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This page was generated on 2025-03-14 11:43 -0400 (Fri, 14 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4781
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4537
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4567
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4519
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4451
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 871/2309HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.3.0  (landing page)
Angelo Velle
Snapshot Date: 2025-03-13 13:40 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: devel
git_last_commit: 3ba788e
git_last_commit_date: 2024-10-29 11:30:48 -0400 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for gINTomics on lconway

To the developers/maintainers of the gINTomics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gINTomics.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gINTomics
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.3.0.tar.gz
StartedAt: 2025-03-13 21:01:33 -0400 (Thu, 13 Mar 2025)
EndedAt: 2025-03-13 21:13:29 -0400 (Thu, 13 Mar 2025)
EllapsedTime: 716.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gINTomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gINTomics_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.3.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 40 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gINTomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2025-03-13 21:05:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:05:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:05:46] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 21:05:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-13 21:05:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13
[2025-03-13 21:05:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:09:23 UTC; unix
[2025-03-13 21:05:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 21:05:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-13 21:05:47] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 21:05:47] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-03-13 21:05:48] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 21:05:48] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:05:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 21:05:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:05:48] [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’
.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’
.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 chr_cov cnv cnv_met coef cov met mirna_cnv omics pval
  significance
Consider adding
  importFrom("stats", "coef", "cov")
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      24.001  2.164  39.113
extract_model_res 14.264  1.358  16.450
plot_ridge        12.646  1.337  16.806
run_multiomics     6.020  0.846   8.706
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00check.log’
for details.

Installation output

gINTomics.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gINTomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘gINTomics’ ...
** this is package ‘gINTomics’ version ‘1.3.0’
** using staged installation
** R
[2025-03-13 15:44:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:44:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:44:46] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:44:46] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-13 15:44:46] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13
[2025-03-13 15:44:46] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:09:23 UTC; unix
[2025-03-13 15:44:46] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 15:44:46] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-13 15:44:47] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 15:44:47] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-03-13 15:44:47] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 15:44:47] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-03-13 15:44:47] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 15:44:47] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:44:47] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 15:44:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 15:44:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:44:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:44:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:44:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-13 15:44:48] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 15:44:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:44:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 15:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:44:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 15:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:44:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 15:44:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:44:49] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2025-03-13 15:45:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:45:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:12] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:45:12] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-13 15:45:12] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13
[2025-03-13 15:45:12] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:09:23 UTC; unix
[2025-03-13 15:45:12] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 15:45:12] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-13 15:45:13] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 15:45:13] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-03-13 15:45:14] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 15:45:14] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 15:45:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:14] [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
[2025-03-13 15:45:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:45:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:48] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:45:48] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-13 15:45:48] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13
[2025-03-13 15:45:48] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:09:23 UTC; unix
[2025-03-13 15:45:48] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 15:45:48] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-13 15:45:48] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 15:45:49] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-03-13 15:45:49] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 15:45:49] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:45:49] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-13 15:46:14] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:46:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:46:14] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:46:14] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-13 15:46:14] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13
[2025-03-13 15:46:14] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:09:23 UTC; unix
[2025-03-13 15:46:14] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 15:46:14] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-13 15:46:15] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 15:46:15] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-03-13 15:46:16] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 15:46:16] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:46:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 15:46:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 15:46:16] [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) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(gINTomics)
[2025-03-13 21:11:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:17] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 21:11:17] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-03-13 21:11:17] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-03-13
[2025-03-13 21:11:17] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-03-13 19:09:23 UTC; unix
[2025-03-13 21:11:17] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.11
[2025-03-13 21:11:17] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-03-13 21:11:17] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-03-02 r87868); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-03-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-03-13 21:11:18] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-03-13 21:11:18] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); AnnotationDbi 1.69.0(2025-03-13); backports 1.5.0(2024-05-23); Biobase 2.67.0(2025-03-13); BiocBaseUtils 1.9.0(2025-03-13); BiocGenerics 0.53.6(2025-03-13); BiocIO 1.17.1(2025-03-13); BiocParallel 1.41.2(2025-03-13); Biostrings 2.75.4(2025-03-13); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); bitops 1.0-9(2024-10-03); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.4.0(2025-01-25); circlize 0.4.16(2024-02-20); cli 3.6.4(2025-02-13); clisymbols 1.2.0(2017-05-21); clue 0.3-66(2024-11-13); cluster 2.1.8.1(2025-03-12); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); ComplexHeatmap 2.23.0(2025-03-13); crayon 1.5.3(2024-06-20); curl 6.2.1(2025-02-19); DBI 1.2.3(2024-06-02); DelayedArray 0.33.6(2025-03-13); digest 0.6.37(2024-08-19); doParallel 1.0.17(2022-02-07); dplyr 1.1.4(2023-11-17); DT 0.33(2024-04-04); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fontawesome 0.5.3(2024-11-16); foreach 1.5.2(2022-02-02); fs 1.6.5(2024-10-30); generics 0.1.3(2022-07-05); GenomeInfoDb 1.43.4(2025-03-13); GenomeInfoDbData 1.2.14(2025-03-12); GenomicAlignments 1.43.0(2025-03-13); GenomicFeatures 1.59.1(2025-03-13); GenomicRanges 1.59.1(2025-03-13); GetoptLong 1.0.5(2020-12-15); gINTomics 1.3.0(2025-03-13); GlobalOptions 0.1.2(2020-06-10); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.15(2024-03-26); httr 1.4.7(2023-08-15); httr2 1.1.1(2025-03-08); igraph 2.1.4(2025-01-23); InteractiveComplexHeatmap 1.15.0(2025-03-13); IRanges 2.41.3(2025-03-13); iterators 1.0.14(2022-02-05); jsonlite 1.9.1(2025-03-03); kableExtra 1.4.0(2024-01-24); KEGGREST 1.47.0(2025-03-13); knitr 1.49(2024-11-08); later 1.4.1(2024-11-27); lattice 0.22-6(2024-03-20); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.19.1(2025-03-13); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.12(2021-09-28); MultiAssayExperiment 1.33.9(2025-03-13); munsell 0.5.1(2024-04-01); OmnipathR 3.15.11(2025-03-13); pillar 1.10.1(2025-01-07); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.0(2025-02-18); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 1.0.14(2025-01-12); RCurl 1.98-1.16(2024-07-11); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); restfulr 0.0.15(2022-06-16); rjson 0.2.23(2024-09-16); rlang 1.1.5(2025-01-17); rmarkdown 2.29(2024-11-04); Rsamtools 2.23.1(2025-03-13); RSQLite 2.3.9(2024-12-03); rstudioapi 0.17.1(2024-10-22); rtracklayer 1.67.1(2025-03-13); rvest 1.0.4(2024-02-12); S4Arrays 1.7.3(2025-03-13); S4Vectors 0.45.4(2025-03-13); scales 1.3.0(2023-11-28); sessioninfo 1.2.3(2025-02-05); shape 1.4.6.1(2024-02-23); shiny 1.10.0(2024-12-14); SparseArray 1.7.6(2025-03-13); stringi 1.8.4(2024-05-06); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.37.0(2025-03-13); svglite 2.1.3(2023-12-08); systemfonts 1.2.1(2025-01-20); testthat 3.2.3(2025-01-13); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.4.0(2023-05-12); UCSC.utils 1.3.1(2025-03-13); vctrs 0.6.5(2023-12-01); viridisLite 0.4.2(2023-05-02); websocket 1.4.2(2024-07-22); withr 3.0.2(2024-10-28); xfun 0.51(2025-02-19); XML 3.99-0.18(2025-01-01); xml2 1.3.7(2025-02-28); xtable 1.8-4(2019-04-21); XVector 0.47.2(2025-03-13); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-03-13 21:11:18] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Contains 6 files.
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:18] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2025-03-13 21:11:25] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:25] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:25] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-03-13 21:11:25] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-13 21:11:25] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-13 21:11:26] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-03-13 21:11:26] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-03-13 21:11:27] [TRACE]   [OmnipathR] HTTP 200 (OK)
[2025-03-13 21:11:27] [TRACE]   [OmnipathR] Downloaded 30.8 Kb in 1.107215s from www.ensembl.org (27.9 Kb/s); Redirect: 0.906586s, DNS look up: 0.003164s, Connection: 0.004796s, Pretransfer: 0.601142s, First byte at: 1.07973s
[2025-03-13 21:11:27] [TRACE]   [OmnipathR] Response headers: [date=Fri, 14 Mar 2025 01:11:27 GMT,content-type=text/html; charset=utf-8,content-length=31578,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Sat, 15 Mar 2025 01:01:49 GMT,set-cookie=ENSEMBL_WWW_SESSION=aa11a9f0082fe7460fc8a21d682299fe082c70019711a77eadcceb8e; 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=Sat, 15 Mar 2025 01:01:49 GMT,set-cookie=ENSEMBL_WWW_SESSION=aa11a9f0082fe7460fc8a21d682299fe082c70019711a77eadcceb8e; 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-10-25-25-69.us-east-2.compute.internal]
[2025-03-13 21:11:28] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:28] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-13 21:11:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-13 21:11:28] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-03-13 21:11:28] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-13 21:11:30] [TRACE]   [OmnipathR] Downloaded 108 Kb in 1.070594s from omabrowser.org (100.9 Kb/s); Redirect: 0s, DNS look up: 0.001259s, Connection: 0.002134s, Pretransfer: 0.20661s, First byte at: 0.309547s
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-03-13 21:11:31] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:31] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-03-13 21:11:31] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:31] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:31] [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`
[2025-03-13 21:11:31] [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`
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:31] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:31] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-13 21:11:32] [TRACE]   [OmnipathR] Downloaded 226.1 Kb in 1.066703s from omnipathdb.org (212 Kb/s); Redirect: 0s, DNS look up: 0.001241s, Connection: 0.002159s, Pretransfer: 0.157827s, First byte at: 0.312218s
[2025-03-13 21:11:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:33] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-03-13 21:11:33] [INFO]    [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:33] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2025-03-13 21:11:34] [SUCCESS] [OmnipathR] Downloaded 11118 interactions.
[2025-03-13 21:11:34] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-13 21:11:34] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2025-03-13 21:11:34] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-13 21:11:34] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-13 21:11:35] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-03-13 21:11:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:35] [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`
[2025-03-13 21:11:35] [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`
[2025-03-13 21:11:35] [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`
[2025-03-13 21:11:35] [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`
[2025-03-13 21:11:35] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:35] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:35] [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`
[2025-03-13 21:11:35] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-13 21:11:35] [TRACE]   [OmnipathR] Downloaded 53.9 Kb in 0.574011s from omnipathdb.org (93.9 Kb/s); Redirect: 0s, DNS look up: 0.001319s, Connection: 0.002323s, Pretransfer: 0.167954s, First byte at: 0.333044s
[2025-03-13 21:11:36] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:36] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2025-03-13 21:11:36] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-03-13 21:11:37] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:37] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2025-03-13 21:11:37] [SUCCESS] [OmnipathR] Downloaded 3868 interactions.
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Orthology targets: 
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:37] [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`
[2025-03-13 21:11:37] [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`
[2025-03-13 21:11:37] [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`
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:37] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:37] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-03-13 21:11:39] [TRACE]   [OmnipathR] Downloaded 805.9 Kb in 1.80621s from omnipathdb.org (446.2 Kb/s); Redirect: 0s, DNS look up: 0.001222s, Connection: 0.002036s, Pretransfer: 0.157404s, First byte at: 0.310289s
[2025-03-13 21:11:40] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:40] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-03-13 21:11:40] [INFO]    [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-13 21:11:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-13 21:11:40] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2025-03-13 21:11:43] [SUCCESS] [OmnipathR] Downloaded 59469 interactions.
  2169 genes were dropped because they have exons located on both strands of
  the same reference sequence or on more than one reference sequence, so cannot
  be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
'select()' returned 1: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
  2169 genes were dropped because they have exons located on both strands of
  the same reference sequence or on more than one reference sequence, so cannot
  be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
'select()' returned 1:many mapping between keys and columns
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 204 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 204 ]
> 
> proc.time()
   user  system elapsed 
196.859  36.913 141.191

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

nameusersystemelapsed
create_multiassay0.7560.1200.881
dot_plotly0.6840.1090.796
extract_model_res14.264 1.35816.450
mirna_hsa0.0240.0040.075
mmultiassay_ov0.1150.0060.178
plot_chr_distribution0.7830.1051.246
plot_heatmap0.6840.1380.929
plot_network0.6460.1100.762
plot_ridge12.646 1.33716.806
plot_tf_distribution0.7570.1330.915
plot_venn0.7680.1270.910
plot_volcano24.001 2.16439.113
run_cnv_integration1.6130.2892.295
run_genomic_enrich0.8740.1061.608
run_genomic_integration1.6640.3072.582
run_met_integration1.2620.2801.616
run_multiomics6.0200.8468.706
run_shiny0.6900.1230.828
run_tf_enrich0.7070.1170.837
run_tf_integration3.0980.3063.482