Angelo Velle
| Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/gINTomics |
| git_branch: devel |
| git_last_commit: 3ba788e |
| git_last_commit_date: 2024-10-29 11:30:48 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-14 11:47 -0400 (Fri, 14 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4781 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4537 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4567 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4519 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4451 |
| 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 871/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gINTomics 1.3.0 (landing page) Angelo Velle
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | 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: 1.3.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL gINTomics |
| StartedAt: 2025-03-13 20:09:23 -0000 (Thu, 13 Mar 2025) |
| EndedAt: 2025-03-13 20:11:12 -0000 (Thu, 13 Mar 2025) |
| EllapsedTime: 108.8 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL gINTomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘gINTomics’ ... ** this is package ‘gINTomics’ version ‘1.3.0’ ** using staged installation ** R [2025-03-13 20:09:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:09:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:09:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:09:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-03-13 20:09:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13 [2025-03-13 20:09:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:20:42 UTC; unix [2025-03-13 20:09:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-13 20:09:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-03-13 20:09:42] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA] [2025-03-13 20:09:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-03-13 20:09:44] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); 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 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); 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 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); 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 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); 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 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); 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 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-13 20:09:44] [INFO] [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-03-13 20:09:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 20:09:44] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:09:44] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 20:09:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 20:09:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:09:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:09:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:09:44] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-03-13 20:09:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-13 20:09:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:09:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-13 20:09:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:09:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-13 20:09:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:09:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-13 20:09:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:09:44] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2025-03-13 20:10:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:07] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:10:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-03-13 20:10:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13 [2025-03-13 20:10:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:20:42 UTC; unix [2025-03-13 20:10:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-13 20:10:07] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-03-13 20:10:07] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA] [2025-03-13 20:10:07] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-03-13 20:10:07] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); 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 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); 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 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); 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 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); 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 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); 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 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-13 20:10:07] [INFO] [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-03-13 20:10:07] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 20:10:07] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:10:07] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 20:10:07] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 20:10:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:10:07] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-03-13 20:10:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-13 20:10:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-13 20:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-13 20:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-13 20:10:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:08] [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 [2025-03-13 20:10:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:10:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:40] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:10:40] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-03-13 20:10:40] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13 [2025-03-13 20:10:40] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:20:42 UTC; unix [2025-03-13 20:10:40] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-13 20:10:40] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-03-13 20:10:40] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA] [2025-03-13 20:10:40] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-03-13 20:10:40] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); 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 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); 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 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); 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 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); 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 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); 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 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-13 20:10:40] [INFO] [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-03-13 20:10:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 20:10:40] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:10:40] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 20:10:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 20:10:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:10:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:10:40] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-03-13 20:10:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-13 20:10:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-13 20:10:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-13 20:10:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-13 20:10:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:10:40] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-13 20:11:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:11:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:11:04] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:11:04] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-03-13 20:11:04] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13 [2025-03-13 20:11:04] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:20:42 UTC; unix [2025-03-13 20:11:04] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.11 [2025-03-13 20:11:04] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-03-13 20:11:05] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-13; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA] [2025-03-13 20:11:05] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0] [2025-03-13 20:11:05] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); 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 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); 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 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); 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 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); 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 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); 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 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01) [2025-03-13 20:11:05] [INFO] [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-03-13 20:11:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-13 20:11:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:11:05] [TRACE] [OmnipathR] Contains 1 files. [2025-03-13 20:11:05] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-13 20:11:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-13 20:11:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:11:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-03-13 20:11:05] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-03-13 20:11:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-13 20:11:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:11:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-13 20:11:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:11:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-13 20:11:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:11:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-13 20:11:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-13 20:11:05] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (gINTomics)