Angelo Velle
| Snapshot Date: 2026-02-27 13:40 -0500 (Fri, 27 Feb 2026) |
| git_url: https://git.bioconductor.org/packages/gINTomics |
| git_branch: devel |
| git_last_commit: 4cacafe |
| git_last_commit_date: 2025-10-29 11:30:01 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-02-28 11:35 -0500 (Sat, 28 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4877 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4570 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 892/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gINTomics 1.7.0 (landing page) Angelo Velle
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for gINTomics in R Universe. | ||||||||||||||
|
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: 1.7.0 |
| 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_1.7.0.tar.gz |
| StartedAt: 2026-02-27 20:21:52 -0500 (Fri, 27 Feb 2026) |
| EndedAt: 2026-02-27 20:30:21 -0500 (Fri, 27 Feb 2026) |
| EllapsedTime: 508.6 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_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.7.0’
* 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
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:24:07] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-02-27 20:24:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-27 20:24:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-27
[2026-02-27 20:24:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-27 20:05:29 UTC; unix
[2026-02-27 20:24:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-27 20:24:07] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-27 20:24:07] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=macOS Sonoma 14.8.3; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-27; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-27 20:24:07] [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; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-02-27 20:24:07] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-02-27); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-02-27); BiocGenerics 0.57.0(2026-02-27); BiocIO 1.21.0(2026-02-27); BiocParallel 1.45.0(2026-02-27); Biostrings 2.79.4(2026-02-27); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-02-27); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-02-27); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-02-27); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); 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 1.47.0(2026-02-27); GenomicFeatures 1.63.1(2026-02-27); GenomicRanges 1.63.1(2026-02-27); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-02-27); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-02-27); IRanges 2.45.0(2026-02-27); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-02-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-02-27); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-02-27); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-02-27); OmnipathR 3.19.6(2026-02-27); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-02-27); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-02-27); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-02-27); S4Vectors 0.49.0(2026-02-27); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-02-27); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-02-27); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-02-27); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-02-27); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-27 20:24:07] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Contains 1 files.
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:24:07] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-02-27 20:24:07] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-27 20:24:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:24:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-27 20:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:24:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-27 20:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:24:08] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-27 20:24:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:24:08] [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 18.073 3.371 57.432
extract_model_res 5.924 0.721 10.404
plot_ridge 4.547 0.813 7.119
run_multiomics 3.007 0.572 6.270
* 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-3.23-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/4.6-arm64/Resources/library’ * installing *source* package ‘gINTomics’ ... ** this is package ‘gINTomics’ version ‘1.7.0’ ** using staged installation ** R [2026-02-27 15:26:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:13] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:13] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-27 15:26:13] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-27 [2026-02-27 15:26:13] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-27 20:05:29 UTC; unix [2026-02-27 15:26:13] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6 [2026-02-27 15:26:13] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-02-27 15:26:14] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=macOS Sonoma 14.8.3; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-27; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-02-27 15:26:14] [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; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-02-27 15:26:14] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-02-27); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-02-27); BiocGenerics 0.57.0(2026-02-27); BiocIO 1.21.0(2026-02-27); BiocParallel 1.45.0(2026-02-27); Biostrings 2.79.4(2026-02-27); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-02-27); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-02-27); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-02-27); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); 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 1.47.0(2026-02-27); GenomicFeatures 1.63.1(2026-02-27); GenomicRanges 1.63.1(2026-02-27); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-02-27); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-02-27); IRanges 2.45.0(2026-02-27); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-02-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-02-27); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-02-27); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-02-27); OmnipathR 3.19.6(2026-02-27); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-02-27); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-02-27); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-02-27); S4Vectors 0.49.0(2026-02-27); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-02-27); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-02-27); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-02-27); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-02-27); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-02-27 15:26:14] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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 [2026-02-27 15:26:14] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-27 15:26:14] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:14] [TRACE] [OmnipathR] Contains 1 files. [2026-02-27 15:26:14] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-27 15:26:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:14] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-02-27 15:26:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-02-27 15:26:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-02-27 15:26:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-27 15:26:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:14] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-02-27 15:26:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:14] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2026-02-27 15:26:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:21] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:21] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:21] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-27 15:26:21] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-27 [2026-02-27 15:26:21] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-27 20:05:29 UTC; unix [2026-02-27 15:26:21] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6 [2026-02-27 15:26:21] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-02-27 15:26:21] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=macOS Sonoma 14.8.3; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-27; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-02-27 15:26:22] [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; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-02-27 15:26:22] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-02-27); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-02-27); BiocGenerics 0.57.0(2026-02-27); BiocIO 1.21.0(2026-02-27); BiocParallel 1.45.0(2026-02-27); Biostrings 2.79.4(2026-02-27); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-02-27); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-02-27); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-02-27); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); 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 1.47.0(2026-02-27); GenomicFeatures 1.63.1(2026-02-27); GenomicRanges 1.63.1(2026-02-27); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-02-27); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-02-27); IRanges 2.45.0(2026-02-27); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-02-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-02-27); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-02-27); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-02-27); OmnipathR 3.19.6(2026-02-27); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-02-27); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-02-27); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-02-27); S4Vectors 0.49.0(2026-02-27); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-02-27); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-02-27); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-02-27); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-02-27); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-02-27 15:26:22] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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 [2026-02-27 15:26:22] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-27 15:26:22] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:22] [TRACE] [OmnipathR] Contains 1 files. [2026-02-27 15:26:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-27 15:26:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:22] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-02-27 15:26:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-02-27 15:26:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-02-27 15:26:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-27 15:26:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-02-27 15:26:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:22] [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 [2026-02-27 15:26:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:31] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:31] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-27 15:26:31] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-27 [2026-02-27 15:26:31] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-27 20:05:29 UTC; unix [2026-02-27 15:26:31] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6 [2026-02-27 15:26:31] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-02-27 15:26:32] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=macOS Sonoma 14.8.3; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-27; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-02-27 15:26:32] [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; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-02-27 15:26:32] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-02-27); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-02-27); BiocGenerics 0.57.0(2026-02-27); BiocIO 1.21.0(2026-02-27); BiocParallel 1.45.0(2026-02-27); Biostrings 2.79.4(2026-02-27); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-02-27); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-02-27); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-02-27); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); 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 1.47.0(2026-02-27); GenomicFeatures 1.63.1(2026-02-27); GenomicRanges 1.63.1(2026-02-27); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-02-27); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-02-27); IRanges 2.45.0(2026-02-27); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-02-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-02-27); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-02-27); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-02-27); OmnipathR 3.19.6(2026-02-27); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-02-27); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-02-27); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-02-27); S4Vectors 0.49.0(2026-02-27); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-02-27); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-02-27); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-02-27); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-02-27); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-02-27 15:26:32] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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 [2026-02-27 15:26:32] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-27 15:26:32] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:32] [TRACE] [OmnipathR] Contains 1 files. [2026-02-27 15:26:32] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-27 15:26:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:32] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-02-27 15:26:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-02-27 15:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-02-27 15:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-27 15:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:32] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-02-27 15:26:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:32] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-02-27 15:26:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-02-27 15:26:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-27 [2026-02-27 15:26:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-27 20:05:29 UTC; unix [2026-02-27 15:26:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6 [2026-02-27 15:26:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-02-27 15:26:40] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=macOS Sonoma 14.8.3; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-27; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-02-27 15:26:40] [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; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-02-27 15:26:40] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-02-27); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-02-27); BiocGenerics 0.57.0(2026-02-27); BiocIO 1.21.0(2026-02-27); BiocParallel 1.45.0(2026-02-27); Biostrings 2.79.4(2026-02-27); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-02-27); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-02-27); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-02-27); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); 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 1.47.0(2026-02-27); GenomicFeatures 1.63.1(2026-02-27); GenomicRanges 1.63.1(2026-02-27); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-02-27); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-02-27); IRanges 2.45.0(2026-02-27); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-02-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-02-27); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-02-27); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-02-27); OmnipathR 3.19.6(2026-02-27); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-02-27); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-02-27); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-02-27); S4Vectors 0.49.0(2026-02-27); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-02-27); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-02-27); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-02-27); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-02-27); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-02-27 15:26:40] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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 [2026-02-27 15:26:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-02-27 15:26:40] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:40] [TRACE] [OmnipathR] Contains 1 files. [2026-02-27 15:26:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-02-27 15:26:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-02-27 15:26:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-02-27 15:26:40] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-02-27 15:26:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-02-27 15:26:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-02-27 15:26:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-02-27 15:26:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-02-27 15:26:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-02-27 15:26:40] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (gINTomics)
gINTomics.Rcheck/tests/testthat.Rout
R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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)
[2026-02-27 20:27:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-02-27 20:27:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-27 20:27:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-27
[2026-02-27 20:27:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-02-27 20:05:29 UTC; unix
[2026-02-27 20:27:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-02-27 20:27:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-02-27 20:27:47] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=macOS Sonoma 14.8.3; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-27; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-27 20:27:47] [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; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=74.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-02-27 20:27:47] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-02-27); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-02-27); BiocGenerics 0.57.0(2026-02-27); BiocIO 1.21.0(2026-02-27); BiocParallel 1.45.0(2026-02-27); Biostrings 2.79.4(2026-02-27); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-02-27); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-02-27); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-02-27); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); 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 1.47.0(2026-02-27); GenomicFeatures 1.63.1(2026-02-27); GenomicRanges 1.63.1(2026-02-27); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-02-27); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-02-27); IRanges 2.45.0(2026-02-27); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-02-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-02-27); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-02-27); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-02-27); OmnipathR 3.19.6(2026-02-27); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-02-27); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-02-27); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-02-27); S4Vectors 0.49.0(2026-02-27); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-02-27); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-02-27); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-02-27); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); testthat 3.3.2(2026-01-11); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-02-27); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-27 20:27:47] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; 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
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Contains 8 files.
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-27 20:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-27 20:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-27 20:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-27 20:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:47] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check("gINTomics")
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2026-02-27 20:27:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-02-27 20:27:54] [INFO] [OmnipathR] Cache record does not exist: `db://organisms`
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Loading database `organisms` from source.
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:54] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:54] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-27 20:27:54] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-27 20:27:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-27 20:27:54] [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]
[2026-02-27 20:27:54] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-27 20:27:54] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-27 20:27:55] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-27 20:27:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 20:27:55] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.604705s from rescued.omnipathdb.org (65.9 Kb/s); Redirect: 0s, DNS look up: 0.023925s, Connection: 0.026489s, Pretransfer: 0.324124s, First byte at: 0.466886s
[2026-02-27 20:27:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 28 Feb 2026 01:27:54 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Sat, 28 Feb 2026 02:27:54 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-27 20:27:55] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Sat, 28 Feb 2026 01:27:54 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Sat, 28 Feb 2026 02:27:54 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-27 20:27:55] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-27 20:27:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:55] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-27 20:27:55] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-27 20:27:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-27 20:27:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-27 20:27:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-27 20:27:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-27 20:27:56] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-27 20:27:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-27 20:27:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-27 20:27:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 20:27:56] [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]
[2026-02-27 20:27:56] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-27 20:27:56] [TRACE] [OmnipathR] Downloaded 5.3 Kb in 0.157073s from omabrowser.org (34 Kb/s); Redirect: 0s, DNS look up: 0.001239s, Connection: 0.016924s, Pretransfer: 0.037073s, First byte at: 0.156909s
[2026-02-27 20:27:56] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 28 Feb 2026 01:27:56 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=yxS8DHnqTkhhPpiHGjBp%2F6okuJK%2B90EJKl5NySCmdGQ7Q0unU8hg9q%2BLPaWDTbNDz7aFD1m6%2FvUXXnz0O1SSBbGvLpan5qBYcF2dccdY"}]}; cf-ray: 9d4c2470c98c3b78-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-27 20:27:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-27 20:27:57] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:27:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:27:57] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-27 20:27:57] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-27 20:27:57] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-27 20:28:34] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-27 20:28:34] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-27 20:28:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:34] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-27 20:28:34] [TRACE] [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-02-27 20:28:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:34] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-02-27 20:28:34] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-27 20:28:35] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-02-27 20:28:35] [INFO] [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-02-27 20:28:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:35] [INFO] [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-02-27 20:28:35] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-27 20:28:35] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 20:28:35] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 20:28:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:35] [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`
[2026-02-27 20:28:35] [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`
[2026-02-27 20:28:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 20:28:35] [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]
[2026-02-27 20:28:37] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 20:28:37] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 1.796161s from omnipathdb.org (8.7 Kb/s); Redirect: 0s, DNS look up: 0.00526s, Connection: 0.008247s, Pretransfer: 0.155407s, First byte at: 1.79601s
[2026-02-27 20:28:37] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 28 Feb 2026 01:28:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 28 Feb 2026 02:28:36 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 20:28:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:38] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2026-02-27 20:28:38] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2026-02-27 20:28:38] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2026-02-27 20:28:38] [INFO] [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2026-02-27 20:28:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:38] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2026-02-27 20:28:39] [SUCCESS] [OmnipathR] Downloaded 11240 interactions.
[2026-02-27 20:28:39] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 20:28:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2026-02-27 20:28:39] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 20:28:39] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 20:28:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-27 20:28:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:40] [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`
[2026-02-27 20:28:40] [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`
[2026-02-27 20:28:40] [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`
[2026-02-27 20:28:40] [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`
[2026-02-27 20:28:40] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:40] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:40] [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`
[2026-02-27 20:28:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 20:28:40] [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]
[2026-02-27 20:28:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 20:28:41] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 1.447935s from omnipathdb.org (10.8 Kb/s); Redirect: 0s, DNS look up: 0.001143s, Connection: 0.002499s, Pretransfer: 0.147086s, First byte at: 1.44778s
[2026-02-27 20:28:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 28 Feb 2026 01:28:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 28 Feb 2026 02:28:41 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 20:28:42] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:42] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2026-02-27 20:28:42] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-02-27 20:28:42] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-02-27 20:28:42] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2026-02-27 20:28:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:42] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2026-02-27 20:28:42] [SUCCESS] [OmnipathR] Downloaded 3788 interactions.
[2026-02-27 20:28:43] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-27 20:28:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2026-02-27 20:28:43] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-27 20:28:43] [TRACE] [OmnipathR] Orthology targets:
[2026-02-27 20:28:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:43] [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`
[2026-02-27 20:28:43] [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`
[2026-02-27 20:28:43] [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`
[2026-02-27 20:28:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-27 20:28:43] [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]
[2026-02-27 20:28:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-27 20:28:48] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 5.027306s from omnipathdb.org (3.1 Kb/s); Redirect: 0s, DNS look up: 0.001115s, Connection: 0.002103s, Pretransfer: 0.145078s, First byte at: 5.026568s
[2026-02-27 20:28:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 28 Feb 2026 01:28:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Sat, 28 Feb 2026 02:28:48 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-27 20:28:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-02-27 20:28:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:51] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2026-02-27 20:28:51] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2026-02-27 20:28:51] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2026-02-27 20:28:51] [INFO] [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2026-02-27 20:28:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-27 20:28:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-27 20:28:51] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2026-02-27 20:28:56] [SUCCESS] [OmnipathR] Downloaded 69655 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 2 | SKIP 0 | PASS 201 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 201 ]
>
> proc.time()
user system elapsed
85.007 20.703 154.918
gINTomics.Rcheck/gINTomics-Ex.timings
| name | user | system | elapsed | |
| create_multiassay | 0.290 | 0.059 | 0.795 | |
| dot_plotly | 0.265 | 0.047 | 0.619 | |
| extract_model_res | 5.924 | 0.721 | 10.404 | |
| mirna_hsa | 0.009 | 0.003 | 0.011 | |
| mmultiassay_ov | 0.053 | 0.004 | 0.057 | |
| plot_chr_distribution | 0.376 | 0.098 | 0.489 | |
| plot_heatmap | 0.369 | 0.094 | 0.476 | |
| plot_network | 0.336 | 0.086 | 0.432 | |
| plot_ridge | 4.547 | 0.813 | 7.119 | |
| plot_tf_distribution | 0.253 | 0.059 | 0.572 | |
| plot_venn | 0.223 | 0.060 | 0.507 | |
| plot_volcano | 18.073 | 3.371 | 57.432 | |
| run_cnv_integration | 0.771 | 0.205 | 1.014 | |
| run_genomic_enrich | 0.325 | 0.073 | 0.402 | |
| run_genomic_integration | 0.682 | 0.182 | 0.890 | |
| run_met_integration | 0.391 | 0.122 | 0.940 | |
| run_multiomics | 3.007 | 0.572 | 6.270 | |
| run_shiny | 0.460 | 0.087 | 0.554 | |
| run_tf_enrich | 0.404 | 0.075 | 0.781 | |
| run_tf_integration | 1.480 | 0.231 | 2.458 | |