Angelo Velle
| Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/gINTomics |
| git_branch: devel |
| git_last_commit: f809e93 |
| git_last_commit_date: 2025-04-15 13:34:55 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 872/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gINTomics 1.5.0 (landing page) Angelo Velle
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the gINTomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: gINTomics |
| Version: 1.5.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL gINTomics |
| StartedAt: 2025-07-31 21:21:29 -0000 (Thu, 31 Jul 2025) |
| EndedAt: 2025-07-31 21:23:19 -0000 (Thu, 31 Jul 2025) |
| EllapsedTime: 110.1 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gINTomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘gINTomics’ ... ** this is package ‘gINTomics’ version ‘1.5.0’ ** using staged installation ** R [2025-07-31 21:21:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:21:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:21:47] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:21:47] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-07-31 21:21:47] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-07-31 [2025-07-31 21:21:47] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-07-31 20:25:46 UTC; unix [2025-07-31 21:21:47] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-31 21:21:47] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-07-31 21:21:48] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-07-31; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-07-31 21:21:48] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-07-31 21:21:49] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-07-31); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-31); BiocBaseUtils 1.11.2(2025-07-31); BiocGenerics 0.55.1(2025-07-31); BiocIO 1.19.0(2025-07-31); BiocParallel 1.43.4(2025-07-31); Biostrings 2.77.2(2025-07-31); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-31); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-31); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-07-31); GenomicFeatures 1.61.6(2025-07-31); GenomicRanges 1.61.1(2025-07-31); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-31); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-31); IRanges 2.43.0(2025-07-31); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-31); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-31); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-31); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-07-31); OmnipathR 3.17.4(2025-07-31); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-07-31); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-31); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-31); S4Vectors 0.47.0(2025-07-31); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-07-31); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-07-31); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-31); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-31); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-07-31 21:21:49] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-07-31 21:21:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-31 21:21:49] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:21:49] [TRACE] [OmnipathR] Contains 1 files. [2025-07-31 21:21:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-31 21:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:21:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:21:49] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-07-31 21:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-31 21:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:21:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-31 21:21:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:21:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-31 21:21:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:21:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-31 21:21:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:21:50] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2025-07-31 21:22:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:22:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:12] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:22:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-07-31 21:22:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-07-31 [2025-07-31 21:22:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-07-31 20:25:46 UTC; unix [2025-07-31 21:22:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-31 21:22:12] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-07-31 21:22:12] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-07-31; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-07-31 21:22:13] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-07-31 21:22:13] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-07-31); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-31); BiocBaseUtils 1.11.2(2025-07-31); BiocGenerics 0.55.1(2025-07-31); BiocIO 1.19.0(2025-07-31); BiocParallel 1.43.4(2025-07-31); Biostrings 2.77.2(2025-07-31); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-31); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-31); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-07-31); GenomicFeatures 1.61.6(2025-07-31); GenomicRanges 1.61.1(2025-07-31); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-31); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-31); IRanges 2.43.0(2025-07-31); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-31); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-31); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-31); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-07-31); OmnipathR 3.17.4(2025-07-31); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-07-31); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-31); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-31); S4Vectors 0.47.0(2025-07-31); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-07-31); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-07-31); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-31); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-31); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-07-31 21:22:13] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-07-31 21:22:13] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-31 21:22:13] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:22:13] [TRACE] [OmnipathR] Contains 1 files. [2025-07-31 21:22:13] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-31 21:22:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:22:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:22:13] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-07-31 21:22:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-31 21:22:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-31 21:22:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-31 21:22:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-31 21:22:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:13] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-07-31 21:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:22:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-07-31 21:22:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-07-31 [2025-07-31 21:22:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-07-31 20:25:46 UTC; unix [2025-07-31 21:22:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-31 21:22:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-07-31 21:22:46] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-07-31; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-07-31 21:22:47] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-07-31 21:22:47] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-07-31); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-31); BiocBaseUtils 1.11.2(2025-07-31); BiocGenerics 0.55.1(2025-07-31); BiocIO 1.19.0(2025-07-31); BiocParallel 1.43.4(2025-07-31); Biostrings 2.77.2(2025-07-31); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-31); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-31); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-07-31); GenomicFeatures 1.61.6(2025-07-31); GenomicRanges 1.61.1(2025-07-31); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-31); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-31); IRanges 2.43.0(2025-07-31); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-31); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-31); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-31); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-07-31); OmnipathR 3.17.4(2025-07-31); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-07-31); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-31); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-31); S4Vectors 0.47.0(2025-07-31); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-07-31); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-07-31); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-31); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-31); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-07-31 21:22:47] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-07-31 21:22:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-31 21:22:47] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:22:47] [TRACE] [OmnipathR] Contains 1 files. [2025-07-31 21:22:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-31 21:22:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:22:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:22:47] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-07-31 21:22:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-31 21:22:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-31 21:22:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-31 21:22:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-31 21:22:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:22:47] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-07-31 21:23:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:23:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:23:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:23:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-07-31 21:23:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-07-31 [2025-07-31 21:23:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-07-31 20:25:46 UTC; unix [2025-07-31 21:23:10] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-07-31 21:23:10] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-07-31 21:23:11] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11); os=openEuler 24.03 (LTS); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-07-31; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=1.7.32 @ /home/biocbuild/bioconductor/quarto-1.7.32/bin/quarto] [2025-07-31 21:23:11] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.47; jpeg=6.2; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.14; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/usr/lib64/libopenblas-r0.3.25.so; lapack=/usr/lib64/libopenblas-r0.3.25.so; lapack_version=3.11.0] [2025-07-31 21:23:11] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-07-31); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-31); BiocBaseUtils 1.11.2(2025-07-31); BiocGenerics 0.55.1(2025-07-31); BiocIO 1.19.0(2025-07-31); BiocParallel 1.43.4(2025-07-31); Biostrings 2.77.2(2025-07-31); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-31); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-31); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-07-31); GenomicFeatures 1.61.6(2025-07-31); GenomicRanges 1.61.1(2025-07-31); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-31); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-31); IRanges 2.43.0(2025-07-31); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-31); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-31); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-31); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-07-31); OmnipathR 3.17.4(2025-07-31); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-07-31); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-31); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-31); S4Vectors 0.47.0(2025-07-31); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-07-31); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-07-31); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-31); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-31); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-07-31 21:23:11] [INFO] [OmnipathR] CURL: version: 8.13.0; headers: 8.13.0; ssl_version: OpenSSL/3.5.0; libz_version: 1.3.1; libssh_version: libssh2/1.11.1; libidn_version: NA; host: aarch64-conda-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-07-31 21:23:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-07-31 21:23:11] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:23:11] [TRACE] [OmnipathR] Contains 1 files. [2025-07-31 21:23:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-07-31 21:23:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-07-31 21:23:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:23:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-07-31 21:23:11] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-07-31 21:23:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-07-31 21:23:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:23:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-07-31 21:23:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:23:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-07-31 21:23:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:23:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-07-31 21:23:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-07-31 21:23:12] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (gINTomics)