Angelo Velle
| Snapshot Date: 2025-08-13 13:45 -0400 (Wed, 13 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/gINTomics |
| git_branch: devel |
| git_last_commit: f809e93 |
| git_last_commit_date: 2025-04-15 13:34:55 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-14 12:08 -0400 (Thu, 14 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 872/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gINTomics 1.5.0 (landing page) Angelo Velle
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the gINTomics package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: gINTomics |
| Version: 1.5.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.5.0.tar.gz |
| StartedAt: 2025-08-13 21:06:27 -0400 (Wed, 13 Aug 2025) |
| EndedAt: 2025-08-13 21:19:45 -0400 (Wed, 13 Aug 2025) |
| EllapsedTime: 797.4 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_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/gINTomics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.5.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 42 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gINTomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-08-13 21:10:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:10:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:10:48] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-13 21:10:48] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-13 21:10:48] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-13
[2025-08-13 21:10:48] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-13 19:09:49 UTC; unix
[2025-08-13 21:10:48] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-13 21:10:48] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-13 21:10:49] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-13 21:10:50] [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=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-13 21:10:50] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-13); BiocBaseUtils 1.11.2(2025-08-13); BiocGenerics 0.55.1(2025-08-13); BiocIO 1.19.0(2025-08-13); BiocParallel 1.43.4(2025-08-13); Biostrings 2.77.2(2025-08-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-08-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-08-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-08-13); GenomicFeatures 1.61.6(2025-08-13); GenomicRanges 1.61.1(2025-08-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-13); IRanges 2.43.0(2025-08-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-08-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.8(2025-08-13); OmnipathR 3.17.4(2025-08-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-08-13); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-13); S4Vectors 0.47.0(2025-08-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-13 21:10:50] [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: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:10:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-13 21:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:10:50] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-13 21:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
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[2025-08-13 21:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
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[2025-08-13 21:10:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:10:50] [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 53.857 6.652 79.898
extract_model_res 13.207 1.260 14.558
plot_ridge 10.277 1.188 11.512
run_multiomics 7.907 0.868 10.419
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/gINTomics.Rcheck/00check.log’
for details.
gINTomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gINTomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘gINTomics’ ... ** this is package ‘gINTomics’ version ‘1.5.0’ ** using staged installation ** R [2025-08-13 15:43:19] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:43:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:19] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:43:19] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-13 15:43:19] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-13 [2025-08-13 15:43:19] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-13 19:09:49 UTC; unix [2025-08-13 15:43:19] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-13 15:43:19] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-13 15:43:20] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-13 15:43:21] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-13 15:43:21] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-13); BiocBaseUtils 1.11.2(2025-08-13); BiocGenerics 0.55.1(2025-08-13); BiocIO 1.19.0(2025-08-13); BiocParallel 1.43.4(2025-08-13); Biostrings 2.77.2(2025-08-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-08-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-08-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-08-13); GenomicFeatures 1.61.6(2025-08-13); GenomicRanges 1.61.1(2025-08-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-13); IRanges 2.43.0(2025-08-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-08-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.8(2025-08-13); OmnipathR 3.17.4(2025-08-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-08-13); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-13); S4Vectors 0.47.0(2025-08-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-13 15:43:21] [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: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-13 15:43:21] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-13 15:43:21] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:43:21] [TRACE] [OmnipathR] Contains 1 files. [2025-08-13 15:43:22] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-13 15:43:22] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:43:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:43:22] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-13 15:43:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-13 15:43:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-13 15:43:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-13 15:43:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:22] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-13 15:43:22] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:22] [TRACE] [OmnipathR] Cache locked: FALSE ** data ** inst ** byte-compile and prepare package for lazy loading [2025-08-13 15:43:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:43:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:43:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-13 15:43:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-13 [2025-08-13 15:43:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-13 19:09:49 UTC; unix [2025-08-13 15:43:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-13 15:43:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-13 15:43:47] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-13 15:43:47] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-13 15:43:48] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-13); BiocBaseUtils 1.11.2(2025-08-13); BiocGenerics 0.55.1(2025-08-13); BiocIO 1.19.0(2025-08-13); BiocParallel 1.43.4(2025-08-13); Biostrings 2.77.2(2025-08-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-08-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-08-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-08-13); GenomicFeatures 1.61.6(2025-08-13); GenomicRanges 1.61.1(2025-08-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-13); IRanges 2.43.0(2025-08-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-08-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.8(2025-08-13); OmnipathR 3.17.4(2025-08-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-08-13); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-13); S4Vectors 0.47.0(2025-08-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-13 15:43:48] [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: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-13 15:43:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-13 15:43:48] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:43:48] [TRACE] [OmnipathR] Contains 1 files. [2025-08-13 15:43:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-13 15:43:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:43:48] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-13 15:43:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-13 15:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-13 15:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-13 15:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-13 15:43:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:43:48] [TRACE] [OmnipathR] Cache locked: FALSE ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-08-13 15:44:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:44:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:24] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:44:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-13 15:44:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-13 [2025-08-13 15:44:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-13 19:09:49 UTC; unix [2025-08-13 15:44:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-13 15:44:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-13 15:44:25] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-13 15:44:25] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-13 15:44:26] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-13); BiocBaseUtils 1.11.2(2025-08-13); BiocGenerics 0.55.1(2025-08-13); BiocIO 1.19.0(2025-08-13); BiocParallel 1.43.4(2025-08-13); Biostrings 2.77.2(2025-08-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-08-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-08-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-08-13); GenomicFeatures 1.61.6(2025-08-13); GenomicRanges 1.61.1(2025-08-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-13); IRanges 2.43.0(2025-08-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-08-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.8(2025-08-13); OmnipathR 3.17.4(2025-08-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-08-13); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-13); S4Vectors 0.47.0(2025-08-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-13 15:44:26] [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: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-13 15:44:26] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-13 15:44:26] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:44:26] [TRACE] [OmnipathR] Contains 1 files. [2025-08-13 15:44:26] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-13 15:44:26] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:44:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:44:26] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-13 15:44:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-13 15:44:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-13 15:44:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-13 15:44:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:26] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-13 15:44:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:26] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-13 15:44:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:44:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:51] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:44:51] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-13 15:44:51] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-13 [2025-08-13 15:44:51] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-13 19:09:49 UTC; unix [2025-08-13 15:44:51] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-13 15:44:51] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-13 15:44:52] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-13 15:44:52] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-13 15:44:52] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-13); BiocBaseUtils 1.11.2(2025-08-13); BiocGenerics 0.55.1(2025-08-13); BiocIO 1.19.0(2025-08-13); BiocParallel 1.43.4(2025-08-13); Biostrings 2.77.2(2025-08-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-08-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-08-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-08-13); GenomicFeatures 1.61.6(2025-08-13); GenomicRanges 1.61.1(2025-08-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-13); IRanges 2.43.0(2025-08-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-08-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.8(2025-08-13); OmnipathR 3.17.4(2025-08-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-08-13); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-13); S4Vectors 0.47.0(2025-08-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-13 15:44:52] [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: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2025-08-13 15:44:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-13 15:44:52] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:44:52] [TRACE] [OmnipathR] Contains 1 files. [2025-08-13 15:44:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-13 15:44:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-13 15:44:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-13 15:44:52] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-13 15:44:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-13 15:44:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:52] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-13 15:44:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-13 15:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-13 15:44:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-13 15:44:53] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (gINTomics)
gINTomics.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.
> library(testthat)
> library(gINTomics)
[2025-08-13 21:16:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:16:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:16:52] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-13 21:16:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-13 21:16:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-13
[2025-08-13 21:16:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-13 19:09:49 UTC; unix
[2025-08-13 21:16:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-13 21:16:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-13 21:16:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-08-13 21:16:53] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-13 21:16:54] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-08-13); backports 1.5.0(2024-05-23); Biobase 2.69.0(2025-08-13); BiocBaseUtils 1.11.2(2025-08-13); BiocGenerics 0.55.1(2025-08-13); BiocIO 1.19.0(2025-08-13); BiocParallel 1.43.4(2025-08-13); Biostrings 2.77.2(2025-08-13); 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 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-08-13); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); DelayedArray 0.35.2(2025-08-13); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.45.2(2025-08-13); GenomicFeatures 1.61.6(2025-08-13); GenomicRanges 1.61.1(2025-08-13); GetoptLong 1.0.5(2020-12-15); ggplot2 3.5.2(2025-04-09); gINTomics 1.5.0(2025-08-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.17.0(2025-08-13); IRanges 2.43.0(2025-08-13); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.49.1(2025-08-13); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-08-13); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.8(2025-08-13); OmnipathR 3.17.4(2025-08-13); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); RCurl 1.98-1.17(2025-03-22); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); Rsamtools 2.25.2(2025-08-13); RSQLite 2.4.2(2025-07-18); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-08-13); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-13); S4Vectors 0.47.0(2025-08-13); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-08-13); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.9.1(2025-08-13); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-13); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); testthat 3.2.3(2025-01-13); textshaping 1.0.1(2025-05-01); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-08-13); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-13 21:16:54] [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: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Contains 7 files.
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:16:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-13 21:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-13 21:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-13 21:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-13 21:16:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:16:54] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check("gINTomics")
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2025-08-13 21:17:01] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:01] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:01] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-08-13 21:17:01] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-08-13 21:17:01] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-13 21:17:01] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-08-13 21:17:01] [TRACE] [OmnipathR] Sending HTTP request.
[2025-08-13 21:17:02] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-08-13 21:17:02] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-13 21:17:02] [TRACE] [OmnipathR] Downloaded 31.1 Kb in 1.025978s from www.ensembl.org (30.3 Kb/s); Redirect: 0.808428s, DNS look up: 0.003164s, Connection: 0.004834s, Pretransfer: 0.687097s, First byte at: 0.998191s
[2025-08-13 21:17:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Thu, 14 Aug 2025 01:17:02 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-31.ebi.ac.uk; HTTP/2 302 ; date: Thu, 14 Aug 2025 01:17:02 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-86.us-east-2.compute.internal; HTTP/2 200 ; date: Thu, 14 Aug 2025 01:17:02 GMT; content-type: text/html; charset=utf-8; content-length: 31834; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Fri, 15 Aug 2025 01:15:05 GMT; set-cookie: ENSEMBL_WWW_SESSION=f9a3907849f3955e0e34502d68ec5299030d9928c9fc5fb30a1b5b8a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Fri, 15 Aug 2025 01:15:05 GMT; set-cookie: ENSEMBL_WWW_SESSION=f9a3907849f3955e0e34502d68ec5299030d9928c9fc5fb30a1b5b8a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; vary: Accept-Encoding; content-encoding: gzip; x-frame-options: SAMEORIGIN; content-security-policy: frame-ancestors 'self'; x-nginx-machine: ip-10-25-25-92.us-east-2.compute.internal
[2025-08-13 21:17:02] [TRACE] [OmnipathR] Response headers: [date=Thu, 14 Aug 2025 01:17:02 GMT,content-type=text/html; charset=utf-8,content-length=31834,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Fri, 15 Aug 2025 01:15:05 GMT,set-cookie=ENSEMBL_WWW_SESSION=f9a3907849f3955e0e34502d68ec5299030d9928c9fc5fb30a1b5b8a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Fri, 15 Aug 2025 01:15:05 GMT,set-cookie=ENSEMBL_WWW_SESSION=f9a3907849f3955e0e34502d68ec5299030d9928c9fc5fb30a1b5b8a; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-92.us-east-2.compute.internal]
[2025-08-13 21:17:03] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-08-13 21:17:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:03] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-13 21:17:04] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:04] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-13 21:17:04] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-08-13 21:17:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-13 21:17:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-13 21:17:05] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-13 21:17:05] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.469137s from omabrowser.org (18.5 Kb/s); Redirect: 0s, DNS look up: 0.001053s, Connection: 0.002137s, Pretransfer: 0.376685s, First byte at: 0.468873s
[2025-08-13 21:17:05] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 14 Aug 2025 01:17:05 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-08-13 21:17:06] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-13 21:17:06] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-08-13 21:17:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:06] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-08-13 21:17:06] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-13 21:17:06] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-08-13 21:17:06] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-08-13 21:17:07] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-08-13 21:17:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:07] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-08-13 21:17:07] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-08-13 21:17:07] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-08-13 21:17:07] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-08-13 21:17:47] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-08-13 21:17:47] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-08-13 21:17:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:47] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-08-13 21:17:48] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Orthology targets:
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:48] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:48] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:48] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-13 21:17:48] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-13 21:17:48] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.310715s from omnipathdb.org (50.4 Kb/s); Redirect: 0s, DNS look up: 0.001185s, Connection: 0.002227s, Pretransfer: 0.15868s, First byte at: 0.310238s
[2025-08-13 21:17:48] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 14 Aug 2025 01:17:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 14 Aug 2025 02:17:48 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-13 21:17:50] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:50] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2025-08-13 21:17:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-08-13 21:17:50] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-08-13 21:17:50] [INFO] [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2025-08-13 21:17:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:50] [INFO] [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2025-08-13 21:17:51] [SUCCESS] [OmnipathR] Downloaded 11240 interactions.
[2025-08-13 21:17:51] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-13 21:17:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2025-08-13 21:17:51] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-13 21:17:51] [TRACE] [OmnipathR] Orthology targets:
[2025-08-13 21:17:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-13 21:17:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:52] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:52] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:52] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:52] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:52] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:52] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-13 21:17:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-13 21:17:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-13 21:17:52] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.311144s from omnipathdb.org (50.4 Kb/s); Redirect: 0s, DNS look up: 0.000993s, Connection: 0.001998s, Pretransfer: 0.158589s, First byte at: 0.310653s
[2025-08-13 21:17:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 14 Aug 2025 01:17:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 14 Aug 2025 02:17:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-13 21:17:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:54] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-08-13 21:17:54] [INFO] [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:54] [INFO] [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2025-08-13 21:17:54] [SUCCESS] [OmnipathR] Downloaded 3788 interactions.
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Orthology targets:
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-08-13 21:17:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-13 21:17:54] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.308314s from omnipathdb.org (50.8 Kb/s); Redirect: 0s, DNS look up: 0.001237s, Connection: 0.002337s, Pretransfer: 0.157118s, First byte at: 0.308038s
[2025-08-13 21:17:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 14 Aug 2025 01:17:54 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 14 Aug 2025 02:17:54 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-13 21:17:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-08-13 21:17:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:57] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2025-08-13 21:17:57] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-08-13 21:17:58] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-08-13 21:17:58] [INFO] [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2025-08-13 21:17:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-13 21:17:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-13 21:17:58] [INFO] [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2025-08-13 21:18:00] [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 4 | SKIP 0 | PASS 204 ]
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 204 ]
>
> proc.time()
user system elapsed
228.503 40.901 178.861
gINTomics.Rcheck/gINTomics-Ex.timings
| name | user | system | elapsed | |
| create_multiassay | 0.826 | 0.132 | 0.973 | |
| dot_plotly | 0.712 | 0.102 | 0.814 | |
| extract_model_res | 13.207 | 1.260 | 14.558 | |
| mirna_hsa | 0.019 | 0.002 | 0.021 | |
| mmultiassay_ov | 0.085 | 0.005 | 0.089 | |
| plot_chr_distribution | 0.614 | 0.089 | 0.706 | |
| plot_heatmap | 0.626 | 0.097 | 0.724 | |
| plot_network | 0.640 | 0.097 | 0.741 | |
| plot_ridge | 10.277 | 1.188 | 11.512 | |
| plot_tf_distribution | 0.632 | 0.099 | 0.733 | |
| plot_venn | 0.615 | 0.101 | 0.720 | |
| plot_volcano | 53.857 | 6.652 | 79.898 | |
| run_cnv_integration | 1.355 | 0.262 | 1.636 | |
| run_genomic_enrich | 0.810 | 0.119 | 0.947 | |
| run_genomic_integration | 1.753 | 0.234 | 2.919 | |
| run_met_integration | 1.333 | 0.250 | 1.897 | |
| run_multiomics | 7.907 | 0.868 | 10.419 | |
| run_shiny | 0.797 | 0.111 | 1.145 | |
| run_tf_enrich | 0.689 | 0.106 | 0.799 | |
| run_tf_integration | 3.771 | 0.315 | 4.391 | |