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) (2025-10-20 r88955) -- "Unsuffered Consequences"	4775
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: 2025-11-02 23:42:57 -0500 (Sun, 02 Nov 2025)

EndedAt: 2025-11-02 23:56:40 -0500 (Sun, 02 Nov 2025)

EllapsedTime: 823.5 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) (2025-10-20 r88955)
* 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
[2025-11-02 23:46:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:46:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:46:50] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 23:46:50] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-02 23:46:50] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-02
[2025-11-02 23:46:50] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-02 20:15:15 UTC; unix
[2025-11-02 23:46:50] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-02 23:46:50] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-02 23:46:50] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); 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=2025-11-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-02 23:46:50] [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]
[2025-11-02 23:46:51] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-02); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-02); BiocBaseUtils 1.13.0(2025-11-02); BiocGenerics 0.57.0(2025-11-02); BiocIO 1.21.0(2025-11-02); BiocParallel 1.45.0(2025-11-02); Biostrings 2.79.1(2025-11-02); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-02); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-02); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-02); 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 1.47.0(2025-11-02); GenomicFeatures 1.63.1(2025-11-02); GenomicRanges 1.63.0(2025-11-02); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-02); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-02); IRanges 2.45.0(2025-11-02); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-02); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2025-11-02); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-02); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.0(2025-11-02); OmnipathR 3.19.0(2025-11-02); 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 1.1.0(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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-02); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-02); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-02); S4Vectors 0.49.0(2025-11-02); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-02); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-02); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.41.0(2025-11-02); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-02); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-02 23:46:51] [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
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:46:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-02 23:46:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:46:51] [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      40.895  6.807  56.193
extract_model_res 10.836  1.088  11.935
plot_ridge         8.163  0.847   9.006
run_multiomics     4.738  0.524   5.882
* 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
[2025-11-02 15:55:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:02] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:02] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-02 15:55:02] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-02
[2025-11-02 15:55:02] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-02 20:15:15 UTC; unix
[2025-11-02 15:55:02] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-02 15:55:02] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-02 15:55:03] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); 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=2025-11-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-02 15:55:03] [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]
[2025-11-02 15:55:03] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-02); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-02); BiocBaseUtils 1.13.0(2025-11-02); BiocGenerics 0.57.0(2025-11-02); BiocIO 1.21.0(2025-11-02); BiocParallel 1.45.0(2025-11-02); Biostrings 2.79.1(2025-11-02); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-02); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-02); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-02); 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 1.47.0(2025-11-02); GenomicFeatures 1.63.1(2025-11-02); GenomicRanges 1.63.0(2025-11-02); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-02); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-02); IRanges 2.45.0(2025-11-02); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-02); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2025-11-02); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-02); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.0(2025-11-02); OmnipathR 3.19.0(2025-11-02); 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 1.1.0(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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-02); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-02); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-02); S4Vectors 0.49.0(2025-11-02); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-02); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-02); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.41.0(2025-11-02); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-02); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-02 15:55:03] [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
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:03] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-11-02 15:55:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:20] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:20] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-02 15:55:20] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-02
[2025-11-02 15:55:20] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-02 20:15:15 UTC; unix
[2025-11-02 15:55:20] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-02 15:55:20] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-02 15:55:21] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); 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=2025-11-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-02 15:55:21] [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]
[2025-11-02 15:55:21] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-02); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-02); BiocBaseUtils 1.13.0(2025-11-02); BiocGenerics 0.57.0(2025-11-02); BiocIO 1.21.0(2025-11-02); BiocParallel 1.45.0(2025-11-02); Biostrings 2.79.1(2025-11-02); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-02); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-02); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-02); 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 1.47.0(2025-11-02); GenomicFeatures 1.63.1(2025-11-02); GenomicRanges 1.63.0(2025-11-02); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-02); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-02); IRanges 2.45.0(2025-11-02); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-02); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2025-11-02); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-02); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.0(2025-11-02); OmnipathR 3.19.0(2025-11-02); 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 1.1.0(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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-02); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-02); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-02); S4Vectors 0.49.0(2025-11-02); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-02); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-02); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.41.0(2025-11-02); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-02); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-02 15:55:21] [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
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-02 15:55:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-02 15:55:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-02 15:55:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:22] [TRACE]   [OmnipathR] Cache locked: FALSE
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2025-11-02 15:55:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:55:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:46] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-02 15:55:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-02
[2025-11-02 15:55:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-02 20:15:15 UTC; unix
[2025-11-02 15:55:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-02 15:55:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-02 15:55:46] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); 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=2025-11-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-02 15:55:46] [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]
[2025-11-02 15:55:47] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-02); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-02); BiocBaseUtils 1.13.0(2025-11-02); BiocGenerics 0.57.0(2025-11-02); BiocIO 1.21.0(2025-11-02); BiocParallel 1.45.0(2025-11-02); Biostrings 2.79.1(2025-11-02); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-02); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-02); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-02); 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 1.47.0(2025-11-02); GenomicFeatures 1.63.1(2025-11-02); GenomicRanges 1.63.0(2025-11-02); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-02); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-02); IRanges 2.45.0(2025-11-02); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-02); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2025-11-02); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-02); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.0(2025-11-02); OmnipathR 3.19.0(2025-11-02); 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 1.1.0(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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-02); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-02); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-02); S4Vectors 0.49.0(2025-11-02); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-02); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-02); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.41.0(2025-11-02); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-02); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-02 15:55:47] [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
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:55:47] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-11-02 15:56:04] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:56:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:56:04] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:56:04] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-02 15:56:04] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-02
[2025-11-02 15:56:04] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-02 20:15:15 UTC; unix
[2025-11-02 15:56:04] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-02 15:56:04] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-02 15:56:05] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); 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=2025-11-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-02 15:56:05] [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]
[2025-11-02 15:56:05] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-02); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-02); BiocBaseUtils 1.13.0(2025-11-02); BiocGenerics 0.57.0(2025-11-02); BiocIO 1.21.0(2025-11-02); BiocParallel 1.45.0(2025-11-02); Biostrings 2.79.1(2025-11-02); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cigarillo 1.1.0(2025-11-02); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-02); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-02); 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 1.47.0(2025-11-02); GenomicFeatures 1.63.1(2025-11-02); GenomicRanges 1.63.0(2025-11-02); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-02); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-02); IRanges 2.45.0(2025-11-02); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-02); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2025-11-02); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-02); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.0(2025-11-02); OmnipathR 3.19.0(2025-11-02); 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 1.1.0(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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-02); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-02); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-02); S4Vectors 0.49.0(2025-11-02); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-02); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-02); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.41.0(2025-11-02); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-02); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-02 15:56:05] [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
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:56:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-02 15:56:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 15:56:05] [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) (2025-10-20 r88955) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu

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> library(testthat)
> library(gINTomics)
[2025-11-02 23:51:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:15] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 23:51:15] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-02 23:51:15] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-11-02
[2025-11-02 23:51:15] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2025-11-02 20:15:15 UTC; unix
[2025-11-02 23:51:15] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.19.0
[2025-11-02 23:51:15] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2025-11-02 23:51:16] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-10-20 r88955); 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=2025-11-02; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.8.25 @ /usr/local/bin/quarto]
[2025-11-02 23:51:16] [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]
[2025-11-02 23:51:16] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.73.0(2025-11-02); backports 1.5.0(2024-05-23); Biobase 2.71.0(2025-11-02); BiocBaseUtils 1.13.0(2025-11-02); BiocGenerics 0.57.0(2025-11-02); BiocIO 1.21.0(2025-11-02); BiocParallel 1.45.0(2025-11-02); Biostrings 2.79.1(2025-11-02); 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); cigarillo 1.1.0(2025-11-02); circlize 0.4.16(2024-02-20); cli 3.6.5(2025-04-23); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-2(2025-09-22); ComplexHeatmap 2.27.0(2025-11-02); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.2.3(2024-06-02); DelayedArray 0.37.0(2025-11-02); 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 1.47.0(2025-11-02); GenomicFeatures 1.63.1(2025-11-02); GenomicRanges 1.63.0(2025-11-02); GetoptLong 1.0.5(2020-12-15); ggplot2 4.0.0(2025-09-11); gINTomics 1.7.0(2025-11-02); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); InteractiveComplexHeatmap 1.19.0(2025-11-02); IRanges 2.45.0(2025-11-02); iterators 1.0.14(2022-02-05); jsonlite 2.0.0(2025-03-27); kableExtra 1.4.0(2024-01-24); KEGGREST 1.51.0(2025-11-02); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.23.0(2025-11-02); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); MethylMix 2.41.0(2025-11-02); mime 0.13(2025-03-17); MultiAssayExperiment 1.37.0(2025-11-02); OmnipathR 3.19.0(2025-11-02); 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 1.1.0(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 2.30(2025-09-28); Rsamtools 2.27.0(2025-11-02); RSQLite 2.4.3(2025-08-20); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.71.0(2025-11-02); rvest 1.0.5(2025-08-29); S4Arrays 1.11.0(2025-11-02); S4Vectors 0.49.0(2025-11-02); S7 0.2.0(2024-11-07); scales 1.4.0(2025-04-24); Seqinfo 1.1.0(2025-11-02); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.11.1(2025-07-03); SparseArray 1.11.1(2025-11-02); stringi 1.8.7(2025-03-27); stringr 1.5.2(2025-09-08); SummarizedExperiment 1.41.0(2025-11-02); svglite 2.2.2(2025-10-21); systemfonts 1.3.1(2025-10-01); testthat 3.2.3(2025-01-13); textshaping 1.0.4(2025-10-10); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.19(2025-08-22); xml2 1.4.1(2025-10-27); xtable 1.8-4(2019-04-21); XVector 0.51.0(2025-11-02); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-02 23:51:16] [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
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Contains 7 files.
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.23-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:16] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2025-11-02 23:51:21] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:21] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:21] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-11-02 23:51:21] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-02 23:51:21] [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]
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-11-02 23:51:21] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-11-02 23:51:22] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-11-02 23:51:22] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-11-02 23:51:22] [TRACE]   [OmnipathR] Downloaded 31.1 Kb in 0.997796s from www.ensembl.org (31.2 Kb/s); Redirect: 0.792026s, DNS look up: 0.021236s, Connection: 0.022627s, Pretransfer: 0.675629s, First byte at: 0.972847s
[2025-11-02 23:51:22] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Mon, 03 Nov 2025 04:51:22 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-33.ebi.ac.uk; HTTP/2 302 ; date: Mon, 03 Nov 2025 04:51:22 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-68.us-east-2.compute.internal; HTTP/2 200 ; date: Mon, 03 Nov 2025 04:51:22 GMT; content-type: text/html; charset=utf-8; content-length: 31856; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Tue, 04 Nov 2025 04:47:14 GMT; set-cookie: ENSEMBL_WWW_SESSION=3ee5b20b4ccb9d980a31424369574dd2057086395c2579b2e0151f45; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Tue, 04 Nov 2025 04:47:14 GMT; set-cookie: ENSEMBL_WWW_SESSION=3ee5b20b4ccb9d980a31424369574dd2057086395c2579b2e0151f45; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; vary: Accept-Encoding; content-encoding: gzip; x-frame-options: SAMEORIGIN; content-security-policy: frame-ancestors 'self'; x-nginx-machine: ip-10-25-25-94.us-east-2.compute.internal
[2025-11-02 23:51:22] [TRACE]   [OmnipathR] Response headers: [date=Mon, 03 Nov 2025 04:51:22 GMT,content-type=text/html; charset=utf-8,content-length=31856,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Tue, 04 Nov 2025 04:47:14 GMT,set-cookie=ENSEMBL_WWW_SESSION=3ee5b20b4ccb9d980a31424369574dd2057086395c2579b2e0151f45; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Tue, 04 Nov 2025 04:47:14 GMT,set-cookie=ENSEMBL_WWW_SESSION=3ee5b20b4ccb9d980a31424369574dd2057086395c2579b2e0151f45; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-94.us-east-2.compute.internal]
[2025-11-02 23:51:24] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:24] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-02 23:51:24] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:24] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-02 23:51:24] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-02 23:51:24] [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]
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] HTTP v2 GET: status 200.
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] Downloaded 8.7 Kb in 0.290385s from omabrowser.org (29.9 Kb/s); Redirect: 0s, DNS look up: 0.037265s, Connection: 0.038018s, Pretransfer: 0.206114s, First byte at: 0.290031s
[2025-11-02 23:51:24] [TRACE]   [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 03 Nov 2025 04:51:24 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-02 23:51:26] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:26] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-02 23:51:26] [INFO]    [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:51:26] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-02 23:51:26] [INFO]    [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-02 23:51:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-02 23:52:06] [INFO]    [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:06] [INFO]    [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-11-02 23:52:06] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:06] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:06] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:06] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-02 23:52:06] [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]
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.295742s from omnipathdb.org (53 Kb/s); Redirect: 0s, DNS look up: 0.004335s, Connection: 0.005016s, Pretransfer: 0.152945s, First byte at: 0.295163s
[2025-11-02 23:52:06] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 03 Nov 2025 04:52:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 03 Nov 2025 05:52:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-02 23:52:11] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:11] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-11-02 23:52:11] [INFO]    [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:11] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2025-11-02 23:52:11] [SUCCESS] [OmnipathR] Downloaded 11240 interactions.
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-02 23:52:11] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:12] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:12] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-02 23:52:12] [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]
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.309096s from omnipathdb.org (50.7 Kb/s); Redirect: 0s, DNS look up: 0.002329s, Connection: 0.003027s, Pretransfer: 0.158327s, First byte at: 0.308523s
[2025-11-02 23:52:12] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 03 Nov 2025 04:52:12 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 03 Nov 2025 05:52:12 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-02 23:52:14] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:14] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-11-02 23:52:14] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:14] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2025-11-02 23:52:14] [SUCCESS] [OmnipathR] Downloaded 3788 interactions.
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Orthology targets: 
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-02 23:52:14] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-02 23:52:14] [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]
[2025-11-02 23:52:15] [TRACE]   [OmnipathR] HTTP v1 GET: status 200.
[2025-11-02 23:52:15] [TRACE]   [OmnipathR] Downloaded 15.7 Kb in 0.308868s from omnipathdb.org (50.7 Kb/s); Redirect: 0s, DNS look up: 0.001974s, Connection: 0.002789s, Pretransfer: 0.158136s, First byte at: 0.308247s
[2025-11-02 23:52:15] [TRACE]   [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 03 Nov 2025 04:52:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 03 Nov 2025 05:52:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-02 23:52:18] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:18] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-11-02 23:52:18] [INFO]    [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-02 23:52:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-11-02 23:52:18] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2025-11-02 23:52:20] [SUCCESS] [OmnipathR] Downloaded 69655 interactions.
'select()' returned many:many mapping between keys and columns
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
response_var and covariates have common colnames, adding '_cov' to covariates
colnames
Generating interactions
Generating interactions
'select()' returned many:many mapping between keys and columns
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 201 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 201 ]
> 
> proc.time()
   user  system elapsed 
269.973  36.656 183.080

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

name	user	system	elapsed
create_multiassay	0.598	0.075	0.675
dot_plotly	0.465	0.038	0.503
extract_model_res	10.836	1.088	11.935
mirna_hsa	0.015	0.002	0.018
mmultiassay_ov	0.098	0.008	0.106
plot_chr_distribution	0.488	0.030	0.519
plot_heatmap	0.466	0.031	0.496
plot_network	0.463	0.061	0.523
plot_ridge	8.163	0.847	9.006
plot_tf_distribution	0.469	0.036	0.505
plot_venn	0.462	0.040	0.502
plot_volcano	40.895	6.807	56.193
run_cnv_integration	0.911	0.140	1.052
run_genomic_enrich	0.449	0.061	0.509
run_genomic_integration	1.002	0.170	1.173
run_met_integration	0.832	0.131	0.964
run_multiomics	4.738	0.524	5.882
run_shiny	0.493	0.084	0.577
run_tf_enrich	0.477	0.064	0.541
run_tf_integration	2.982	0.421	3.402