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##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL gINTomics
###
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'gINTomics' ...
** this is package 'gINTomics' version '1.5.0'
** using staged installation
** R
[2025-07-13 16:25:13] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:25:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:25:13] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:25:13] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-13 16:25:13] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-13
[2025-07-13 16:25:13] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-13 19:56:43 UTC; windows
[2025-07-13 16:25:13] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.1
[2025-07-13 16:25:13] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmps1Lxo0/file16d2411634458". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmps1Lxo0/file16d2411634458 -V' had status 1
[2025-07-13 16:25:16] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-07-13; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-07-13 16:25:16] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-07-13 16:25:17] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.0(2025-07-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-13); BiocBaseUtils 1.11.1(2025-07-13); BiocGenerics 0.55.0(2025-07-13); BiocIO 1.19.0(2025-07-13); BiocParallel 1.43.4(2025-07-13); Biostrings 2.77.2(2025-07-13); 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 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.1(2025-07-13); GenomicFeatures 1.61.4(2025-07-13); GenomicRanges 1.61.1(2025-07-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.0(2025-07-13); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-13); IRanges 2.43.0(2025-07-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.3(2025-07-13); OmnipathR 3.17.1(2025-07-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.1(2025-07-13); RSQLite 2.4.1(2025-06-08); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-13); S4Vectors 0.47.0(2025-07-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.1(2025-07-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.0(2025-07-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-13 16:25:17] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; 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, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:25:17] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-13 16:25:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:25:18] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-13 16:25:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:25:18] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-13 16:25:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:25:18] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-13 16:25:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:25:18] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-07-13 16:26:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:26:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:01] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:26:01] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-13 16:26:01] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-13
[2025-07-13 16:26:01] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-13 19:56:43 UTC; windows
[2025-07-13 16:26:01] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.1
[2025-07-13 16:26:01] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp65l5Jj/file1527c23765af6". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/Rtmp65l5Jj/file1527c23765af6 -V' had status 1
[2025-07-13 16:26:03] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-07-13; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-07-13 16:26:03] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-07-13 16:26:04] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.0(2025-07-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-13); BiocBaseUtils 1.11.1(2025-07-13); BiocGenerics 0.55.0(2025-07-13); BiocIO 1.19.0(2025-07-13); BiocParallel 1.43.4(2025-07-13); Biostrings 2.77.2(2025-07-13); 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 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.1(2025-07-13); GenomicFeatures 1.61.4(2025-07-13); GenomicRanges 1.61.1(2025-07-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.0(2025-07-13); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-13); IRanges 2.43.0(2025-07-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.3(2025-07-13); OmnipathR 3.17.1(2025-07-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.1(2025-07-13); RSQLite 2.4.1(2025-06-08); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-13); S4Vectors 0.47.0(2025-07-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.1(2025-07-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.0(2025-07-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-13 16:26:04] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; 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, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:04] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:04] [TRACE]   [OmnipathR] Cache locked: FALSE
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-07-13 16:26:56] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:26:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:56] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:26:56] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-13 16:26:56] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-13
[2025-07-13 16:26:56] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-13 19:56:43 UTC; windows
[2025-07-13 16:26:56] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.1
[2025-07-13 16:26:56] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpSYJEfl/file20a54757f6cbb". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpSYJEfl/file20a54757f6cbb -V' had status 1
[2025-07-13 16:26:57] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-07-13; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-07-13 16:26:57] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-07-13 16:26:58] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.0(2025-07-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-13); BiocBaseUtils 1.11.1(2025-07-13); BiocGenerics 0.55.0(2025-07-13); BiocIO 1.19.0(2025-07-13); BiocParallel 1.43.4(2025-07-13); Biostrings 2.77.2(2025-07-13); 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 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.1(2025-07-13); GenomicFeatures 1.61.4(2025-07-13); GenomicRanges 1.61.1(2025-07-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.0(2025-07-13); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-13); IRanges 2.43.0(2025-07-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.3(2025-07-13); OmnipathR 3.17.1(2025-07-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.1(2025-07-13); RSQLite 2.4.1(2025-06-08); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-13); S4Vectors 0.47.0(2025-07-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.1(2025-07-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.0(2025-07-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-13 16:26:58] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; 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, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:58] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:26:58] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-07-13 16:27:16] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:27:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:27:16] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:27:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-07-13 16:27:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-07-13
[2025-07-13 16:27:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-07-13 19:56:43 UTC; windows
[2025-07-13 16:27:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.1
[2025-07-13 16:27:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
ERROR: Unknown command "TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpCsunyJ/filed7c04545b9c". Did you mean command "update"?
Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=",  :
  running command '"quarto" TMPDIR=F:/biocbuild/bbs-3.22-bioc/tmpdir/RtmpCsunyJ/filed7c04545b9c -V' had status 1
[2025-07-13 16:27:18] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-07-13; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA @ C:\PROGRA~1\Quarto\bin\quarto.exe]
[2025-07-13 16:27:18] [INFO]    [OmnipathR] External libraries: [cairo=1.18.4; cairoFT=; pango=; png=1.6.48; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.13.0; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.8.1; deflate=1.24; PCRE=10.45 2025-02-05; ICU=77.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-07-13 16:27:18] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.0(2025-07-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-07-13); BiocBaseUtils 1.11.1(2025-07-13); BiocGenerics 0.55.0(2025-07-13); BiocIO 1.19.0(2025-07-13); BiocParallel 1.43.4(2025-07-13); Biostrings 2.77.2(2025-07-13); 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 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-07-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-07-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.1(2025-07-13); GenomicFeatures 1.61.4(2025-07-13); GenomicRanges 1.61.1(2025-07-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-07-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.0(2025-07-13); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-07-13); IRanges 2.43.0(2025-07-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-07-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-07-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-07-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.3(2025-07-13); OmnipathR 3.17.1(2025-07-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.1(2025-07-13); RSQLite 2.4.1(2025-06-08); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-07-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-07-13); S4Vectors 0.47.0(2025-07-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.1(2025-07-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.0(2025-07-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-07-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-07-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-07-13 16:27:18] [INFO]    [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; 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, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-07-13 16:27:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-07-13 16:27:18] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:27:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:27:19] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-07-13 16:27:19] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (gINTomics)