Angelo Velle
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| 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 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| 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 878/2325 | 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 | | ||||||||
|
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: 2025-11-13 20:15:18 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 20:31:46 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 988.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: gINTomics.Rcheck |
| Warnings: 0 |
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### 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
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* 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 13.7.8
* 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
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:17:22] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-13 20:17:22] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-13 20:17:22] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13
[2025-11-13 20:17:22] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix
[2025-11-13 20:17:22] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-13 20:17:22] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-13 20:17:22] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-13 20:17:22] [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=1.2.11; 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=70.2; 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]
[2025-11-13 20:17:22] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); 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(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); OmnipathR 3.19.0(2025-11-13); 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 1.2.0(2025-11-04); 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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-13); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-13 20:17:22] [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
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Contains 1 files.
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:17:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-13 20:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:17:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-13 20:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
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[2025-11-13 20:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
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[2025-11-13 20:17:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:17:22] [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 19.686 2.870 333.877
extract_model_res 5.816 0.462 8.247
plot_ridge 4.028 0.496 6.133
run_multiomics 2.952 0.359 6.254
* 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 [2025-11-13 15:28:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-13 15:28:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13 [2025-11-13 15:28:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix [2025-11-13 15:28:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-11-13 15:28:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-13 15:28:31] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-13 15:28:31] [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=1.2.11; 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=70.2; 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] [2025-11-13 15:28:31] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); 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(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); OmnipathR 3.19.0(2025-11-13); 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 1.2.0(2025-11-04); 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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-13); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-13 15:28:31] [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 [2025-11-13 15:28:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-13 15:28:31] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:31] [TRACE] [OmnipathR] Contains 1 files. [2025-11-13 15:28:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-13 15:28:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:31] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-11-13 15:28:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-13 15:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-13 15:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-13 15:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-13 15:28:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:31] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2025-11-13 15:28:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:38] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:38] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-13 15:28:38] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13 [2025-11-13 15:28:38] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix [2025-11-13 15:28:38] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-11-13 15:28:38] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-13 15:28:38] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-13 15:28:38] [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; curl=8.7.1; zlib=1.2.11; 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=70.2; 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] [2025-11-13 15:28:39] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); 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(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); OmnipathR 3.19.0(2025-11-13); 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 1.2.0(2025-11-04); 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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-13); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-13 15:28:39] [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 [2025-11-13 15:28:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-13 15:28:39] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:39] [TRACE] [OmnipathR] Contains 1 files. [2025-11-13 15:28:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-13 15:28:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:39] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-11-13 15:28:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-13 15:28:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-13 15:28:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-13 15:28:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-13 15:28:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:39] [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 [2025-11-13 15:28:49] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:49] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:49] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-13 15:28:49] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13 [2025-11-13 15:28:49] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix [2025-11-13 15:28:49] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-11-13 15:28:49] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-13 15:28:49] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-13 15:28:50] [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=1.2.11; 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=70.2; 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] [2025-11-13 15:28:50] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); 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(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); OmnipathR 3.19.0(2025-11-13); 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 1.2.0(2025-11-04); 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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-13); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-13 15:28:50] [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 [2025-11-13 15:28:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-13 15:28:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:50] [TRACE] [OmnipathR] Contains 1 files. [2025-11-13 15:28:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-13 15:28:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:50] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-11-13 15:28:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-13 15:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-13 15:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-13 15:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-13 15:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-11-13 15:28:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:57] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:57] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-11-13 15:28:57] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13 [2025-11-13 15:28:57] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix [2025-11-13 15:28:57] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0 [2025-11-13 15:28:57] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2025-11-13 15:28:57] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-11-13 15:28:57] [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=1.2.11; 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=70.2; 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] [2025-11-13 15:28:58] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); 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(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); OmnipathR 3.19.0(2025-11-13); 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 1.2.0(2025-11-04); 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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-13); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-11-13 15:28:58] [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 [2025-11-13 15:28:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-11-13 15:28:58] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:58] [TRACE] [OmnipathR] Contains 1 files. [2025-11-13 15:28:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-11-13 15:28:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-11-13 15:28:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-11-13 15:28:58] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-11-13 15:28:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-11-13 15:28:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-11-13 15:28:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-11-13 15:28:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-11-13 15:28:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-11-13 15:28:58] [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) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
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> library(testthat)
> library(gINTomics)
[2025-11-13 20:25:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:19] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-13 20:25:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-13 20:25:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13
[2025-11-13 20:25:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix
[2025-11-13 20:25:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-13 20:25:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-13 20:25:19] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-13 20:25:20] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6; curl=8.7.1; zlib=1.2.11; 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=70.2; 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]
[2025-11-13 20:25:20] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); 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(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); OmnipathR 3.19.0(2025-11-13); 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 1.2.0(2025-11-04); 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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-13); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); testthat 3.3.0(2025-11-13); textshaping 1.0.4(2025-10-10); 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 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-13 20:25:20] [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
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Contains 8 files.
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:25:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-13 20:25:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-13 20:25:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-13 20:25:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-13 20:25:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:20] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check("gINTomics")
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2025-11-13 20:25:28] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:25:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:28] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:25:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:25:28] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-11-13 20:25:28] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-13 20:25:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:25:28] [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]
[2025-11-13 20:25:28] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:25:28] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-13 20:27:28] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-11-13 20:27:33] [TRACE] [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-13 20:27:33] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-13 20:27:33] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:27:33] [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]
[2025-11-13 20:27:33] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:27:33] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-13 20:28:34] [WARN] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-11-13 20:28:39] [TRACE] [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-13 20:28:39] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-13 20:28:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:28:39] [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]
[2025-11-13 20:28:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:28:39] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-13 20:30:10] [ERROR] [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-11-13 20:30:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-13 20:30:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13
[2025-11-13 20:30:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix
[2025-11-13 20:30:10] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-13 20:30:10] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-13 20:30:10] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-13 20:30:10] [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=1.2.11; 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=70.2; 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]
[2025-11-13 20:30:11] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocFileCache 3.1.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); biomaRt 2.67.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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); clusterProfiler 4.19.1(2025-11-13); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dbplyr 2.5.1(2025-09-10); DelayedArray 0.37.0(2025-11-13); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); DOSE 4.5.0(2025-11-13); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.9.0(2025-11-13); enrichplot 1.31.0(2025-11-13); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.37.0(2025-11-13); filelock 1.0.3(2023-12-11); fontawesome 0.5.3(2024-11-16); fontBitstreamVera 0.1.1(2017-02-01); fontLiberation 0.1.0(2016-10-15); fontquiver 0.2.1(2017-02-01); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); gdtools 0.4.4(2025-10-06); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.2(2025-10-07); ggplot2 4.0.0(2025-09-11); ggplotify 0.1.3(2025-09-20); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); ggtangle 0.0.8(2025-11-06); ggtree 4.1.1(2025-11-13); ggvenn 0.1.19(2025-10-08); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-11-12); GOSemSim 2.37.0(2025-11-13); graph 1.89.0(2025-11-13); graphite 1.57.0(2025-11-13); graphlayouts 1.2.2(2025-01-23); gridExtra 2.3(2017-09-09); gridGraphics 0.5-1(2020-12-13); gson 0.1.0(2023-03-07); gtable 0.3.6(2024-10-25); gtools 3.9.5(2023-11-20); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); limma 3.67.0(2025-11-13); locfit 1.5-9.12(2025-03-05); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); nlme 3.1-168(2025-03-31); OmnipathR 3.19.0(2025-11-13); org.Hs.eg.db 3.22.0(2025-11-12); org.Mm.eg.db 3.22.0(2025-11-12); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); plyr 1.8.9(2023-10-02); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); 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 1.2.0(2025-11-04); qvalue 2.43.0(2025-11-13); 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); randomForest 4.7-1.2(2024-09-22); 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); reactome.db 1.94.0(2025-11-12); ReactomePA 1.55.0(2025-11-13); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.7.0(2025-11-13); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.11.1(2025-11-13); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); testthat 3.3.0(2025-11-13); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); tidytree 0.4.6(2023-12-12); timechange 0.3.0(2024-01-18); treeio 1.35.0(2025-11-13); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-11-12); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-11-12); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); visNetwork 2.1.4(2025-09-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-11-13 20:30:11] [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
[2025-11-13 20:30:11] [ERROR] [OmnipathR] Failed to download Ensembl organisms table.
[2025-11-13 20:30:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-13 20:30:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-13
[2025-11-13 20:30:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-13 20:05:04 UTC; unix
[2025-11-13 20:30:11] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-13 20:30:11] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-13 20:30:12] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-11-04 r88984); os=macOS Ventura 13.7.8; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-13; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-13 20:30:12] [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=1.2.11; 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=70.2; 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]
[2025-11-13 20:30:12] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-13); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-13); BiocFileCache 3.1.0(2025-11-13); BiocGenerics 0.57.0(2025-11-13); BiocIO 1.21.0(2025-11-13); BiocParallel 1.45.0(2025-11-13); biomaRt 2.67.0(2025-11-13); Biostrings 2.79.2(2025-11-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); callr 3.7.6(2024-03-25); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-13); 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); clusterProfiler 4.19.1(2025-11-13); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-13); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); dbplyr 2.5.1(2025-09-10); DelayedArray 0.37.0(2025-11-13); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.38(2025-11-12); doParallel 1.0.17(2022-02-07); DOSE 4.5.0(2025-11-13); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.9.0(2025-11-13); enrichplot 1.31.0(2025-11-13); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.37.0(2025-11-13); filelock 1.0.3(2023-12-11); fontawesome 0.5.3(2024-11-16); fontBitstreamVera 0.1.1(2017-02-01); fontLiberation 0.1.0(2016-10-15); fontquiver 0.2.1(2017-02-01); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); gdtools 0.4.4(2025-10-06); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2025-11-13); GenomicFeatures 1.63.1(2025-11-13); GenomicRanges 1.63.0(2025-11-13); GetoptLong 1.0.5(2020-12-15); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.2(2025-10-07); ggplot2 4.0.0(2025-09-11); ggplotify 0.1.3(2025-09-20); ggraph 2.2.2(2025-08-24); ggrepel 0.9.6(2024-09-07); ggridges 0.5.7(2025-08-27); ggtangle 0.0.8(2025-11-06); ggtree 4.1.1(2025-11-13); ggvenn 0.1.19(2025-10-08); gINTomics 1.7.0(2025-11-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.22.0(2025-11-12); GOSemSim 2.37.0(2025-11-13); graph 1.89.0(2025-11-13); graphite 1.57.0(2025-11-13); graphlayouts 1.2.2(2025-01-23); gridExtra 2.3(2017-09-09); gridGraphics 0.5-1(2020-12-13); gson 0.1.0(2023-03-07); gtable 0.3.6(2024-10-25); gtools 3.9.5(2023-11-20); hms 1.1.4(2025-10-17); 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 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-13); IRanges 2.45.0(2025-11-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-13); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); limma 3.67.0(2025-11-13); locfit 1.5-9.12(2025-03-05); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.1(2025-11-13); nlme 3.1-168(2025-03-31); OmnipathR 3.19.0(2025-11-13); org.Hs.eg.db 3.22.0(2025-11-12); org.Mm.eg.db 3.22.0(2025-11-12); otel 0.2.0(2025-08-29); patchwork 1.3.2(2025-08-25); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); plyr 1.8.9(2023-10-02); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); 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 1.2.0(2025-11-04); qvalue 2.43.0(2025-11-13); 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); randomForest 4.7-1.2(2024-09-22); 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); reactome.db 1.94.0(2025-11-12); ReactomePA 1.55.0(2025-11-13); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-13); RSQLite 2.4.4(2025-11-10); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-13); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-13); S4Vectors 0.49.0(2025-11-13); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.7.0(2025-11-13); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.11.1(2025-11-13); statmod 1.5.1(2025-10-09); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.0(2025-11-13); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); testthat 3.3.0(2025-11-13); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidygraph 1.3.1(2024-01-30); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); tidytree 0.4.6(2023-12-12); timechange 0.3.0(2024-01-18); treeio 1.35.0(2025-11-13); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.22.0(2025-11-12); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-11-12); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridis 0.6.5(2024-01-29); viridisLite 0.4.2(2023-05-02); visNetwork 2.1.4(2025-09-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-13); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-11-13 20:30:12] [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
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Accessing Ensembl organisms table from rescued repo.
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:12] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:12] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-11-13 20:30:12] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-11-13 20:30:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:30:12] [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]
[2025-11-13 20:30:12] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-13 20:30:12] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-11-13 20:30:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.67302s from rescued.omnipathdb.org (59.2 Kb/s); Redirect: 0s, DNS look up: 0.00094s, Connection: 0.002074s, Pretransfer: 0.343266s, First byte at: 0.51773s
[2025-11-13 20:30:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 14 Nov 2025 01:30:12 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: Fri, 14 Nov 2025 02:30:12 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-13 20:30:12] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 14 Nov 2025 01:30:12 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=Fri, 14 Nov 2025 02:30:12 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2025-11-13 20:30:13] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2025-11-13 20:30:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:13] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-13 20:30:14] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:14] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-13 20:30:14] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-11-13 20:30:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-13 20:30:14] [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]
[2025-11-13 20:30:14] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-13 20:30:14] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.504259s from omabrowser.org (17.2 Kb/s); Redirect: 0s, DNS look up: 0.00081s, Connection: 0.001444s, Pretransfer: 0.401686s, First byte at: 0.504066s
[2025-11-13 20:30:14] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 14 Nov 2025 01:30:14 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
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-13 20:30:16] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-13 20:30:16] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:16] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-13 20:30:16] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-13 20:30:16] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-13 20:30:36] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:36] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-11-13 20:30:36] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Orthology targets:
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:36] [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`
[2025-11-13 20:30:36] [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`
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-13 20:30:36] [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]
[2025-11-13 20:30:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-13 20:30:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.508229s from omnipathdb.org (30.8 Kb/s); Redirect: 0s, DNS look up: 0.002078s, Connection: 0.003014s, Pretransfer: 0.341337s, First byte at: 0.507996s
[2025-11-13 20:30:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 14 Nov 2025 01:30:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 14 Nov 2025 02:30:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-13 20:30:38] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:38] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-11-13 20:30:38] [INFO] [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:38] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2025-11-13 20:30:38] [SUCCESS] [OmnipathR] Downloaded 11240 interactions.
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Orthology targets:
[2025-11-13 20:30:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-13 20:30:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:39] [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`
[2025-11-13 20:30:39] [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`
[2025-11-13 20:30:39] [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`
[2025-11-13 20:30:39] [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`
[2025-11-13 20:30:39] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:39] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:39] [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`
[2025-11-13 20:30:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-13 20:30:39] [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]
[2025-11-13 20:30:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-13 20:30:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.336729s from omnipathdb.org (46.5 Kb/s); Redirect: 0s, DNS look up: 0.001202s, Connection: 0.002091s, Pretransfer: 0.171292s, First byte at: 0.336365s
[2025-11-13 20:30:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 14 Nov 2025 01:30:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 14 Nov 2025 02:30:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-13 20:30:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:40] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2025-11-13 20:30:40] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-11-13 20:30:40] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-11-13 20:30:40] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2025-11-13 20:30:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:40] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2025-11-13 20:30:40] [SUCCESS] [OmnipathR] Downloaded 3788 interactions.
[2025-11-13 20:30:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-13 20:30:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-11-13 20:30:41] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-13 20:30:41] [TRACE] [OmnipathR] Orthology targets:
[2025-11-13 20:30:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:41] [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`
[2025-11-13 20:30:41] [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`
[2025-11-13 20:30:41] [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`
[2025-11-13 20:30:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-13 20:30:41] [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]
[2025-11-13 20:30:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-13 20:30:41] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.337657s from omnipathdb.org (46.4 Kb/s); Redirect: 0s, DNS look up: 0.002014s, Connection: 0.003261s, Pretransfer: 0.169692s, First byte at: 0.337108s
[2025-11-13 20:30:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 14 Nov 2025 01:30:41 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 14 Nov 2025 02:30:41 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-13 20:30:43] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-13 20:30:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:43] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2025-11-13 20:30:43] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-11-13 20:30:43] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-11-13 20:30:43] [INFO] [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2025-11-13 20:30:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-13 20:30:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-13 20:30:43] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2025-11-13 20:30:44] [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 3 | SKIP 0 | PASS 201 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 201 ]
>
> proc.time()
user system elapsed
80.452 15.280 388.346
gINTomics.Rcheck/gINTomics-Ex.timings
| name | user | system | elapsed | |
| create_multiassay | 0.262 | 0.042 | 0.599 | |
| dot_plotly | 0.250 | 0.035 | 0.613 | |
| extract_model_res | 5.816 | 0.462 | 8.247 | |
| mirna_hsa | 0.012 | 0.001 | 0.013 | |
| mmultiassay_ov | 0.058 | 0.003 | 0.063 | |
| plot_chr_distribution | 0.250 | 0.043 | 0.425 | |
| plot_heatmap | 0.211 | 0.035 | 0.399 | |
| plot_network | 0.201 | 0.034 | 0.364 | |
| plot_ridge | 4.028 | 0.496 | 6.133 | |
| plot_tf_distribution | 0.229 | 0.046 | 0.595 | |
| plot_venn | 0.244 | 0.052 | 0.574 | |
| plot_volcano | 19.686 | 2.870 | 333.877 | |
| run_cnv_integration | 0.513 | 0.089 | 1.053 | |
| run_genomic_enrich | 0.227 | 0.043 | 0.699 | |
| run_genomic_integration | 0.438 | 0.102 | 1.377 | |
| run_met_integration | 0.374 | 0.090 | 1.212 | |
| run_multiomics | 2.952 | 0.359 | 6.254 | |
| run_shiny | 0.280 | 0.050 | 0.619 | |
| run_tf_enrich | 0.225 | 0.039 | 0.513 | |
| run_tf_integration | 1.314 | 0.123 | 2.560 | |