15:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:15:03] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:15:04] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:15:04] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:15:04] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bibtex 0.5.1(2023-01-26); BiocManager 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); ggrepel 0.9.6(2024-09-07); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); igraph 2.2.1(2025-10-27); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); readr 2.1.6(2025-11-14); 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 2.4.5(2025-11-30); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 1.6.0(2025-11-04); 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 0.58(2025-11-19); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13) [2025-12-08 17:15:04] [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 [2025-12-08 17:15:05] [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. [2025-12-08 17:15:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:15:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:15:05] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:15:05] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:15:05] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:15:17] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:15:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:15:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:15:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:15:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:15:17] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`. [2025-12-08 17:15:17] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-12-08 17:15:20] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-12-08 17:15:20] [INFO] [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1] [2025-12-08 17:15:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:15:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:15:20] [INFO] [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`. [2025-12-08 17:15:20] [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 [2025-12-08 17:15:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-12-08 17:15:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:15:39] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:15:39] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:15:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:15:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:15:40] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 5. [2025-12-08 17:15:40] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-5.html [2025-12-08 17:15:40] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:40] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:15:40] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:40] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:15:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:15:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:15:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:40] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:15:40] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:15:45] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:45] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:15:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:15:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:15:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:45] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:15:45] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:15:50] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:50] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:15:50] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:15:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:15:50] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:50] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:15:50] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:15:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:15:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:15:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:15:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:15:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:15:50] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:15:50] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:15:51] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:15:51] [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 [2025-12-08 17:15:51] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:15:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:15:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:15:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:15:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:15:51] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:15:52] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:15:52] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:15:52] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:15:52] [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 [2025-12-08 17:15:52] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:15:52] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:15:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:15:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:15:52] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 6. [2025-12-08 17:15:52] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-6.html [2025-12-08 17:15:52] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:52] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:15:52] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:52] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:15:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:15:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:15:52] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:52] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:15:52] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:15:57] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:15:57] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:15:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:15:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:15:57] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:15:57] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:15:58] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:03] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:03] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:03] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:16:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:16:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:16:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:16:03] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:16:03] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:16:03] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:16:04] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:16:04] [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 [2025-12-08 17:16:04] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-12-08 17:16:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-12-08 17:16:04] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:16:04] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:16:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:16:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:16:04] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 7. [2025-12-08 17:16:04] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-7.html [2025-12-08 17:16:04] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:04] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:16:04] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:04] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:04] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:04] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:04] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:04] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:09] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:09] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:09] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:09] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:09] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:09] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:09] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:09] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:14] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:14] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:14] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:14] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:16:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:16:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:16:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:16:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:16:15] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:16:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:16:15] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:16:15] [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 [2025-12-08 17:16:16] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:16:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:16:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:16:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:16:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:16:16] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:16:17] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:16:17] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:16:17] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:16:17] [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 [2025-12-08 17:16:17] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:16:17] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:16:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:16:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:16:17] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 8. [2025-12-08 17:16:17] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-8.html [2025-12-08 17:16:17] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:17] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:16:17] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:17] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:17] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:17] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:17] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:17] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:22] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:22] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:22] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:22] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:27] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:27] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:27] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:27] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:16:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:16:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:16:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:16:27] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:16:28] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:16:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:16:28] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:16:28] [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 [2025-12-08 17:16:29] [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. [2025-12-08 17:16:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:16:31] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`. [2025-12-08 17:16:31] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz` [2025-12-08 17:16:31] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. | | | 0% | |==============================================================================================================| 100% --- finished re-building ‘pw_sc.Rmd’ --- re-building ‘tf_bk.Rmd’ using rmarkdown [2025-12-08 17:16:40] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:16:40] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:16:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:16:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:16:40] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 9. [2025-12-08 17:16:40] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-9.html [2025-12-08 17:16:40] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:40] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:16:40] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:40] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:40] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:40] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:40] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:45] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:45] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:45] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:45] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:45] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:50] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:50] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:50] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:50] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:50] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:50] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:50] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:16:50] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:16:50] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:16:50] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:16:50] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:16:51] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:16:51] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:16:51] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:16:51] [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 [2025-12-08 17:16:52] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:16:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:16:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:16:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:16:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:16:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:16:53] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:16:53] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:16:53] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:16:53] [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 [2025-12-08 17:16:53] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:16:53] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:16:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:16:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:16:53] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 10. [2025-12-08 17:16:53] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-10.html [2025-12-08 17:16:53] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:53] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:16:53] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:53] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:53] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:53] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:16:58] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:16:58] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:16:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:16:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:16:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:16:58] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:16:58] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:03] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:03] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:03] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:17:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:17:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:17:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:17:03] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:17:04] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:17:04] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:17:04] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:17:04] [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 [2025-12-08 17:17:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-12-08 17:17:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-12-08 17:17:05] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:17:05] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:17:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:17:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:17:05] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 11. [2025-12-08 17:17:05] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-11.html [2025-12-08 17:17:05] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:05] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:17:05] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:05] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:05] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:05] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:05] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:05] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:10] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:10] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:10] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:10] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:10] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:10] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:10] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:10] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:15] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:15] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:15] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:15] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:15] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:17:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:17:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:17:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:17:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:17:16] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:17:16] [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; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:17:16] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:17:16] [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 [2025-12-08 17:17:16] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:17:16] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:17:16] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:17:16] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:17:16] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:17:16] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:17:17] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:17:17] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:17:17] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:17:17] [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 [2025-12-08 17:17:17] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:17:17] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:17:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:17:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:17:17] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 12. [2025-12-08 17:17:17] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-12.html [2025-12-08 17:17:17] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:17] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:17:17] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:17] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:17] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:17] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:17] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:17] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:22] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:22] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:22] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:22] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:22] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:27] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:27] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:27] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:27] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:27] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:17:27] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:17:27] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:17:27] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:17:27] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:17:28] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:17:28] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:17:28] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:17:28] [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 [2025-12-08 17:17:29] [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. [2025-12-08 17:17:29] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:17:29] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:17:29] [TRACE] [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:17:29] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:17:29] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:17:35] [INFO] [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:17:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:17:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:17:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:17:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:17:35] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`. [2025-12-08 17:17:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-12-08 17:17:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-12-08 17:17:36] [INFO] [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1] [2025-12-08 17:17:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:17:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:17:36] [INFO] [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`. [2025-12-08 17:17:36] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-12-08 17:17:42] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any Quitting from tf_bk.Rmd:117-120 [collectri] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 [2025-12-08 17:17:48] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:17:48] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:17:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:17:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:17:48] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 13. [2025-12-08 17:17:48] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-13.html [2025-12-08 17:17:48] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:48] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:17:48] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:48] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:48] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:48] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:48] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:48] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:48] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:53] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:53] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:53] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:53] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:53] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:53] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:58] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:17:58] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:17:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:17:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:17:58] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:17:58] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:17:58] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:17:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:17:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:17:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:17:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:17:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:17:59] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:17:59] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:17:59] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:18:00] [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 [2025-12-08 17:18:01] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:18:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:18:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:18:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:18:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:18:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:18:01] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:18:01] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:18:01] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:18:01] [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 [2025-12-08 17:18:01] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:18:01] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:18:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:18:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:18:02] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 14. [2025-12-08 17:18:02] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-14.html [2025-12-08 17:18:02] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:02] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:18:02] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:02] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:02] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:02] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:02] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:02] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:07] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:07] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:07] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:07] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:07] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:07] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:07] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:07] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:12] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:12] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:12] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:12] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:18:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:18:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:18:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:18:12] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:18:12] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:18:12] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:18:13] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:18:13] [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 [2025-12-08 17:18:14] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-12-08 17:18:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-12-08 17:18:14] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-12-08 17:18:14] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:18:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:18:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:18:14] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 15. [2025-12-08 17:18:14] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-15.html [2025-12-08 17:18:14] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:14] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:18:14] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:14] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:14] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:14] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:14] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:19] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:19] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:19] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:19] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:19] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:19] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:24] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:24] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:24] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:24] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:24] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:24] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:18:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:18:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:18:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:18:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:18:25] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:18:25] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:18:25] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:18:25] [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 [2025-12-08 17:18:26] [ERROR] [OmnipathR] Failed to download Ensembl organisms table. [2025-12-08 17:18:26] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:18:26] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:18:26] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:18:26] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:18:26] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:18:27] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:18:27] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:18:27] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:18:27] [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 [2025-12-08 17:18:27] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo. [2025-12-08 17:18:27] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available. [2025-12-08 17:18:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-12-08 17:18:27] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-12-08 17:18:27] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 16. [2025-12-08 17:18:27] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-16.html [2025-12-08 17:18:27] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:27] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-12-08 17:18:27] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:27] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:27] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:27] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:27] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:27] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:27] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 1/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:32] [TRACE] [OmnipathR] Attempt 2/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:32] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:32] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:32] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:32] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:32] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:32] [WARN] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 2/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:37] [TRACE] [OmnipathR] Attempt 3/3: `https://rescued.omnipathdb.org/ensembl-species.html` [2025-12-08 17:18:37] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`. [2025-12-08 17:18:37] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-12-08 17:18:38] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-12-08 17:18:38] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0] [2025-12-08 17:18:38] [TRACE] [OmnipathR] Sending HTTP request. [2025-12-08 17:18:38] [ERROR] [OmnipathR] Failed to download `https://rescued.omnipathdb.org/ensembl-species.html` (attempt 3/3); error: unused arguments (req_prep, resend_count = n) [2025-12-08 17:18:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-12-08 17:18:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-12-08 [2025-12-08 17:18:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-12-08 20:11:27 UTC; unix [2025-12-08 17:18:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.2 [2025-12-08 17:18:38] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-12-08 17:18:38] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-12-08; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto] [2025-12-08 17:18:38] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-12-08 17:18:39] [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 1.30.27(2025-11-14); BiocParallel 1.45.0(2025-12-08); BiocStyle 2.39.0(2025-12-08); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); bookdown 0.46(2025-12-05); 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 2.17.0(2025-12-08); deldir 2.0-4(2024-02-28); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); 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 1.37.2(2025-12-08); fitdistrplus 1.2-4(2025-07-03); fs 1.6.6(2025-04-12); future 1.68.0(2025-11-17); future.apply 1.20.0(2025-06-06); generics 0.1.4(2025-05-09); ggplot2 4.0.1(2025-11-14); 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 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.1(2025-10-27); 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 0.10.0(2025-11-02); 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 3.19.2(2025-12-08); otel 0.2.0(2025-08-29); 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 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); RANN 2.6.2(2024-08-25); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0.8.1(2025-12-08); RcppAnnoy 0.0.22(2024-01-23); RcppHNSW 0.6.0(2024-02-04); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); RefManageR 1.4.0(2022-09-30); reshape2 1.4.5(2025-11-12); reticulate 1.44.1(2025-11-14); 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 2.4.5(2025-11-30); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); 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 5.3.1(2025-10-29); SeuratObject 5.2.0(2025-08-27); shiny 1.12.0(2025-12-03); sp 2.2-0(2025-02-01); spam 2.11-1(2025-01-20); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.6-0(2025-11-22); spatstat.geom 3.6-1(2025-11-20); spatstat.random 3.4-3(2025-11-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-5(2025-11-17); spatstat.utils 3.2-0(2025-09-20); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); 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 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); uwot 0.2.4(2025-11-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.1(2025-12-01); xtable 1.8-4(2019-04-21); yaml 2.3.11(2025-11-28); zip 2.3.3(2025-05-13); zoo 1.8-14(2025-04-10) [2025-12-08 17:18:39] [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 [2025-12-08 17:18:39] [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. [2025-12-08 17:18:39] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:18:40] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`. [2025-12-08 17:18:40] [INFO] [OmnipathR] Loaded from cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz` [2025-12-08 17:18:40] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-12-08 17:18:45] [TRACE] [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any Quitting from tf_sc.Rmd:85-88 [collectri] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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