Multiple platform build/check report for BioC 3.22 - CHECK results for gINTomics on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4814
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4603
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4547
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4553
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*

CHECK results for gINTomics on lconway

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.

raw results

Summary

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: 2025-09-21 21:25:26 -0400 (Sun, 21 Sep 2025)

EndedAt: 2025-09-21 21:54:55 -0400 (Sun, 21 Sep 2025)

EllapsedTime: 1768.4 seconds

RetCode: 1

Status: ERROR

CheckDir: gINTomics.Rcheck

Warnings: NA

Command output

##############################################################################
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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 Patched (2025-09-10 r88807)
* 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
[2025-09-21 21:29:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:29:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:29:50] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 21:29:50] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 21:29:50] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 21:29:50] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 21:29:50] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 21:29:50] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 21:29:51] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 21:29:51] [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]
[2025-09-21 21:29:52] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); 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(2025-09-21); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.35.3(2025-09-21); 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 0.34.0(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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.5.0(2025-09-21); 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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); OmnipathR 3.17.4(2025-09-21); 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 1.3.3(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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); 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(2025-09-21); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.3(2025-09-02); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-21 21:29:52] [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
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:29:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-21 21:29:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:29:52] [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 ... ERROR
Running examples in ‘gINTomics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_volcano
> ### Title: plotting volcano
> ### Aliases: plot_volcano
> 
> ### ** Examples
> 
> # Example usage:
> library(MultiAssayExperiment)
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

> data("mmultiassay_ov")
> tmp <- lapply(experiments(mmultiassay_ov), function(x) x[1:20,])
> mmultiassay_ov <- MultiAssayExperiment(experiments = tmp)
> multiomics_integration <- run_multiomics(data = mmultiassay_ov)
--------------Running gene genomic integration--------------
Generating interactions
---------------Running miRNA CNV integration----------------
Generating interactions
removing response variables with zero standard deviation
Warning in .data_check(response_var = response_var, covariates = covariates,  :
  No genes left in common between response_var and interactions
-------------------Running TF integration-------------------
Warning in import_tf_target_interactions(organism = org[species]) :
  'import_tf_target_interactions' is deprecated.
Use 'tf_target' instead.
See help("Deprecated")
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-09-21 21:33:59] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:33:59] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:33:59] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-09-21 21:33:59] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:33:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:33:59] [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]
[2025-09-21 21:34:00] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:34:00] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:35:01] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:35:06] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:35:06] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:35:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:35:06] [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]
[2025-09-21 21:35:06] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:35:06] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:36:36] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:36:42] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:36:42] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:36:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:36:42] [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]
[2025-09-21 21:36:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:36:42] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:38:12] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:38:12] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 21:38:12] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 21:38:12] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 21:38:12] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 21:38:12] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 21:38:13] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 21:38:13] [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]
[2025-09-21 21:38:14] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocFileCache 2.99.6(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); biomaRt 2.65.14(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); 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); 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 4.17.0(2025-09-21); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-09-21); 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 0.35.3(2025-09-21); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.3.0(2025-09-21); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.7.4(2025-09-21); enrichplot 1.29.2(2025-09-21); 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 1.35.6(2025-09-21); filelock 1.0.3(2023-12-11); 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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.1(2025-09-16); 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 0.0.7(2025-06-30); ggtree 3.99.0(2025-09-21); ggvenn 0.1.10(2023-03-31); gINTomics 1.5.0(2025-09-21); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.21.0(2025-09-10); GOSemSim 2.35.1(2025-09-21); graph 1.87.0(2025-09-21); graphite 1.55.0(2025-09-21); 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 1.1.3(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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); knitr 1.50(2025-03-16); labeling 0.4.3(2023-08-29); 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 3.65.4(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); nlme 3.1-168(2025-03-31); OmnipathR 3.17.4(2025-09-21); org.Hs.eg.db 3.21.0(2025-09-10); org.Mm.eg.db 3.21.0(2025-09-10); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); qvalue 2.41.0(2025-09-21); 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 1.92.0(2025-09-10); ReactomePA 1.53.0(2025-09-21); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reshape2 1.4.4(2020-04-09); 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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.5.0(2025-09-21); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.9.1(2025-09-21); statmod 1.5.0(2023-01-06); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.3(2025-09-02); 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 1.33.0(2025-09-21); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.21.0(2025-09-10); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-09-10); tzdb 0.5.0(2025-03-15); uuid 1.2-1(2024-07-29); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-09-21 21:38:14] [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
Error in `map_int()`:
ℹ In index: 1.
ℹ With name: hsa.
Caused by error in `map_int()`:
ℹ In index: 1.
Caused by error in `req_perform()`:
! HTTP 504 Gateway Timeout.
Backtrace:
     ▆
  1. ├─gINTomics::run_multiomics(data = mmultiassay_ov)
  2. │ └─gINTomics::run_tf_integration(...)
  3. │   └─gINTomics:::.def_tf_integration(...)
  4. │     └─gINTomics:::.download_tf(genes = colnames(expression), species = species)
  5. │       └─OmnipathR::import_tf_target_interactions(organism = org[species])
  6. │         └─OmnipathR::tf_target(...)
  7. │           ├─rlang::exec(omnipath_query, !!!args)
  8. │           └─OmnipathR (local) `<fn>`(organisms = `<dbl>`, query_type = "interactions", datasets = "tf_target")
  9. │             └─environment() %>% as.list %>% c(list(...)) %>% ...
 10. ├─OmnipathR:::omnipath_check_param(.)
 11. │ └─param$organisms %<>% map_int(ncbi_taxid)
 12. ├─purrr::map_int(., ncbi_taxid)
 13. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 14. │   ├─purrr:::with_indexed_errors(...)
 15. │   │ └─base::withCallingHandlers(...)
 16. │   ├─purrr:::call_with_cleanup(...)
 17. │   └─OmnipathR (local) .f(.x[[i]], ...)
 18. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 19. ├─purrr::map_int(., taxon_name, "ncbi")
 20. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 21. │   ├─purrr:::with_indexed_errors(...)
 22. │   │ └─base::withCallingHandlers(...)
 23. │   ├─purrr:::call_with_cleanup(...)
 24. │   └─OmnipathR (local) .f(.x[[i]], ...)
 25. │     ├─... %>% if_null_len0(NA)
 26. │     └─OmnipathR::get_db("organisms")
 27. │       └─OmnipathR::load_db(key, param = param)
 28. │         ├─rlang::exec(loader, !!!param)
 29. │         └─OmnipathR (local) `<fn>`()
 30. │           ├─... %>% ...
 31. │           └─OmnipathR::ensembl_organisms()
 32. │             ├─... %>% ...
 33. │             └─OmnipathR::ensembl_organisms_raw()
 34. │               └─... %>% html_table()
 35. ├─OmnipathR:::if_null_len0(., NA)
 36. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 37. ├─OmnipathR:::is_empty_2(.)
 38. │ └─value %>% ...
 39. ├─dplyr::pull(., name_type)
 40. ├─dplyr::filter(...)
 41. ├─dplyr::mutate(...)
 42. ├─dplyr::full_join(...)
 43. ├─dplyr::full_join(...)
 44. ├─dplyr::rename(., common_name_ensembl = common_name)
 45. ├─dplyr::mutate(...)
 46. ├─dplyr::select(...)
 47. ├─rvest::html_table(.)
 48. ├─rvest::html_element(., "table")
 49. ├─xml2::read_html(.)
 50. ├─OmnipathR:::download_to_cache(., http_headers = user_agent())
 51. │ └─OmnipathR:::download_base(...)
 52. │   ├─base::tryCatch(exec(fun, url, !!!args), error = identity)
 53. │   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 54. │   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 55. │   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 56. │   ├─rlang::exec(fun, url, !!!args)
 57. │   └─OmnipathR (local) `<fn>`("https://www.ensembl.org/info/about/species.html")
 58. │     └─req %>% omnipath_httr2_perform(path = path)
 59. ├─OmnipathR:::omnipath_httr2_perform(., path = path)
 60. │ └─req %>% req_perform(path = path)
 61. └─httr2::req_perform(., path = path)
 62.   └─httr2:::handle_resp(req, resp, error_call = error_call)
 63.     └─httr2:::resp_failure_cnd(req, resp, error_call = error_call)
 64.       ├─rlang::catch_cnd(...)
 65.       │ ├─rlang::eval_bare(...)
 66.       │ ├─base::tryCatch(...)
 67.       │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 68.       │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 69.       │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 70.       │ └─base::force(expr)
 71.       └─rlang::abort(...)
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
extract_model_res 15.380  1.538  20.248
plot_ridge        12.064  1.418  16.194
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  names(tested)[1] (`actual`) not equal to "data" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('data')
  ── Failure ('test-outputs_shiny.R:184:3'): .build_histo works ──────────────────
  `tested` has type 'object', not 'list'.
  ── Failure ('test-outputs_shiny.R:186:3'): .build_histo works ──────────────────
  names(tested)[1] (`actual`) not equal to "data" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('data')
  
  [ FAIL 9 | WARN 5 | SKIP 0 | PASS 193 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/gINTomics.Rcheck/00check.log’
for details.

Installation output

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
[2025-09-21 15:46:29] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:46:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:46:29] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:46:29] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 15:46:29] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 15:46:29] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 15:46:29] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 15:46:29] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 15:46:31] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 15:46:31] [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=8.6.13; 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]
[2025-09-21 15:46:32] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); 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(2025-09-21); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.35.3(2025-09-21); 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 0.34.0(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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.5.0(2025-09-21); 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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); OmnipathR 3.17.4(2025-09-21); 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 1.3.3(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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); 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(2025-09-21); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.3(2025-09-02); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-21 15:46:32] [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
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:46:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:46:32] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-09-21 15:46:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:46:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:46:57] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:46:57] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 15:46:57] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 15:46:57] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 15:46:57] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 15:46:57] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 15:46:58] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 15:46:58] [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]
[2025-09-21 15:47:00] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); 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(2025-09-21); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.35.3(2025-09-21); 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 0.34.0(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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.5.0(2025-09-21); 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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); OmnipathR 3.17.4(2025-09-21); 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 1.3.3(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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); 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(2025-09-21); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.3(2025-09-02); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-21 15:47:00] [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
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-21 15:47:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:00] [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
[2025-09-21 15:47:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:47:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:36] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:47:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 15:47:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 15:47:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 15:47:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 15:47:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 15:47:37] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 15:47:38] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; 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]
[2025-09-21 15:47:39] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); 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(2025-09-21); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.35.3(2025-09-21); 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 0.34.0(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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.5.0(2025-09-21); 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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); OmnipathR 3.17.4(2025-09-21); 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 1.3.3(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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); 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(2025-09-21); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.3(2025-09-02); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-21 15:47:39] [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: 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
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:47:39] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-09-21 15:48:03] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:48:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:48:03] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:48:03] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 15:48:03] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 15:48:03] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 15:48:03] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 15:48:03] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 15:48:04] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 15:48:05] [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]
[2025-09-21 15:48:06] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); 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(2025-09-21); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.35.3(2025-09-21); 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 0.34.0(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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.5.0(2025-09-21); 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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); OmnipathR 3.17.4(2025-09-21); 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 1.3.3(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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); 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(2025-09-21); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); textshaping 1.0.3(2025-09-02); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-21 15:48:06] [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
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Contains 1 files.
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:48:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 15:48:06] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (gINTomics)

Tests output

gINTomics.Rcheck/tests/testthat.Rout.fail


R version 4.5.1 Patched (2025-09-10 r88807) -- "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.
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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(gINTomics)
[2025-09-21 21:38:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:38:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:33] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 21:38:33] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 21:38:33] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 21:38:33] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 21:38:33] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 21:38:33] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 21:38:34] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 21:38:35] [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]
[2025-09-21 21:38:35] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); 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); 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(2025-09-21); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.35.3(2025-09-21); 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 0.34.0(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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.5.0(2025-09-21); 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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); OmnipathR 3.17.4(2025-09-21); 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 1.3.3(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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); 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(2025-09-21); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); testthat 3.2.3(2025-01-13); textshaping 1.0.3(2025-09-02); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-09-21 21:38:35] [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
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Contains 2 files.
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:35] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2025-09-21 21:38:42] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:42] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:38:42] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-09-21 21:38:42] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:38:42] [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]
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:38:42] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:40:13] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:40:18] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:40:18] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:40:18] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:40:18] [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]
[2025-09-21 21:40:18] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:40:18] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:41:49] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:41:54] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:41:54] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:41:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:41:54] [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]
[2025-09-21 21:41:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:41:54] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:43:24] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:43:24] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 21:43:24] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 21:43:24] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 21:43:24] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 21:43:24] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 21:43:26] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 21:43:26] [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]
[2025-09-21 21:43:26] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocFileCache 2.99.6(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); biomaRt 2.65.14(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); 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); 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 4.17.0(2025-09-21); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-09-21); 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 0.35.3(2025-09-21); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.3.0(2025-09-21); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.7.4(2025-09-21); enrichplot 1.29.2(2025-09-21); 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 1.35.6(2025-09-21); filelock 1.0.3(2023-12-11); 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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.1(2025-09-16); 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 0.0.7(2025-06-30); ggtree 3.99.0(2025-09-21); ggvenn 0.1.10(2023-03-31); gINTomics 1.5.0(2025-09-21); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.21.0(2025-09-10); GOSemSim 2.35.1(2025-09-21); graph 1.87.0(2025-09-21); graphite 1.55.0(2025-09-21); 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 1.1.3(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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 3.65.4(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); nlme 3.1-168(2025-03-31); OmnipathR 3.17.4(2025-09-21); org.Hs.eg.db 3.21.0(2025-09-10); org.Mm.eg.db 3.21.0(2025-09-10); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); qvalue 2.41.0(2025-09-21); 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 1.92.0(2025-09-10); ReactomePA 1.53.0(2025-09-21); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reshape2 1.4.4(2020-04-09); 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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.5.0(2025-09-21); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.9.1(2025-09-21); statmod 1.5.0(2023-01-06); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); testthat 3.2.3(2025-01-13); textshaping 1.0.3(2025-09-02); 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 1.33.0(2025-09-21); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.21.0(2025-09-10); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-09-10); tzdb 0.5.0(2025-03-15); uuid 1.2-1(2024-07-29); 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 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-09-21 21:43:26] [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
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2025-09-21 21:43:28] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-09-21 21:43:28] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:43:28] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2025-09-21 21:43:28] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:43:28] [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]
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:43:28] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:44:59] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:45:04] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:45:04] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:45:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:45:04] [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]
[2025-09-21 21:45:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:45:04] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:46:34] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:46:39] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:46:39] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:46:39] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:46:39] [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]
[2025-09-21 21:46:39] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:46:39] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:48:10] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:48:10] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 21:48:10] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 21:48:10] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 21:48:10] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 21:48:10] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 21:48:11] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 21:48:11] [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]
[2025-09-21 21:48:12] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocFileCache 2.99.6(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); biomaRt 2.65.14(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); 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); 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 4.17.0(2025-09-21); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-09-21); 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 0.35.3(2025-09-21); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.3.0(2025-09-21); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.7.4(2025-09-21); enrichplot 1.29.2(2025-09-21); 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 1.35.6(2025-09-21); filelock 1.0.3(2023-12-11); 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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.1(2025-09-16); 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 0.0.7(2025-06-30); ggtree 3.99.0(2025-09-21); ggvenn 0.1.10(2023-03-31); gINTomics 1.5.0(2025-09-21); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.21.0(2025-09-10); GOSemSim 2.35.1(2025-09-21); graph 1.87.0(2025-09-21); graphite 1.55.0(2025-09-21); 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 1.1.3(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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 3.65.4(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); nlme 3.1-168(2025-03-31); OmnipathR 3.17.4(2025-09-21); org.Hs.eg.db 3.21.0(2025-09-10); org.Mm.eg.db 3.21.0(2025-09-10); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); qvalue 2.41.0(2025-09-21); 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 1.92.0(2025-09-10); ReactomePA 1.53.0(2025-09-21); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reshape2 1.4.4(2020-04-09); 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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.5.0(2025-09-21); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.9.1(2025-09-21); statmod 1.5.0(2023-01-06); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); testthat 3.2.3(2025-01-13); textshaping 1.0.3(2025-09-02); 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 1.33.0(2025-09-21); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.21.0(2025-09-10); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-09-10); tzdb 0.5.0(2025-03-15); uuid 1.2-1(2024-07-29); 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); waldo 0.6.2(2025-07-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-09-21 21:48:12] [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: 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
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-09-21 21:48:13] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-09-21 21:48:13] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-09-21 21:48:13] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2025-09-21 21:48:13] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:48:13] [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]
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:48:13] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:49:44] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:49:49] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:49:49] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:49:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:49:49] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-09-21 21:49:49] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:49:49] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:51:20] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:51:25] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-09-21 21:51:25] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-09-21 21:51:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:51:25] [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]
[2025-09-21 21:51:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-09-21 21:51:25] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-09-21 21:52:56] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-09-21 21:52:56] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-09-21 21:52:56] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-09-21
[2025-09-21 21:52:56] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-09-21 19:11:42 UTC; unix
[2025-09-21 21:52:56] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-09-21 21:52:56] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-09-21 21:52:57] [INFO]    [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-09-10 r88807); 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=2025-09-21; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-09-21 21:52:57] [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=8.6.13; 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]
[2025-09-21 21:52:57] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.71.1(2025-09-21); ape 5.8-1(2024-12-16); aplot 0.2.9(2025-09-12); backports 1.5.0(2024-05-23); Biobase 2.69.1(2025-09-21); BiocBaseUtils 1.11.2(2025-09-21); BiocFileCache 2.99.6(2025-09-21); BiocGenerics 0.55.1(2025-09-21); BiocIO 1.19.0(2025-09-21); BiocParallel 1.43.4(2025-09-21); biomaRt 2.65.14(2025-09-21); Biostrings 2.77.2(2025-09-21); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); 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); 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 4.17.0(2025-09-21); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.25.2(2025-09-21); 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 0.35.3(2025-09-21); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); DOSE 4.3.0(2025-09-21); dplyr 1.1.4(2023-11-17); DT 0.34.0(2025-09-02); edgeR 4.7.4(2025-09-21); enrichplot 1.29.2(2025-09-21); 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 1.35.6(2025-09-21); filelock 1.0.3(2023-12-11); 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 1.45.4(2025-09-21); GenomicFeatures 1.61.6(2025-09-21); GenomicRanges 1.61.4(2025-09-21); GetoptLong 1.0.5(2020-12-15); ggforce 0.5.0(2025-06-18); ggfun 0.2.0(2025-07-15); ggiraph 0.9.1(2025-09-16); 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 0.0.7(2025-06-30); ggtree 3.99.0(2025-09-21); ggvenn 0.1.10(2023-03-31); gINTomics 1.5.0(2025-09-21); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); GO.db 3.21.0(2025-09-10); GOSemSim 2.35.1(2025-09-21); graph 1.87.0(2025-09-21); graphite 1.55.0(2025-09-21); 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 1.1.3(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(2025-09-21); IRanges 2.43.2(2025-09-21); 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(2025-09-21); 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 3.65.4(2025-09-21); 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 1.21.0(2025-09-21); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.39.0(2025-09-21); mime 0.13(2025-03-17); MultiAssayExperiment 1.35.9(2025-09-21); nlme 3.1-168(2025-03-31); OmnipathR 3.17.4(2025-09-21); org.Hs.eg.db 3.21.0(2025-09-10); org.Mm.eg.db 3.21.0(2025-09-10); 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 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); qvalue 2.41.0(2025-09-21); 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 1.92.0(2025-09-10); ReactomePA 1.53.0(2025-09-21); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); reshape2 1.4.4(2020-04-09); 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 2.25.3(2025-09-21); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.69.1(2025-09-21); rvest 1.0.5(2025-08-29); S4Arrays 1.9.1(2025-09-21); S4Vectors 0.47.2(2025-09-21); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 0.99.2(2025-09-21); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); shiny.gosling 1.5.0(2025-09-21); shinydashboard 0.7.3(2025-04-21); shinyjs 2.1.0(2021-12-23); SparseArray 1.9.1(2025-09-21); statmod 1.5.0(2023-01-06); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.39.2(2025-09-21); svglite 2.2.1(2025-05-12); systemfonts 1.2.3(2025-04-30); testthat 3.2.3(2025-01-13); textshaping 1.0.3(2025-09-02); 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 1.33.0(2025-09-21); tweenr 2.0.3(2024-02-26); TxDb.Hsapiens.UCSC.hg38.knownGene 3.21.0(2025-09-10); TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0(2025-09-10); tzdb 0.5.0(2025-03-15); uuid 1.2-1(2024-07-29); 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); waldo 0.6.2(2025-07-11); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.49.1(2025-09-21); yaml 2.3.10(2024-07-26); yulab.utils 0.2.1(2025-08-19); zip 2.3.3(2025-05-13)
[2025-09-21 21:52:57] [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
'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 9 | WARN 5 | SKIP 0 | PASS 193 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-downloads.R:6:3'): .download_mirna_target works ────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map_int(., ncbi_taxid)`: i In index: 1.
i With name: hsa.
Caused by error in `map_int()`:
i In index: 1.
Caused by error in `req_perform()`:
! HTTP 504 Gateway Timeout.
Backtrace:
     ▆
  1. ├─gINTomics:::.download_mirna_target(...) at test-downloads.R:6:3
  2. │ └─OmnipathR::import_mirnatarget_interactions(organism = org[species])
  3. │   └─OmnipathR::mirna_target(...)
  4. │     ├─rlang::exec(omnipath_query, !!!args)
  5. │     └─OmnipathR (local) `<fn>`(organisms = `<dbl>`, query_type = "interactions", datasets = "mirnatarget")
  6. │       └─environment() %>% as.list %>% c(list(...)) %>% ...
  7. ├─OmnipathR:::omnipath_check_param(.)
  8. │ └─param$organisms %<>% map_int(ncbi_taxid)
  9. ├─purrr::map_int(., ncbi_taxid)
 10. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 11. │   ├─purrr:::with_indexed_errors(...)
 12. │   │ └─base::withCallingHandlers(...)
 13. │   ├─purrr:::call_with_cleanup(...)
 14. │   └─OmnipathR (local) .f(.x[[i]], ...)
 15. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 16. ├─purrr::map_int(., taxon_name, "ncbi")
 17. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 18. │   ├─purrr:::with_indexed_errors(...)
 19. │   │ └─base::withCallingHandlers(...)
 20. │   ├─purrr:::call_with_cleanup(...)
 21. │   └─OmnipathR (local) .f(.x[[i]], ...)
 22. │     ├─... %>% if_null_len0(NA)
 23. │     └─OmnipathR::get_db("organisms")
 24. │       └─OmnipathR::load_db(key, param = param)
 25. │         ├─rlang::exec(loader, !!!param)
 26. │         └─OmnipathR (local) `<fn>`()
 27. │           ├─... %>% ...
 28. │           └─OmnipathR::ensembl_organisms()
 29. │             ├─... %>% ...
 30. │             └─OmnipathR::ensembl_organisms_raw()
 31. │               └─... %>% html_table()
 32. ├─OmnipathR:::if_null_len0(., NA)
 33. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 34. ├─OmnipathR:::is_empty_2(.)
 35. │ └─value %>% ...
 36. ├─dplyr::pull(., name_type)
 37. ├─dplyr::filter(...)
 38. ├─dplyr::mutate(...)
 39. ├─dplyr::full_join(...)
 40. ├─dplyr::full_join(...)
 41. ├─dplyr::rename(., common_name_ensembl = common_name)
 42. ├─dplyr::mutate(...)
 43. ├─dplyr::select(...)
 44. ├─rvest::html_table(.)
 45. ├─rvest::html_element(., "table")
 46. ├─xml2::read_html(.)
 47. ├─OmnipathR:::download_to_cache(., http_headers = user_agent())
 48. │ └─OmnipathR:::download_base(...)
 49. │   └─base::stop(result)
 50. ├─purrr (local) `<fn>`(`<ht2__504>`)
 51. │ └─cli::cli_abort(...)
 52. │   └─rlang::abort(...)
 53. │     └─rlang:::signal_abort(cnd, .file)
 54. │       └─base::signalCondition(cnd)
 55. └─purrr (local) `<fn>`(`<prrr_rr_>`)
 56.   └─cli::cli_abort(...)
 57.     └─rlang::abort(...)
── Error ('test-downloads.R:16:3'): .download_tf_mirna works ───────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map_int(., ncbi_taxid)`: i In index: 1.
i With name: hsa.
Caused by error in `map_int()`:
i In index: 1.
Caused by error in `req_perform()`:
! HTTP 504 Gateway Timeout.
Backtrace:
     ▆
  1. ├─gINTomics:::.download_tf_mirna(...) at test-downloads.R:16:3
  2. │ └─OmnipathR::import_tf_mirna_interactions(...)
  3. │   └─OmnipathR::tf_mirna(...)
  4. │     ├─rlang::exec(omnipath_query, !!!args)
  5. │     └─OmnipathR (local) `<fn>`(...)
  6. │       └─environment() %>% as.list %>% c(list(...)) %>% ...
  7. ├─OmnipathR:::omnipath_check_param(.)
  8. │ └─param$organisms %<>% map_int(ncbi_taxid)
  9. ├─purrr::map_int(., ncbi_taxid)
 10. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 11. │   ├─purrr:::with_indexed_errors(...)
 12. │   │ └─base::withCallingHandlers(...)
 13. │   ├─purrr:::call_with_cleanup(...)
 14. │   └─OmnipathR (local) .f(.x[[i]], ...)
 15. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 16. ├─purrr::map_int(., taxon_name, "ncbi")
 17. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 18. │   ├─purrr:::with_indexed_errors(...)
 19. │   │ └─base::withCallingHandlers(...)
 20. │   ├─purrr:::call_with_cleanup(...)
 21. │   └─OmnipathR (local) .f(.x[[i]], ...)
 22. │     ├─... %>% if_null_len0(NA)
 23. │     └─OmnipathR::get_db("organisms")
 24. │       └─OmnipathR::load_db(key, param = param)
 25. │         ├─rlang::exec(loader, !!!param)
 26. │         └─OmnipathR (local) `<fn>`()
 27. │           ├─... %>% ...
 28. │           └─OmnipathR::ensembl_organisms()
 29. │             ├─... %>% ...
 30. │             └─OmnipathR::ensembl_organisms_raw()
 31. │               └─... %>% html_table()
 32. ├─OmnipathR:::if_null_len0(., NA)
 33. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 34. ├─OmnipathR:::is_empty_2(.)
 35. │ └─value %>% ...
 36. ├─dplyr::pull(., name_type)
 37. ├─dplyr::filter(...)
 38. ├─dplyr::mutate(...)
 39. ├─dplyr::full_join(...)
 40. ├─dplyr::full_join(...)
 41. ├─dplyr::rename(., common_name_ensembl = common_name)
 42. ├─dplyr::mutate(...)
 43. ├─dplyr::select(...)
 44. ├─rvest::html_table(.)
 45. ├─rvest::html_element(., "table")
 46. ├─xml2::read_html(.)
 47. ├─OmnipathR:::download_to_cache(., http_headers = user_agent())
 48. │ └─OmnipathR:::download_base(...)
 49. │   └─base::stop(result)
 50. ├─purrr (local) `<fn>`(`<ht2__504>`)
 51. │ └─cli::cli_abort(...)
 52. │   └─rlang::abort(...)
 53. │     └─rlang:::signal_abort(cnd, .file)
 54. │       └─base::signalCondition(cnd)
 55. └─purrr (local) `<fn>`(`<prrr_rr_>`)
 56.   └─cli::cli_abort(...)
 57.     └─rlang::abort(...)
── Error ('test-downloads.R:26:3'): .download_tf works ─────────────────────────
<purrr_error_indexed/rlang_error/error/condition>
Error in `map_int(., ncbi_taxid)`: i In index: 1.
i With name: hsa.
Caused by error in `map_int()`:
i In index: 1.
Caused by error in `req_perform()`:
! HTTP 504 Gateway Timeout.
Backtrace:
     ▆
  1. ├─gINTomics:::.download_tf(genes = colnames(expression), species = species) at test-downloads.R:26:3
  2. │ └─OmnipathR::import_tf_target_interactions(organism = org[species])
  3. │   └─OmnipathR::tf_target(...)
  4. │     ├─rlang::exec(omnipath_query, !!!args)
  5. │     └─OmnipathR (local) `<fn>`(organisms = `<dbl>`, query_type = "interactions", datasets = "tf_target")
  6. │       └─environment() %>% as.list %>% c(list(...)) %>% ...
  7. ├─OmnipathR:::omnipath_check_param(.)
  8. │ └─param$organisms %<>% map_int(ncbi_taxid)
  9. ├─purrr::map_int(., ncbi_taxid)
 10. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 11. │   ├─purrr:::with_indexed_errors(...)
 12. │   │ └─base::withCallingHandlers(...)
 13. │   ├─purrr:::call_with_cleanup(...)
 14. │   └─OmnipathR (local) .f(.x[[i]], ...)
 15. │     └─name %>% map_int(taxon_name, "ncbi") %>% as.integer
 16. ├─purrr::map_int(., taxon_name, "ncbi")
 17. │ └─purrr:::map_("integer", .x, .f, ..., .progress = .progress)
 18. │   ├─purrr:::with_indexed_errors(...)
 19. │   │ └─base::withCallingHandlers(...)
 20. │   ├─purrr:::call_with_cleanup(...)
 21. │   └─OmnipathR (local) .f(.x[[i]], ...)
 22. │     ├─... %>% if_null_len0(NA)
 23. │     └─OmnipathR::get_db("organisms")
 24. │       └─OmnipathR::load_db(key, param = param)
 25. │         ├─rlang::exec(loader, !!!param)
 26. │         └─OmnipathR (local) `<fn>`()
 27. │           ├─... %>% ...
 28. │           └─OmnipathR::ensembl_organisms()
 29. │             ├─... %>% ...
 30. │             └─OmnipathR::ensembl_organisms_raw()
 31. │               └─... %>% html_table()
 32. ├─OmnipathR:::if_null_len0(., NA)
 33. │ └─value1 %>% is_empty_2 %>% if (value2) value1
 34. ├─OmnipathR:::is_empty_2(.)
 35. │ └─value %>% ...
 36. ├─dplyr::pull(., name_type)
 37. ├─dplyr::filter(...)
 38. ├─dplyr::mutate(...)
 39. ├─dplyr::full_join(...)
 40. ├─dplyr::full_join(...)
 41. ├─dplyr::rename(., common_name_ensembl = common_name)
 42. ├─dplyr::mutate(...)
 43. ├─dplyr::select(...)
 44. ├─rvest::html_table(.)
 45. ├─rvest::html_element(., "table")
 46. ├─xml2::read_html(.)
 47. ├─OmnipathR:::download_to_cache(., http_headers = user_agent())
 48. │ └─OmnipathR:::download_base(...)
 49. │   └─base::stop(result)
 50. ├─purrr (local) `<fn>`(`<ht2__504>`)
 51. │ └─cli::cli_abort(...)
 52. │   └─rlang::abort(...)
 53. │     └─rlang:::signal_abort(cnd, .file)
 54. │       └─base::signalCondition(cnd)
 55. └─purrr (local) `<fn>`(`<prrr_rr_>`)
 56.   └─cli::cli_abort(...)
 57.     └─rlang::abort(...)
── Failure ('test-outputs_shiny.R:66:3'): .build_venn works ────────────────────
`venn` has type 'object', not 'list'.
── Failure ('test-outputs_shiny.R:68:3'): .build_venn works ────────────────────
names(venn)[1] (`actual`) not equal to "data" (`expected`).

`actual` is NULL
`expected` is a character vector ('data')
── Failure ('test-outputs_shiny.R:149:3'): .build_ridge works ──────────────────
`tested` has type 'object', not 'list'.
── Failure ('test-outputs_shiny.R:151:3'): .build_ridge works ──────────────────
names(tested)[1] (`actual`) not equal to "data" (`expected`).

`actual` is NULL
`expected` is a character vector ('data')
── Failure ('test-outputs_shiny.R:184:3'): .build_histo works ──────────────────
`tested` has type 'object', not 'list'.
── Failure ('test-outputs_shiny.R:186:3'): .build_histo works ──────────────────
names(tested)[1] (`actual`) not equal to "data" (`expected`).

`actual` is NULL
`expected` is a character vector ('data')

[ FAIL 9 | WARN 5 | SKIP 0 | PASS 193 ]
Error: Test failures
Execution halted

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

name	user	system	elapsed
create_multiassay	0.866	0.138	1.127
dot_plotly	0.976	0.111	1.709
extract_model_res	15.380	1.538	20.248
mirna_hsa	0.022	0.003	0.026
mmultiassay_ov	0.094	0.005	0.099
plot_chr_distribution	0.670	0.108	0.832
plot_heatmap	0.652	0.107	0.770
plot_network	0.660	0.109	0.777
plot_ridge	12.064	1.418	16.194
plot_tf_distribution	0.719	0.117	0.896
plot_venn	0.634	0.099	0.737