Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 872/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
gINTomics 1.5.0 (landing page) Angelo Velle
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the gINTomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: gINTomics |
Version: 1.5.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.5.0.tar.gz |
StartedAt: 2025-08-08 19:39:09 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 19:43:31 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 262.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: gINTomics.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/gINTomics.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gINTomics/DESCRIPTION’ ... OK * this is package ‘gINTomics’ version ‘1.5.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 42 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘gINTomics’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2025-08-08 19:40:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:40:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:40:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 19:40:37] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 19:40:37] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 19:40:37] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 19:40:37] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 19:40:37] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 19:40:37] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 19:40:38] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 19:40:38] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-08); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-08); BiocBaseUtils 1.11.2(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocIO 1.19.0(2025-08-08); BiocParallel 1.43.4(2025-08-08); Biostrings 2.77.2(2025-08-08); 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(2025-08-08); 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(2025-08-08); 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 1.45.2(2025-08-08); GenomicFeatures 1.61.6(2025-08-08); GenomicRanges 1.61.1(2025-08-08); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-08); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-08); IRanges 2.43.0(2025-08-08); 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(2025-08-08); 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(2025-08-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-08); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-08-08); OmnipathR 3.17.4(2025-08-08); 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 2.25.2(2025-08-08); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-08); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 19:40:38] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2025-08-08 19:40:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 19:40:38] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 19:40:38] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 19:40:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 19:40:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:40:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:40:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 19:40:38] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 19:40:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 19:40:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:40:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 19:40:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:40:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 19:40:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:40:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 19:40:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:40:38] [TRACE] [OmnipathR] Cache locked: FALSE .build_histo: no visible binding for global variable ‘chr_cov’ .build_histo: no visible binding for global variable ‘significance’ .build_ridge: no visible binding for global variable ‘coef’ .build_ridge: no visible binding for global variable ‘significance’ .circos_preprocess: no visible binding for global variable ‘cnv_met’ .find_deg: no visible global function definition for ‘combn’ .find_deg: no visible global function definition for ‘contrasts.fit’ .prepare_cnv_heatmap: no visible binding for global variable ‘cnv’ .prepare_gen_heatmap: no visible binding for global variable ‘met’ .prepare_gen_heatmap: no visible binding for global variable ‘cnv’ .prepare_met_heatmap: no visible binding for global variable ‘met’ .prepare_mirna_heatmap: no visible binding for global variable ‘mirna_cnv’ .prepare_network: no visible binding for global variable ‘omics’ .prepare_reactive_histo_tf: no visible binding for global variable ‘Freq’ .prepare_reactive_venn: no visible binding for global variable ‘cnv_met’ .prepare_reactive_venn: no visible binding for global variable ‘pval’ .reactive_cnv_test_plots: no visible binding for global variable ‘x’ .reactive_cnv_test_plots: no visible binding for global variable ‘y’ .reactive_transcExpr_plots: no visible binding for global variable ‘x’ .reactive_transcExpr_plots: no visible binding for global variable ‘y’ .run_reactive_tf_enrich: no visible binding for '<<-' assignment to ‘bg_process’ .server_enrich_bg : <anonymous>: no visible binding for global variable ‘bg_process’ .server_enrich_bgTF: no visible binding for '<<-' assignment to ‘bg_process’ .server_enrich_bgTF : <anonymous>: no visible binding for global variable ‘bg_process’ .shiny_preprocess: no visible binding for global variable ‘cov’ plot_tf_distribution: no visible binding for global variable ‘Freq’ Undefined global functions or variables: Freq bg_process chr_cov cnv cnv_met coef combn contrasts.fit cov met mirna_cnv omics pval significance x y Consider adding importFrom("stats", "coef", "cov") importFrom("utils", "combn") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: mmultiassay_ov.Rd: MultiAssayExperiment-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot_volcano 14.407 1.366 25.926 extract_model_res 4.925 0.317 5.318 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/gINTomics.Rcheck/00check.log’ for details.
gINTomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gINTomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘gINTomics’ ... ** this is package ‘gINTomics’ version ‘1.5.0’ ** using staged installation ** R [2025-08-08 15:24:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:24:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:42] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:24:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 15:24:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 15:24:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 15:24:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 15:24:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 15:24:42] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 15:24:42] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 15:24:42] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-08); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-08); BiocBaseUtils 1.11.2(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocIO 1.19.0(2025-08-08); BiocParallel 1.43.4(2025-08-08); Biostrings 2.77.2(2025-08-08); 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(2025-08-08); 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(2025-08-08); 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 1.45.2(2025-08-08); GenomicFeatures 1.61.6(2025-08-08); GenomicRanges 1.61.1(2025-08-08); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-08); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-08); IRanges 2.43.0(2025-08-08); 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(2025-08-08); 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(2025-08-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-08); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-08-08); OmnipathR 3.17.4(2025-08-08); 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 2.25.2(2025-08-08); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-08); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 15:24:42] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2025-08-08 15:24:42] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 15:24:42] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:24:42] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 15:24:42] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 15:24:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:24:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:24:42] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 15:24:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 15:24:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 15:24:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 15:24:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:42] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 15:24:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:42] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2025-08-08 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:49] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:24:49] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 15:24:49] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 15:24:49] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 15:24:49] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 15:24:49] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 15:24:49] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 15:24:49] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 15:24:49] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-08); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-08); BiocBaseUtils 1.11.2(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocIO 1.19.0(2025-08-08); BiocParallel 1.43.4(2025-08-08); Biostrings 2.77.2(2025-08-08); 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(2025-08-08); 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(2025-08-08); 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 1.45.2(2025-08-08); GenomicFeatures 1.61.6(2025-08-08); GenomicRanges 1.61.1(2025-08-08); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-08); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-08); IRanges 2.43.0(2025-08-08); 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(2025-08-08); 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(2025-08-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-08); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-08-08); OmnipathR 3.17.4(2025-08-08); 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 2.25.2(2025-08-08); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-08); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 15:24:49] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2025-08-08 15:24:49] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 15:24:49] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:24:49] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 15:24:49] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:24:49] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:49] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 15:24:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:24:49] [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 [2025-08-08 15:25:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:25:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:00] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:25:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 15:25:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 15:25:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 15:25:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 15:25:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 15:25:00] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 15:25:01] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 15:25:01] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-08); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-08); BiocBaseUtils 1.11.2(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocIO 1.19.0(2025-08-08); BiocParallel 1.43.4(2025-08-08); Biostrings 2.77.2(2025-08-08); 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(2025-08-08); 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(2025-08-08); 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 1.45.2(2025-08-08); GenomicFeatures 1.61.6(2025-08-08); GenomicRanges 1.61.1(2025-08-08); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-08); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-08); IRanges 2.43.0(2025-08-08); 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(2025-08-08); 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(2025-08-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-08); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-08-08); OmnipathR 3.17.4(2025-08-08); 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 2.25.2(2025-08-08); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-08); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 15:25:01] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2025-08-08 15:25:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 15:25:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:25:01] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 15:25:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 15:25:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:25:01] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 15:25:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 15:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 15:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 15:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 15:25:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:01] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-08 15:25:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:25:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:08] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:25:08] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 15:25:08] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 15:25:08] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 15:25:08] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 15:25:08] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 15:25:08] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 15:25:09] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 15:25:09] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-08); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-08); BiocBaseUtils 1.11.2(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocIO 1.19.0(2025-08-08); BiocParallel 1.43.4(2025-08-08); Biostrings 2.77.2(2025-08-08); 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(2025-08-08); 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(2025-08-08); 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 1.45.2(2025-08-08); GenomicFeatures 1.61.6(2025-08-08); GenomicRanges 1.61.1(2025-08-08); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-08); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-08); IRanges 2.43.0(2025-08-08); 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(2025-08-08); 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(2025-08-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-08); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-08-08); OmnipathR 3.17.4(2025-08-08); 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 2.25.2(2025-08-08); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-08); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 15:25:09] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2025-08-08 15:25:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 15:25:09] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:25:09] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 15:25:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 15:25:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:25:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:25:09] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 15:25:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 15:25:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 15:25:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 15:25:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 15:25:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:25:09] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (gINTomics)
gINTomics.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(gINTomics) [2025-08-08 19:42:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:28] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 19:42:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 19:42:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 19:42:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 19:42:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 19:42:28] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 19:42:29] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 19:42:29] [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=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 19:42:29] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-08); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-08); BiocBaseUtils 1.11.2(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocIO 1.19.0(2025-08-08); BiocParallel 1.43.4(2025-08-08); Biostrings 2.77.2(2025-08-08); 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); brio 1.1.5(2024-04-24); 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(2025-08-08); 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(2025-08-08); 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 1.45.2(2025-08-08); GenomicFeatures 1.61.6(2025-08-08); GenomicRanges 1.61.1(2025-08-08); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-08); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-08); IRanges 2.43.0(2025-08-08); 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(2025-08-08); 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(2025-08-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-08); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.6(2025-08-08); OmnipathR 3.17.4(2025-08-08); 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 2.25.2(2025-08-08); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-08); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); testthat 3.2.3(2025-01-13); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 19:42:29] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; 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 [2025-08-08 19:42:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 19:42:29] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 19:42:29] [TRACE] [OmnipathR] Contains 7 files. [2025-08-08 19:42:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 19:42:29] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 19:42:29] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 19:42:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 19:42:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 19:42:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 19:42:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:29] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 19:42:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:29] [TRACE] [OmnipathR] Cache locked: FALSE > > test_check("gINTomics") [2025-08-08 19:42:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 19:42:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget] [2025-08-08 19:42:31] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-08-08 19:42:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:31] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-08-08 19:42:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:31] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-08-08 19:42:31] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-08-08 19:42:31] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-08-08 19:42:31] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-08-08 19:42:31] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-08-08 19:42:31] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-08-08 19:42:31] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-08-08 19:42:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-08 19:42:31] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-08-08 19:42:31] [TRACE] [OmnipathR] Sending HTTP request. [2025-08-08 19:42:32] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-08-08 19:42:32] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 19:42:32] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 0.686298s from www.ensembl.org (45.5 Kb/s); Redirect: 0.481253s, DNS look up: 0.011506s, Connection: 0.015972s, Pretransfer: 0.356033s, First byte at: 0.655526s [2025-08-08 19:42:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Fri, 08 Aug 2025 23:42:31 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-32.ebi.ac.uk; HTTP/2 302 ; date: Fri, 08 Aug 2025 23:42:32 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-86.us-east-2.compute.internal; HTTP/2 200 ; date: Fri, 08 Aug 2025 23:42:32 GMT; content-type: text/html; charset=utf-8; content-length: 31944; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Sat, 09 Aug 2025 23:40:30 GMT; set-cookie: ENSEMBL_WWW_SESSION=9d9d6bd2ab3ec31c0cd2e8be68e5a4ee01da72e89fc22b57753fdc67; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Sat, 09 Aug 2025 23:40:30 GMT; set-cookie: ENSEMBL_WWW_SESSION=9d9d6bd2ab3ec31c0cd2e8be68e5a4ee01da72e89fc22b57753fdc67; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; vary: Accept-Encoding; content-encoding: gzip; x-frame-options: SAMEORIGIN; content-security-policy: frame-ancestors 'self'; x-nginx-machine: ip-10-25-25-73.us-east-2.compute.internal [2025-08-08 19:42:32] [TRACE] [OmnipathR] Response headers: [date=Fri, 08 Aug 2025 23:42:32 GMT,content-type=text/html; charset=utf-8,content-length=31944,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Sat, 09 Aug 2025 23:40:30 GMT,set-cookie=ENSEMBL_WWW_SESSION=9d9d6bd2ab3ec31c0cd2e8be68e5a4ee01da72e89fc22b57753fdc67; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Sat, 09 Aug 2025 23:40:30 GMT,set-cookie=ENSEMBL_WWW_SESSION=9d9d6bd2ab3ec31c0cd2e8be68e5a4ee01da72e89fc22b57753fdc67; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-73.us-east-2.compute.internal] [2025-08-08 19:42:32] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-08-08 19:42:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:32] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-08-08 19:42:32] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 19:42:32] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-08-08 19:42:32] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-08-08 19:42:32] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-08-08 19:42:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:32] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-08-08 19:42:32] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-08 19:42:32] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-08-08 19:42:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-08-08 19:42:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 19:42:32] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-08 19:42:33] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 19:42:33] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.457167s from omabrowser.org (19 Kb/s); Redirect: 0s, DNS look up: 0.004758s, Connection: 0.005712s, Pretransfer: 0.365032s, First byte at: 0.457014s [2025-08-08 19:42:33] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 08 Aug 2025 23:42:33 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip [2025-08-08 19:42:34] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-08 19:42:34] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-08-08 19:42:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:34] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-08-08 19:42:34] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 19:42:34] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-08-08 19:42:34] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-08 19:42:34] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-08-08 19:42:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:34] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-08-08 19:42:34] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-08-08 19:42:34] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-08 19:42:34] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-08 19:42:47] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-08-08 19:42:47] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-08-08 19:42:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:47] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-08-08 19:42:47] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-08-08 19:42:47] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 19:42:47] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 19:42:47] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:47] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:47] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:47] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:47] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:47] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:47] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 19:42:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-08 19:42:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 19:42:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.306774s from omnipathdb.org (51.1 Kb/s); Redirect: 0s, DNS look up: 0.000961s, Connection: 0.00189s, Pretransfer: 0.155634s, First byte at: 0.306557s [2025-08-08 19:42:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 08 Aug 2025 23:42:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 00:42:47 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 19:42:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:49] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`. [2025-08-08 19:42:49] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`. [2025-08-08 19:42:49] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`. [2025-08-08 19:42:49] [INFO] [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1] [2025-08-08 19:42:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:49] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`. [2025-08-08 19:42:49] [SUCCESS] [OmnipathR] Downloaded 11118 interactions. [2025-08-08 19:42:49] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 19:42:49] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna] [2025-08-08 19:42:49] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 19:42:49] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 19:42:49] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 19:42:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:49] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:49] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 19:42:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-08 19:42:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 19:42:50] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.312633s from omnipathdb.org (50.1 Kb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.002016s, Pretransfer: 0.160873s, First byte at: 0.312399s [2025-08-08 19:42:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 08 Aug 2025 23:42:50 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 00:42:50 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 19:42:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:51] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`. [2025-08-08 19:42:51] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2025-08-08 19:42:51] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`. [2025-08-08 19:42:51] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1] [2025-08-08 19:42:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:51] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`. [2025-08-08 19:42:51] [SUCCESS] [OmnipathR] Downloaded 3868 interactions. [2025-08-08 19:42:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 19:42:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target] [2025-08-08 19:42:51] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 19:42:51] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 19:42:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 19:42:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-08 19:42:51] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 19:42:51] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.307517s from omnipathdb.org (50.9 Kb/s); Redirect: 0s, DNS look up: 0.000868s, Connection: 0.001932s, Pretransfer: 0.156085s, First byte at: 0.30731s [2025-08-08 19:42:51] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 08 Aug 2025 23:42:51 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 00:42:51 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 19:42:53] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic` [2025-08-08 19:42:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:53] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`. [2025-08-08 19:42:53] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`. [2025-08-08 19:42:53] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`. [2025-08-08 19:42:53] [INFO] [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1] [2025-08-08 19:42:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 19:42:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 19:42:53] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`. [2025-08-08 19:42:54] [SUCCESS] [OmnipathR] Downloaded 59469 interactions. 'select()' returned many:many mapping between keys and columns Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames response_var and covariates have common colnames, adding '_cov' to covariates colnames response_var and covariates have common colnames, adding '_cov' to covariates colnames response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames response_var and covariates have common colnames, adding '_cov' to covariates colnames response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions response_var and covariates have common colnames, adding '_cov' to covariates colnames Generating interactions Generating interactions 'select()' returned many:many mapping between keys and columns [ FAIL 0 | WARN 4 | SKIP 0 | PASS 204 ] [ FAIL 0 | WARN 4 | SKIP 0 | PASS 204 ] > > proc.time() user system elapsed 68.871 12.446 64.291
gINTomics.Rcheck/gINTomics-Ex.timings
name | user | system | elapsed | |
create_multiassay | 0.210 | 0.027 | 0.251 | |
dot_plotly | 0.216 | 0.025 | 0.243 | |
extract_model_res | 4.925 | 0.317 | 5.318 | |
mirna_hsa | 0.006 | 0.001 | 0.008 | |
mmultiassay_ov | 0.047 | 0.002 | 0.049 | |
plot_chr_distribution | 0.200 | 0.041 | 0.238 | |
plot_heatmap | 0.198 | 0.038 | 0.234 | |
plot_network | 0.202 | 0.039 | 0.239 | |
plot_ridge | 3.463 | 0.327 | 3.828 | |
plot_tf_distribution | 0.181 | 0.022 | 0.205 | |
plot_venn | 0.165 | 0.024 | 0.204 | |
plot_volcano | 14.407 | 1.366 | 25.926 | |
run_cnv_integration | 0.289 | 0.049 | 0.340 | |
run_genomic_enrich | 0.173 | 0.020 | 0.192 | |
run_genomic_integration | 0.343 | 0.058 | 0.412 | |
run_met_integration | 0.300 | 0.060 | 0.386 | |
run_multiomics | 2.062 | 0.145 | 2.804 | |
run_shiny | 0.180 | 0.027 | 0.218 | |
run_tf_enrich | 0.171 | 0.023 | 0.196 | |
run_tf_integration | 0.909 | 0.062 | 0.981 | |