Back to Multiple platform build/check report for BioC 3.21:   simplified   long
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This page was generated on 2025-01-20 11:46 -0500 (Mon, 20 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4777
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4502
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4461
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4416
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4403
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 862/2286HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gINTomics 1.3.0  (landing page)
Angelo Velle
Snapshot Date: 2025-01-19 13:40 -0500 (Sun, 19 Jan 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 -0500 (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    ERROR  skippedskipped
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 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for gINTomics on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: gINTomics
Version: 1.3.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gINTomics_1.3.0.tar.gz
StartedAt: 2025-01-20 07:45:15 -0000 (Mon, 20 Jan 2025)
EndedAt: 2025-01-20 08:04:29 -0000 (Mon, 20 Jan 2025)
EllapsedTime: 1154.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gINTomics.Rcheck
Warnings: 5

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gINTomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gINTomics_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 ... WARNING
Found the following significant warnings:
  Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:46:43] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:46:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:46:43] [TRACE]   [OmnipathR] Cache locked: FALSE

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:49:50] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:49:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 07:49:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 07:49:50] [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 ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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      15.492  1.347 467.976
extract_model_res 12.714  0.380  13.115
plot_ridge        10.213  0.240  10.470
run_multiomics     5.682  0.311   7.003
* 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: 5 WARNINGs, 6 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gINTomics.Rcheck/00check.log’
for details.

Installation output

gINTomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL gINTomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘gINTomics’ ...
** using staged installation
** R
Warning: program compiled against libxml 212 using older 211
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:31] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:31] [TRACE]   [OmnipathR] Cache locked: FALSE



** data
** inst
** byte-compile and prepare package for lazy loading
Warning: program compiled against libxml 212 using older 211
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 20:20:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:20:54] [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
Warning: program compiled against libxml 212 using older 211
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:25] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:25] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
Warning: program compiled against libxml 212 using older 211
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:48] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-19 20:21:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-19 20:21:48] [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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(testthat)
> library(gINTomics)
Warning: program compiled against libxml 212 using older 211
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:42] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Contains 6 files.
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:42] [TRACE]   [OmnipathR] Cache locked: FALSE



> 
> test_check("gINTomics")
[2025-01-20 08:01:48] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=mirnatarget]
[2025-01-20 08:01:48] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-01-20 08:01:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:01:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:48] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-01-20 08:01:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:01:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:01:48] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-01-20 08:01:48] [TRACE]   [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-01-20 08:01:48] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-01-20 08:01:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-01-20 08:02:25] [TRACE]   [OmnipathR] HTTP 200
[2025-01-20 08:02:25] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-01-20 08:02:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:25] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:25] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-01-20 08:02:25] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-20 08:02:25] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-01-20 08:02:25] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-01-20 08:02:25] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:26] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-01-20 08:02:26] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-20 08:02:26] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-01-20 08:02:26] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-01-20 08:02:28] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:28] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-01-20 08:02:28] [INFO]    [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] Orthology targets: 
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:28] [INFO]    [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:28] [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`
[2025-01-20 08:02:28] [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`
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:28] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:28] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:29] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=mirnatarget&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:29] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `unknown` to `started`.
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds`.
[2025-01-20 08:02:29] [INFO]    [OmnipathR] Download ready [key=41c8055b20002c0dbf8ddf485403332479b715a1, version=1]
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:29] [INFO]    [OmnipathR] Cache item `41c8055b20002c0dbf8ddf485403332479b715a1` version 1: status changed from `started` to `ready`.
[2025-01-20 08:02:30] [SUCCESS] [OmnipathR] Downloaded 11118 interactions.
[2025-01-20 08:02:30] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=TransmiR,organisms=9606,query_type=interactions,datasets=tf_mirna]
[2025-01-20 08:02:30] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-01-20 08:02:30] [TRACE]   [OmnipathR] Orthology targets: 
[2025-01-20 08:02:32] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-01-20 08:02:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:32] [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`
[2025-01-20 08:02:32] [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`
[2025-01-20 08:02:32] [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`
[2025-01-20 08:02:32] [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`
[2025-01-20 08:02:32] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:32] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:32] [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`
[2025-01-20 08:02:33] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=TransmiR&datasets=tf_mirna&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:33] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `unknown` to `started`.
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds`.
[2025-01-20 08:02:33] [INFO]    [OmnipathR] Download ready [key=2e2b496d72e1686af2bd8a26a0b6d2f96d90e687, version=1]
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:33] [INFO]    [OmnipathR] Cache item `2e2b496d72e1686af2bd8a26a0b6d2f96d90e687` version 1: status changed from `started` to `ready`.
[2025-01-20 08:02:33] [SUCCESS] [OmnipathR] Downloaded 3868 interactions.
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [organisms=9606,query_type=interactions,datasets=tf_target]
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Organism(s): 9606
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Orthology targets: 
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:33] [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`
[2025-01-20 08:02:33] [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`
[2025-01-20 08:02:33] [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`
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:33] [INFO]    [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:56] [INFO]    [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=tf_target&organisms=9606&fields=sources,references,curation_effort&license=academic`
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:56] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `unknown` to `started`.
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds`.
[2025-01-20 08:02:56] [INFO]    [OmnipathR] Download ready [key=6ed1bdfc7230bcb2925f9cb360e0b77190c82237, version=1]
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 08:02:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 08:02:56] [INFO]    [OmnipathR] Cache item `6ed1bdfc7230bcb2925f9cb360e0b77190c82237` version 1: status changed from `started` to `ready`.
[2025-01-20 08:02:59] [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 
196.033  14.419 180.105

Example timings

gINTomics.Rcheck/gINTomics-Ex.timings

nameusersystemelapsed
create_multiassay0.7590.0120.774
dot_plotly0.6180.0120.632
extract_model_res12.714 0.38013.115
mirna_hsa0.0180.0000.018
mmultiassay_ov0.0880.0110.100
plot_chr_distribution0.5950.0190.616
plot_heatmap0.5900.0080.600
plot_network0.5830.0160.601
plot_ridge10.213 0.24010.470
plot_tf_distribution0.6050.0000.606
plot_venn0.5870.0040.591
plot_volcano 15.492 1.347467.976
run_cnv_integration1.1380.0321.173
run_genomic_enrich0.6280.0200.650
run_genomic_integration1.3430.0881.433
run_met_integration1.1580.0321.192
run_multiomics5.6820.3117.003
run_shiny0.7530.0960.852
run_tf_enrich0.5910.0710.665
run_tf_integration3.5930.3233.928