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This page was generated on 2025-03-19 11:40 -0400 (Wed, 19 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" 4742
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 873/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.3.0  (landing page)
Angelo Velle
Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 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)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

INSTALL results for gINTomics on nebbiolo1

To the developers/maintainers of the gINTomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gINTomics
Version: 1.3.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL gINTomics
StartedAt: 2025-03-18 15:49:30 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 15:50:52 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 81.4 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL gINTomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘gINTomics’ ...
** this is package ‘gINTomics’ version ‘1.3.0’
** using staged installation
** R
[2025-03-18 15:49:44] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:49:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:49:44] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:49:44] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-18 15:49:44] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-18
[2025-03-18 15:49:44] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-18 19:10:06 UTC; unix
[2025-03-18 15:49:44] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-18 15:49:44] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-18 15:49:44] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-03-18 15:49:45] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-18 15:49:46] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-18); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-18); BiocBaseUtils 1.9.0(2025-03-18); BiocGenerics 0.53.6(2025-03-18); BiocIO 1.17.1(2025-03-18); BiocParallel 1.41.2(2025-03-18); Biostrings 2.75.4(2025-03-18); 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(2025-03-18); 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(2025-03-18); 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(2025-03-18); GenomeInfoDbData 1.2.14(2025-03-14); GenomicAlignments 1.43.0(2025-03-18); GenomicFeatures 1.59.1(2025-03-18); GenomicRanges 1.59.1(2025-03-18); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-18); 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(2025-03-18); IRanges 2.41.3(2025-03-18); 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(2025-03-18); knitr 1.50(2025-03-16); 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(2025-03-18); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-18); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-18); 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(2025-03-18); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-18); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-18); S4Vectors 0.45.4(2025-03-18); 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(2025-03-18); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-18); 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 0.5.0(2025-03-15); UCSC.utils 1.3.1(2025-03-18); 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 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-18); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-18 15:49:46] [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
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:49:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:49:46] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-03-18 15:50:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:50:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-18 15:50:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-18
[2025-03-18 15:50:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-18 19:10:06 UTC; unix
[2025-03-18 15:50:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-18 15:50:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-18 15:50:04] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-03-18 15:50:04] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-18 15:50:05] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-18); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-18); BiocBaseUtils 1.9.0(2025-03-18); BiocGenerics 0.53.6(2025-03-18); BiocIO 1.17.1(2025-03-18); BiocParallel 1.41.2(2025-03-18); Biostrings 2.75.4(2025-03-18); 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(2025-03-18); 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(2025-03-18); 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(2025-03-18); GenomeInfoDbData 1.2.14(2025-03-14); GenomicAlignments 1.43.0(2025-03-18); GenomicFeatures 1.59.1(2025-03-18); GenomicRanges 1.59.1(2025-03-18); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-18); 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(2025-03-18); IRanges 2.41.3(2025-03-18); 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(2025-03-18); knitr 1.50(2025-03-16); 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(2025-03-18); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-18); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-18); 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(2025-03-18); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-18); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-18); S4Vectors 0.45.4(2025-03-18); 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(2025-03-18); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-18); 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 0.5.0(2025-03-15); UCSC.utils 1.3.1(2025-03-18); 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 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-18); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-18 15:50:05] [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
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 15:50:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:05] [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
[2025-03-18 15:50:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:50:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:27] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:27] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-18 15:50:27] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-18
[2025-03-18 15:50:27] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-18 19:10:06 UTC; unix
[2025-03-18 15:50:27] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-18 15:50:27] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-18 15:50:27] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-03-18 15:50:27] [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=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-18 15:50:28] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-18); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-18); BiocBaseUtils 1.9.0(2025-03-18); BiocGenerics 0.53.6(2025-03-18); BiocIO 1.17.1(2025-03-18); BiocParallel 1.41.2(2025-03-18); Biostrings 2.75.4(2025-03-18); 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(2025-03-18); 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(2025-03-18); 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(2025-03-18); GenomeInfoDbData 1.2.14(2025-03-14); GenomicAlignments 1.43.0(2025-03-18); GenomicFeatures 1.59.1(2025-03-18); GenomicRanges 1.59.1(2025-03-18); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-18); 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(2025-03-18); IRanges 2.41.3(2025-03-18); 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(2025-03-18); knitr 1.50(2025-03-16); 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(2025-03-18); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-18); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-18); 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(2025-03-18); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-18); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-18); S4Vectors 0.45.4(2025-03-18); 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(2025-03-18); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-18); 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 0.5.0(2025-03-15); UCSC.utils 1.3.1(2025-03-18); 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 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-18); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-18 15:50:28] [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
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:28] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-18 15:50:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:50:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:45] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:45] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-18 15:50:45] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-18
[2025-03-18 15:50:45] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-03-18 19:10:06 UTC; unix
[2025-03-18 15:50:45] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-18 15:50:45] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-18 15:50:46] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-13 r87965); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-03-18 15:50:46] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-03-18 15:50:46] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-18); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-18); BiocBaseUtils 1.9.0(2025-03-18); BiocGenerics 0.53.6(2025-03-18); BiocIO 1.17.1(2025-03-18); BiocParallel 1.41.2(2025-03-18); Biostrings 2.75.4(2025-03-18); 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(2025-03-18); 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(2025-03-18); 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(2025-03-18); GenomeInfoDbData 1.2.14(2025-03-14); GenomicAlignments 1.43.0(2025-03-18); GenomicFeatures 1.59.1(2025-03-18); GenomicRanges 1.59.1(2025-03-18); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-18); 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(2025-03-18); IRanges 2.41.3(2025-03-18); 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(2025-03-18); knitr 1.50(2025-03-16); 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(2025-03-18); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-18); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-18); 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(2025-03-18); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-18); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-18); S4Vectors 0.45.4(2025-03-18); 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(2025-03-18); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-18); 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 0.5.0(2025-03-15); UCSC.utils 1.3.1(2025-03-18); 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 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-18); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-18 15:50:46] [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
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 15:50:46] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (gINTomics)