Build/check report for BioC 3.23 - CHECK results for gINTomics on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4877
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 nebbiolo1

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: 1.7.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings gINTomics_1.7.0.tar.gz

StartedAt: 2026-03-02 00:16:43 -0500 (Mon, 02 Mar 2026)

EndedAt: 2026-03-02 00:30:55 -0500 (Mon, 02 Mar 2026)

EllapsedTime: 852.7 seconds

RetCode: 0

Status: OK

CheckDir: gINTomics.Rcheck

Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings gINTomics_1.7.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.7.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 42 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gINTomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-03-02 00:20:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:20:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:20:42] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-02 00:20:42] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-02 00:20:42] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-01
[2026-03-02 00:20:42] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-01 20:11:55 UTC; unix
[2026-03-02 00:20:42] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-02 00:20:42] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-02 00:20:43] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-02 00:20:43] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-02 00:20:43] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-03-01); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-03-01); BiocGenerics 0.57.0(2026-03-01); BiocIO 1.21.0(2026-03-01); BiocParallel 1.45.0(2026-03-01); Biostrings 2.79.4(2026-03-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-03-01); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-03-01); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-03-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2026-03-01); GenomicFeatures 1.63.1(2026-03-01); GenomicRanges 1.63.1(2026-03-01); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-03-01); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-03-01); IRanges 2.45.0(2026-03-01); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-03-01); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-03-01); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-03-01); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-03-01); OmnipathR 3.19.6(2026-03-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-03-01); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-03-01); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-03-01); S4Vectors 0.49.0(2026-03-01); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-03-01); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-03-01); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-03-01); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-03-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-02 00:20:43] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:20:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:20:43] [TRACE]   [OmnipathR] Cache locked: FALSE
.build_histo: no visible binding for global variable ‘chr_cov’
.build_histo: no visible binding for global variable ‘significance’
.build_ridge: no visible binding for global variable ‘coef’
.build_ridge: no visible binding for global variable ‘significance’
.circos_preprocess: no visible binding for global variable ‘cnv_met’
.find_deg: no visible global function definition for ‘combn’
.find_deg: no visible global function definition for ‘contrasts.fit’
.prepare_cnv_heatmap: no visible binding for global variable ‘cnv’
.prepare_gen_heatmap: no visible binding for global variable ‘met’
.prepare_gen_heatmap: no visible binding for global variable ‘cnv’
.prepare_met_heatmap: no visible binding for global variable ‘met’
.prepare_mirna_heatmap: no visible binding for global variable
  ‘mirna_cnv’
.prepare_network: no visible binding for global variable ‘omics’
.prepare_reactive_histo_tf: no visible binding for global variable
  ‘Freq’
.prepare_reactive_venn: no visible binding for global variable
  ‘cnv_met’
.prepare_reactive_venn: no visible binding for global variable ‘pval’
.reactive_cnv_test_plots: no visible binding for global variable ‘x’
.reactive_cnv_test_plots: no visible binding for global variable ‘y’
.reactive_transcExpr_plots: no visible binding for global variable ‘x’
.reactive_transcExpr_plots: no visible binding for global variable ‘y’
.run_reactive_tf_enrich: no visible binding for '<<-' assignment to
  ‘bg_process’
.server_enrich_bg : <anonymous>: no visible binding for global variable
  ‘bg_process’
.server_enrich_bgTF: no visible binding for '<<-' assignment to
  ‘bg_process’
.server_enrich_bgTF : <anonymous>: no visible binding for global
  variable ‘bg_process’
.shiny_preprocess: no visible binding for global variable ‘cov’
plot_tf_distribution: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
  Freq bg_process chr_cov cnv cnv_met coef combn contrasts.fit cov met
  mirna_cnv omics pval significance x y
Consider adding
  importFrom("stats", "coef", "cov")
  importFrom("utils", "combn")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mmultiassay_ov.Rd: MultiAssayExperiment-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
plot_volcano      44.572  8.480  67.706
extract_model_res 11.541  1.579  13.100
plot_ridge         8.173  1.372   9.495
run_multiomics     4.474  0.495   5.611
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/gINTomics.Rcheck/00check.log’
for details.

Installation output

gINTomics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL gINTomics
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘gINTomics’ ...
** this is package ‘gINTomics’ version ‘1.7.0’
** using staged installation
** R
[2026-03-01 15:54:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:54:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:16] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:54:16] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-01 15:54:16] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-01
[2026-03-01 15:54:16] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-01 20:11:55 UTC; unix
[2026-03-01 15:54:16] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-01 15:54:16] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-01 15:54:16] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-01 15:54:16] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-01 15:54:17] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-03-01); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-03-01); BiocGenerics 0.57.0(2026-03-01); BiocIO 1.21.0(2026-03-01); BiocParallel 1.45.0(2026-03-01); Biostrings 2.79.4(2026-03-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-03-01); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-03-01); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-03-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2026-03-01); GenomicFeatures 1.63.1(2026-03-01); GenomicRanges 1.63.1(2026-03-01); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-03-01); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-03-01); IRanges 2.45.0(2026-03-01); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-03-01); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-03-01); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-03-01); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-03-01); OmnipathR 3.19.6(2026-03-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-03-01); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-03-01); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-03-01); S4Vectors 0.49.0(2026-03-01); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-03-01); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-03-01); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-03-01); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-03-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-01 15:54:17] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:17] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:17] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2026-03-01 15:54:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:54:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:54:34] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-01 15:54:34] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-01
[2026-03-01 15:54:34] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-01 20:11:55 UTC; unix
[2026-03-01 15:54:34] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-01 15:54:34] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-01 15:54:35] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-01 15:54:35] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-01 15:54:35] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-03-01); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-03-01); BiocGenerics 0.57.0(2026-03-01); BiocIO 1.21.0(2026-03-01); BiocParallel 1.45.0(2026-03-01); Biostrings 2.79.4(2026-03-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-03-01); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-03-01); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-03-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2026-03-01); GenomicFeatures 1.63.1(2026-03-01); GenomicRanges 1.63.1(2026-03-01); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-03-01); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-03-01); IRanges 2.45.0(2026-03-01); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-03-01); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-03-01); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-03-01); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-03-01); OmnipathR 3.19.6(2026-03-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-03-01); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-03-01); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-03-01); S4Vectors 0.49.0(2026-03-01); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-03-01); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-03-01); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-03-01); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-03-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-01 15:54:35] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:35] [TRACE]   [OmnipathR] Cache locked: FALSE
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2026-03-01 15:54:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:54:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:54:59] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:54:59] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-01 15:54:59] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-01
[2026-03-01 15:54:59] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-01 20:11:55 UTC; unix
[2026-03-01 15:54:59] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-01 15:54:59] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-01 15:55:00] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-01 15:55:00] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-01 15:55:00] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-03-01); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-03-01); BiocGenerics 0.57.0(2026-03-01); BiocIO 1.21.0(2026-03-01); BiocParallel 1.45.0(2026-03-01); Biostrings 2.79.4(2026-03-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-03-01); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-03-01); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-03-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2026-03-01); GenomicFeatures 1.63.1(2026-03-01); GenomicRanges 1.63.1(2026-03-01); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-03-01); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-03-01); IRanges 2.45.0(2026-03-01); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-03-01); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-03-01); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-03-01); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-03-01); OmnipathR 3.19.6(2026-03-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-03-01); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-03-01); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-03-01); S4Vectors 0.49.0(2026-03-01); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-03-01); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-03-01); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-03-01); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-03-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-01 15:55:00] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:00] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2026-03-01 15:55:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:55:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:18] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:55:18] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-01 15:55:18] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-01
[2026-03-01 15:55:18] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-01 20:11:55 UTC; unix
[2026-03-01 15:55:18] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-01 15:55:18] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-01 15:55:19] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-01; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-01 15:55:19] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-01 15:55:19] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-03-01); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-03-01); BiocGenerics 0.57.0(2026-03-01); BiocIO 1.21.0(2026-03-01); BiocParallel 1.45.0(2026-03-01); Biostrings 2.79.4(2026-03-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2026-03-01); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-03-01); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-03-01); dichromat 2.0-0.1(2022-05-02); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2026-03-01); GenomicFeatures 1.63.1(2026-03-01); GenomicRanges 1.63.1(2026-03-01); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-03-01); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-03-01); IRanges 2.45.0(2026-03-01); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-03-01); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-03-01); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-03-01); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-03-01); OmnipathR 3.19.6(2026-03-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-03-01); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-03-01); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-03-01); S4Vectors 0.49.0(2026-03-01); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-03-01); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-03-01); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-03-01); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-03-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-01 15:55:19] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Contains 1 files.
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-01 15:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-01 15:55:19] [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


R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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> library(testthat)
> library(gINTomics)
[2026-03-02 00:25:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:28] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-03-02 00:25:28] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-02 00:25:28] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2026-03-01
[2026-03-02 00:25:28] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-01 20:11:55 UTC; unix
[2026-03-02 00:25:28] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.6
[2026-03-02 00:25:28] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-02 00:25:29] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2026-01-15 r89304); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2026-03-02 00:25:29] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; zstd=1.5.5; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-03-02 00:25:29] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2026-03-01); backports 1.5.0(2024-05-23); Biobase 2.71.0(2026-03-01); BiocGenerics 0.57.0(2026-03-01); BiocIO 1.21.0(2026-03-01); BiocParallel 1.45.0(2026-03-01); Biostrings 2.79.4(2026-03-01); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cigarillo 1.1.0(2026-03-01); circlize 0.4.17(2025-12-08); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-67(2026-02-18); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.1(2026-03-01); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); DelayedArray 0.37.0(2026-03-01); digest 0.6.39(2025-11-19); doParallel 1.0.17(2022-02-07); dplyr 1.2.0(2026-02-03); DT 0.34.0(2025-09-02); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicAlignments 1.47.0(2026-03-01); GenomicFeatures 1.63.1(2026-03-01); GenomicRanges 1.63.1(2026-03-01); GetoptLong 1.1.0(2025-11-28); ggplot2 4.0.2(2026-02-03); gINTomics 1.7.0(2026-03-01); GlobalOptions 0.1.3(2025-11-28); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); InteractiveComplexHeatmap 1.19.1(2026-03-01); IRanges 2.45.0(2026-03-01); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.1(2026-03-01); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2026-03-01); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2026-03-01); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.2(2026-03-01); OmnipathR 3.19.6(2026-03-01); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RCurl 1.98-1.17(2025-03-22); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); restfulr 0.0.16(2025-06-27); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); Rsamtools 2.27.0(2026-03-01); RSQLite 2.4.6(2026-02-06); rstudioapi 0.18.0(2026-01-16); rtracklayer 1.71.3(2026-03-01); rvest 1.0.5(2025-08-29); S4Arrays 1.11.1(2026-03-01); S4Vectors 0.49.0(2026-03-01); S7 0.2.1(2025-11-14); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2026-03-01); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.13.0(2026-02-20); SparseArray 1.11.10(2026-03-01); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.41.1(2026-03-01); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); testthat 3.3.2(2026-01-11); textshaping 1.0.4(2025-10-10); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.51.0(2026-03-01); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-02 00:25:29] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Contains 8 files.
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:29] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2026-03-02 00:25:34] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Checking on-disk cache for database `organisms`.
[2026-03-02 00:25:34] [INFO]    [OmnipathR] Cache record does not exist: `db://organisms`
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Loading database `organisms` from source.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:34] [INFO]    [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:34] [INFO]    [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-03-02 00:25:34] [INFO]    [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Sending HTTP request.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Downloaded 39.9 Kb in 0.433771s from rescued.omnipathdb.org (91.9 Kb/s); Redirect: 0s, DNS look up: 0.001625s, Connection: 0.002235s, Pretransfer: 0.151354s, First byte at: 0.293208s
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 05:25:34 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Mon, 02 Mar 2026 06:25:34 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-03-02 00:25:34] [TRACE]   [OmnipathR] Response headers: [Server=nginx,Date=Mon, 02 Mar 2026 05:25:34 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Mon, 02 Mar 2026 06:25:34 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-03-02 00:25:36] [INFO]    [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:36] [INFO]    [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-02 00:25:36] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:36] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-02 00:25:36] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] Downloaded 3.8 Kb in 0.379894s from omabrowser.org (10 Kb/s); Redirect: 0s, DNS look up: 0.000774s, Connection: 0.013571s, Pretransfer: 0.053684s, First byte at: 0.379761s
[2026-03-02 00:25:36] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 02 Mar 2026 05:25:36 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=7TZyJfUV4WUdGPdM3rquXqYjxuqL6fZcb1GRTcyvKxZu62nTUSbab9dfqLwvET23pSwY0FpueVquR5LKAa40o2QqjEnZIZxfU3AWPUWY"}]}; cf-ray: 9d5dfb570a8b9e01-IAD; alt-svc: h3=":443"; ma=86400
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-03-02 00:25:38] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:38] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-02 00:25:38] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:25:38] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-02 00:25:38] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-02 00:25:38] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-03-02 00:26:09] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-03-02 00:26:09] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-03-02 00:26:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:09] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-03-02 00:26:09] [TRACE]   [OmnipathR] Saving database `organisms` to on-disk cache.
[2026-03-02 00:26:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:10] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `unknown` to `started`.
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2279cf45097ad11a757767cb09e3eb8d227f0445-1.rds`.
[2026-03-02 00:26:10] [INFO]    [OmnipathR] Download ready [key=2279cf45097ad11a757767cb09e3eb8d227f0445, version=1]
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:10] [INFO]    [OmnipathR] Cache item `2279cf45097ad11a757767cb09e3eb8d227f0445` version 1: status changed from `started` to `ready`.
[2026-03-02 00:26:10] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:10] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:10] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:10] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-02 00:26:10] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 00:26:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 00:26:12] [TRACE]   [OmnipathR] Downloaded 15.6 Kb in 1.640853s from omnipathdb.org (9.5 Kb/s); Redirect: 0s, DNS look up: 0.00153s, Connection: 0.002407s, Pretransfer: 0.157146s, First byte at: 1.640285s
[2026-03-02 00:26:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 05:26:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 02 Mar 2026 06:26:12 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-03-02 00:26:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:14] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2026-03-02 00:26:14] [INFO]    [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:14] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2026-03-02 00:26:15] [SUCCESS] [OmnipathR] Downloaded 11240 interactions.
[2026-03-02 00:26:15] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 00:26:15] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2026-03-02 00:26:15] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 00:26:15] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 00:26:15] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:16] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:16] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:16] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-02 00:26:16] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 00:26:17] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 00:26:17] [TRACE]   [OmnipathR] Downloaded 15.6 Kb in 1.249398s from omnipathdb.org (12.5 Kb/s); Redirect: 0s, DNS look up: 0.0019s, Connection: 0.002671s, Pretransfer: 0.148782s, First byte at: 1.248742s
[2026-03-02 00:26:17] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 05:26:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 02 Mar 2026 06:26:17 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-03-02 00:26:19] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:19] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2026-03-02 00:26:19] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:19] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2026-03-02 00:26:19] [SUCCESS] [OmnipathR] Downloaded 3788 interactions.
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Organism(s): 9606
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Orthology targets: 
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-03-02 00:26:19] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-03-02 00:26:26] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2026-03-02 00:26:26] [TRACE]   [OmnipathR] Downloaded 15.6 Kb in 7.392033s from omnipathdb.org (2.1 Kb/s); Redirect: 0s, DNS look up: 0.002089s, Connection: 0.015756s, Pretransfer: 0.15501s, First byte at: 7.391113s
[2026-03-02 00:26:26] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 02 Mar 2026 05:26:26 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Mon, 02 Mar 2026 06:26:26 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-03-02 00:26:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2026-03-02 00:26:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:29] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2026-03-02 00:26:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2026-03-02 00:26:30] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2026-03-02 00:26:30] [INFO]    [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2026-03-02 00:26:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-02 00:26:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2026-03-02 00:26:30] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2026-03-02 00:26:32] [SUCCESS] [OmnipathR] Downloaded 69655 interactions.
'select()' returned many:many mapping between keys and columns
Generating interactions
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
calcNormFactors has been renamed to normLibSizes
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
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
Generating interactions
calcNormFactors has been renamed to normLibSizes
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
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
calcNormFactors has been renamed to normLibSizes
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
calcNormFactors has been renamed to normLibSizes
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
calcNormFactors has been renamed to normLibSizes
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
calcNormFactors has been renamed to normLibSizes
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
calcNormFactors has been renamed to normLibSizes
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
Generating interactions
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
'select()' returned many:many mapping between keys and columns
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 201 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 201 ]
> 
> proc.time()
   user  system elapsed 
206.586  31.619 159.077

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

name	user	system	elapsed
create_multiassay	0.571	0.104	0.675
dot_plotly	0.571	0.166	0.737
extract_model_res	11.541	1.579	13.100
mirna_hsa	0.014	0.002	0.017
mmultiassay_ov	0.102	0.003	0.105
plot_chr_distribution	0.479	0.060	0.537
plot_heatmap	0.470	0.045	0.512
plot_network	0.506	0.071	0.573
plot_ridge	8.173	1.372	9.495
plot_tf_distribution	0.463	0.043	0.504
plot_venn	0.492	0.046	0.534
plot_volcano	44.572	8.480	67.706
run_cnv_integration	0.860	0.079	0.933
run_genomic_enrich	0.489	0.044	0.533
run_genomic_integration	1.025	0.148	1.160
run_met_integration	0.857	0.081	0.930
run_multiomics	4.474	0.495	5.611
run_shiny	0.499	0.072	0.567
run_tf_enrich	0.593	0.097	0.687
run_tf_integration	2.965	0.411	3.341