Multiple platform build/check report for BioC 3.21 - INSTALL results for gINTomics on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4667
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4573
lconway	macOS 12.7.1 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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*
INSTALL results for gINTomics on lconway

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: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gINTomics
StartedAt: 2025-04-16 15:42:30 -0400 (Wed, 16 Apr 2025)
EndedAt: 2025-04-16 15:44:29 -0400 (Wed, 16 Apr 2025)
EllapsedTime: 118.9 seconds
RetCode: 0
Status: OK
Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gINTomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘gINTomics’ ...
** this is package ‘gINTomics’ version ‘1.4.0’
** using staged installation
** R
[2025-04-16 15:42:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:42:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:42:48] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:42:48] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-16 15:42:48] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-04-16 15:42:48] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-16 19:09:23 UTC; unix
[2025-04-16 15:42:48] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-16 15:42:48] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-16 15:42:49] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-16; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-04-16 15:42:49] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-16 15:42:50] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.70.0(2025-04-16); backports 1.5.0(2024-05-23); Biobase 2.68.0(2025-04-16); BiocBaseUtils 1.10.0(2025-04-16); BiocGenerics 0.54.0(2025-04-16); BiocIO 1.18.0(2025-04-16); BiocParallel 1.42.0(2025-04-16); Biostrings 2.76.0(2025-04-16); 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 0.5.0(2025-03-21); 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 2.24.0(2025-04-16); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); DelayedArray 0.34.0(2025-04-16); 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 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-04-16); GenomeInfoDbData 1.2.14(2025-04-10); GenomicAlignments 1.44.0(2025-04-16); GenomicFeatures 1.60.0(2025-04-16); GenomicRanges 1.60.0(2025-04-16); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.4.0(2025-04-16); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.16.0(2025-04-16); IRanges 2.42.0(2025-04-16); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.48.0(2025-04-16); 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 1.20.0(2025-04-16); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.38.0(2025-04-16); mime 0.13(2025-03-17); MultiAssayExperiment 1.34.0(2025-04-16); munsell 0.5.1(2024-04-01); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); 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 1.9.1(2025-04-12); 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 1.98-1.17(2025-03-22); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.24.0(2025-04-16); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.68.0(2025-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-04-16); S4Vectors 0.46.0(2025-04-16); 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 1.8.0(2025-04-16); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.0(2025-04-16); svglite 2.1.3(2023-12-08); systemfonts 1.2.2(2025-04-04); 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 1.4.0(2025-04-16); 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 0.48.0(2025-04-16); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-16 15:42:50] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:42:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-16 15:42:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:42:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-16 15:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:42:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-16 15:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:42:51] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-16 15:42:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:42:51] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-04-16 15:43:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:43:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:15] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:43:15] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-16 15:43:15] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-04-16 15:43:15] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-16 19:09:23 UTC; unix
[2025-04-16 15:43:15] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-16 15:43:15] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-16 15:43:16] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-16; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-04-16 15:43:16] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-16 15:43:17] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.70.0(2025-04-16); backports 1.5.0(2024-05-23); Biobase 2.68.0(2025-04-16); BiocBaseUtils 1.10.0(2025-04-16); BiocGenerics 0.54.0(2025-04-16); BiocIO 1.18.0(2025-04-16); BiocParallel 1.42.0(2025-04-16); Biostrings 2.76.0(2025-04-16); 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 0.5.0(2025-03-21); 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 2.24.0(2025-04-16); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); DelayedArray 0.34.0(2025-04-16); 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 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-04-16); GenomeInfoDbData 1.2.14(2025-04-10); GenomicAlignments 1.44.0(2025-04-16); GenomicFeatures 1.60.0(2025-04-16); GenomicRanges 1.60.0(2025-04-16); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.4.0(2025-04-16); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.16.0(2025-04-16); IRanges 2.42.0(2025-04-16); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.48.0(2025-04-16); 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 1.20.0(2025-04-16); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.38.0(2025-04-16); mime 0.13(2025-03-17); MultiAssayExperiment 1.34.0(2025-04-16); munsell 0.5.1(2024-04-01); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); 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 1.9.1(2025-04-12); 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 1.98-1.17(2025-03-22); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.24.0(2025-04-16); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.68.0(2025-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-04-16); S4Vectors 0.46.0(2025-04-16); 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 1.8.0(2025-04-16); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.0(2025-04-16); svglite 2.1.3(2023-12-08); systemfonts 1.2.2(2025-04-04); 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 1.4.0(2025-04-16); 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 0.48.0(2025-04-16); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-16 15:43:17] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-16 15:43:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:17] [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
[2025-04-16 15:43:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:43:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:53] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:43:53] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-16 15:43:53] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-04-16 15:43:53] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-16 19:09:23 UTC; unix
[2025-04-16 15:43:53] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-16 15:43:53] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-16 15:43:53] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-16; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-04-16 15:43:53] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-16 15:43:54] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.70.0(2025-04-16); backports 1.5.0(2024-05-23); Biobase 2.68.0(2025-04-16); BiocBaseUtils 1.10.0(2025-04-16); BiocGenerics 0.54.0(2025-04-16); BiocIO 1.18.0(2025-04-16); BiocParallel 1.42.0(2025-04-16); Biostrings 2.76.0(2025-04-16); 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 0.5.0(2025-03-21); 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 2.24.0(2025-04-16); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); DelayedArray 0.34.0(2025-04-16); 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 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-04-16); GenomeInfoDbData 1.2.14(2025-04-10); GenomicAlignments 1.44.0(2025-04-16); GenomicFeatures 1.60.0(2025-04-16); GenomicRanges 1.60.0(2025-04-16); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.4.0(2025-04-16); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.16.0(2025-04-16); IRanges 2.42.0(2025-04-16); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.48.0(2025-04-16); 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 1.20.0(2025-04-16); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.38.0(2025-04-16); mime 0.13(2025-03-17); MultiAssayExperiment 1.34.0(2025-04-16); munsell 0.5.1(2024-04-01); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); 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 1.9.1(2025-04-12); 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 1.98-1.17(2025-03-22); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.24.0(2025-04-16); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.68.0(2025-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-04-16); S4Vectors 0.46.0(2025-04-16); 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 1.8.0(2025-04-16); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.0(2025-04-16); svglite 2.1.3(2023-12-08); systemfonts 1.2.2(2025-04-04); 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 1.4.0(2025-04-16); 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 0.48.0(2025-04-16); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-16 15:43:54] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:43:54] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-04-16 15:44:19] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:44:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:44:19] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:44:19] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-16 15:44:19] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-04-16
[2025-04-16 15:44:19] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-16 19:09:23 UTC; unix
[2025-04-16 15:44:19] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-16 15:44:19] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-16 15:44:19] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-04-16; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-04-16 15:44:20] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-04-16 15:44:20] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.70.0(2025-04-16); backports 1.5.0(2024-05-23); Biobase 2.68.0(2025-04-16); BiocBaseUtils 1.10.0(2025-04-16); BiocGenerics 0.54.0(2025-04-16); BiocIO 1.18.0(2025-04-16); BiocParallel 1.42.0(2025-04-16); Biostrings 2.76.0(2025-04-16); 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 0.5.0(2025-03-21); 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 2.24.0(2025-04-16); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); DelayedArray 0.34.0(2025-04-16); 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 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-04-16); GenomeInfoDbData 1.2.14(2025-04-10); GenomicAlignments 1.44.0(2025-04-16); GenomicFeatures 1.60.0(2025-04-16); GenomicRanges 1.60.0(2025-04-16); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.4.0(2025-04-16); 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 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.16.0(2025-04-16); IRanges 2.42.0(2025-04-16); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.48.0(2025-04-16); 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 1.20.0(2025-04-16); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.38.0(2025-04-16); mime 0.13(2025-03-17); MultiAssayExperiment 1.34.0(2025-04-16); munsell 0.5.1(2024-04-01); OmnipathR 3.16.0(2025-04-16); pillar 1.10.2(2025-04-05); 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 1.9.1(2025-04-12); 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 1.98-1.17(2025-03-22); 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 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.24.0(2025-04-16); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.68.0(2025-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-04-16); S4Vectors 0.46.0(2025-04-16); 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 1.8.0(2025-04-16); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.0(2025-04-16); svglite 2.1.3(2023-12-08); systemfonts 1.2.2(2025-04-04); 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 1.4.0(2025-04-16); 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 0.48.0(2025-04-16); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-16 15:44:20] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Contains 1 files.
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:44:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-04-16 15:44:20] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (gINTomics)