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This page was generated on 2024-12-02 12:03 -0500 (Mon, 02 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4739
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4482
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4510
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4462
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 865/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.2.0  (landing page)
Angelo Velle
Snapshot Date: 2024-11-28 13:00 -0500 (Thu, 28 Nov 2024)
git_url: https://git.bioconductor.org/packages/gINTomics
git_branch: RELEASE_3_20
git_last_commit: eb9ddba
git_last_commit_date: 2024-10-29 11:30:48 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for gINTomics on nebbiolo2

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: 1.2.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gINTomics_1.2.0.tar.gz
StartedAt: 2024-11-29 00:37:32 -0500 (Fri, 29 Nov 2024)
EndedAt: 2024-11-29 00:49:39 -0500 (Fri, 29 Nov 2024)
EllapsedTime: 726.6 seconds
RetCode: 0
Status:   OK  
CheckDir: gINTomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gINTomics_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gINTomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘gINTomics/DESCRIPTION’ ... OK
* this is package ‘gINTomics’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* 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
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:44:18] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:44:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-29 00:44:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:44:18] [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 ... OK
* 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      10.757  1.309  18.281
extract_model_res  9.166  0.666   9.832
plot_ridge         6.508  0.457   6.965
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/gINTomics.Rcheck/00check.log’
for details.

Installation output

gINTomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gINTomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘gINTomics’ ...
** using staged installation
** R
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:44:52] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:44:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:44:52] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:08] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-28 15:45:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-28 15:45:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-28 15:45:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:09] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-28 15:45:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:09] [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
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:29] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:29] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:45] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-28 15:45:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-28 15:45:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-28 15:45:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-28 15:45:46] [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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(gINTomics)
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Contains 6 files.
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:23] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2024-11-29 00:47:27] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:27] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:27] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-11-29 00:47:27] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] HTTP 200
[2024-11-29 00:47:27] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:27] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-29 00:47:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-29 00:47:28] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-11-29 00:47:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-11-29 00:47:29] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-11-29 00:47:29] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-11-29 00:47:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:29] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2024-11-29 00:47:29] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2024-11-29 00:47:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-29 00:47:30] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-29 00:47:30] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:30] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:30] [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`
[2024-11-29 00:47:30] [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`
[2024-11-29 00:47:30] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:30] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:30] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:31] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:31] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2024-11-29 00:47:31] [INFO]    [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:31] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2024-11-29 00:47:31] [SUCCESS] [OmnipathR] Downloaded 11118 interactions.
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-29 00:47:31] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-29 00:47:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-11-29 00:47:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:32] [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`
[2024-11-29 00:47:32] [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`
[2024-11-29 00:47:32] [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`
[2024-11-29 00:47:32] [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`
[2024-11-29 00:47:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:32] [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`
[2024-11-29 00:47:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:33] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2024-11-29 00:47:33] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:33] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2024-11-29 00:47:33] [SUCCESS] [OmnipathR] Downloaded 3868 interactions.
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Orthology targets: 
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:33] [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`
[2024-11-29 00:47:33] [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`
[2024-11-29 00:47:33] [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`
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:35] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:35] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2024-11-29 00:47:35] [INFO]    [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-29 00:47:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-29 00:47:35] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2024-11-29 00:47:37] [SUCCESS] [OmnipathR] Downloaded 59469 interactions.
  2162 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
  2162 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 
129.094   9.961  80.471

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

nameusersystemelapsed
create_multiassay0.4770.0240.501
dot_plotly0.3870.0140.401
extract_model_res9.1660.6669.832
mirna_hsa0.0130.0020.015
mmultiassay_ov0.0950.0030.098
plot_chr_distribution0.3550.0100.364
plot_heatmap0.3660.0160.382
plot_network0.3960.0280.424
plot_ridge6.5080.4576.965
plot_tf_distribution0.3630.0010.364
plot_venn0.3520.0080.360
plot_volcano10.757 1.30918.281
run_cnv_integration0.6720.0180.690
run_genomic_enrich0.3640.0080.372
run_genomic_integration0.7810.0700.851
run_met_integration0.6900.0450.735
run_multiomics3.4810.1734.404
run_shiny0.3650.0160.381
run_tf_enrich0.3770.0110.388
run_tf_integration2.0860.0722.159