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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL gINTomics
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘gINTomics’ ...
** this is package ‘gINTomics’ version ‘1.3.0’
** using staged installation
** R
[2025-03-21 20:10:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:10:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:29] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:10:29] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-21 20:10:29] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-21
[2025-03-21 20:10:29] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-21 19:21:20 UTC; unix
[2025-03-21 20:10:29] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-21 20:10:29] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-21 20:10:29] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-21; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA]
[2025-03-21 20:10:29] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-03-21 20:10:31] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-21); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-21); BiocBaseUtils 1.9.0(2025-03-21); BiocGenerics 0.53.6(2025-03-21); BiocIO 1.17.1(2025-03-21); BiocParallel 1.41.2(2025-03-21); Biostrings 2.75.4(2025-03-21); 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 2.23.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-21); GenomicFeatures 1.59.1(2025-03-21); GenomicRanges 1.59.1(2025-03-21); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-21); 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(2025-03-21); IRanges 2.41.3(2025-03-21); 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(2025-03-21); 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(2025-03-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-21); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-21); 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(2025-03-21); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-21); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-21); S4Vectors 0.45.4(2025-03-21); 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 1.7.7(2025-03-21); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-21 20:10:31] [INFO]    [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:31] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-03-21 20:10:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:10:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:10:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-21 20:10:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-21
[2025-03-21 20:10:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-21 19:21:20 UTC; unix
[2025-03-21 20:10:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-21 20:10:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-21 20:10:54] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-21; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA]
[2025-03-21 20:10:54] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-03-21 20:10:55] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-21); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-21); BiocBaseUtils 1.9.0(2025-03-21); BiocGenerics 0.53.6(2025-03-21); BiocIO 1.17.1(2025-03-21); BiocParallel 1.41.2(2025-03-21); Biostrings 2.75.4(2025-03-21); 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 2.23.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-21); GenomicFeatures 1.59.1(2025-03-21); GenomicRanges 1.59.1(2025-03-21); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-21); 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(2025-03-21); IRanges 2.41.3(2025-03-21); 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(2025-03-21); 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(2025-03-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-21); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-21); 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(2025-03-21); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-21); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-21); S4Vectors 0.45.4(2025-03-21); 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 1.7.7(2025-03-21); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-21 20:10:55] [INFO]    [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-21 20:10:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:10:55] [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
[2025-03-21 20:11:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:11:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:26] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:11:26] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-21 20:11:26] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-21
[2025-03-21 20:11:26] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-21 19:21:20 UTC; unix
[2025-03-21 20:11:26] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-21 20:11:26] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-21 20:11:27] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-21; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA]
[2025-03-21 20:11:27] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-03-21 20:11:27] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-21); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-21); BiocBaseUtils 1.9.0(2025-03-21); BiocGenerics 0.53.6(2025-03-21); BiocIO 1.17.1(2025-03-21); BiocParallel 1.41.2(2025-03-21); Biostrings 2.75.4(2025-03-21); 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 2.23.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-21); GenomicFeatures 1.59.1(2025-03-21); GenomicRanges 1.59.1(2025-03-21); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-21); 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(2025-03-21); IRanges 2.41.3(2025-03-21); 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(2025-03-21); 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(2025-03-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-21); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-21); 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(2025-03-21); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-21); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-21); S4Vectors 0.45.4(2025-03-21); 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 1.7.7(2025-03-21); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-21 20:11:27] [INFO]    [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:27] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-21 20:11:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:11:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:51] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:11:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-21 20:11:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-21
[2025-03-21 20:11:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-21 19:21:20 UTC; unix
[2025-03-21 20:11:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-21 20:11:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-21 20:11:52] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-02-19 r87757); os=openEuler 24.03 (LTS-SP1); system=aarch64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=UTC; date=2025-03-21; pandoc=2.12 @ /home/biocbuild/bin/ (via rmarkdown); quarto=NA]
[2025-03-21 20:11:52] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.51.0; png=1.6.40; jpeg=6.2; tiff=LIBTIFF, Version 4.6.0; tcl=8.6.14; curl=8.4.0; zlib=1.2.13; bzlib=1.0.8, 13-Jul-2019; xz=5.4.7; deflate=; PCRE=10.42 2022-12-11; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.38; readline=8.2; BLAS=/home/biocbuild/R/R-devel_2025-02-19/lib/libRblas.so; lapack=/home/biocbuild/R/R-devel_2025-02-19/lib/libRlapack.so; lapack_version=3.12.0]
[2025-03-21 20:11:52] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-21); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-21); BiocBaseUtils 1.9.0(2025-03-21); BiocGenerics 0.53.6(2025-03-21); BiocIO 1.17.1(2025-03-21); BiocParallel 1.41.2(2025-03-21); Biostrings 2.75.4(2025-03-21); 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 2.23.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-21); GenomicFeatures 1.59.1(2025-03-21); GenomicRanges 1.59.1(2025-03-21); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-21); 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(2025-03-21); IRanges 2.41.3(2025-03-21); 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(2025-03-21); 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(2025-03-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); MultiAssayExperiment 1.33.9(2025-03-21); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-21); 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(2025-03-21); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-21); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-21); S4Vectors 0.45.4(2025-03-21); 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 1.7.7(2025-03-21); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-21); 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(2025-03-21); 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(2025-03-21); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-21 20:11:52] [INFO]    [OmnipathR] CURL: version: 8.4.0; headers: 8.4.0; ssl_version: OpenSSL/3.0.12; libz_version: 1.2.13; libssh_version: libssh/0.10.5/openssl/zlib; libidn_version: 2.3.4; host: aarch64-openEuler-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-devel_2025-02-19/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-21 20:11:52] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (gINTomics)