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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 913/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.12.0  (landing page)
Christian Arnold
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: RELEASE_3_21
git_last_commit: 21e7fc4
git_last_commit_date: 2025-04-15 12:51:24 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GRaNIE on merida1

To the developers/maintainers of the GRaNIE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRaNIE.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: GRaNIE
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.12.0.tar.gz
StartedAt: 2025-10-14 04:45:56 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 05:01:20 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 923.4 seconds
RetCode: 0
Status:   OK  
CheckDir: GRaNIE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GRaNIE_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 37 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 ‘GRaNIE’ 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 whether startup messages can be suppressed ... 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
.performIHW: no visible binding for global variable 'adj_pvalue'
Undefined global functions or variables:
  adj_pvalue
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
generateStatsSummary           12.978  0.204  13.890
addConnections_TF_peak          8.522  1.756  13.711
addSNPData                      8.002  0.747  11.273
plotDiagnosticPlots_peakGene    8.294  0.158   9.689
plotCommunitiesStats            7.770  0.113   8.828
plotCommunitiesEnrichment       7.130  0.197   8.505
plotDiagnosticPlots_TFPeaks     7.116  0.150   8.375
plotGeneralGraphStats           6.076  0.125   6.949
plotPCA_all                     5.926  0.171   6.859
calculateCommunitiesEnrichment  5.709  0.234   6.726
visualizeGRN                    5.732  0.129   6.620
plotTFEnrichment                4.628  0.091   5.365
plot_stats_connectionSummary    4.258  0.108   5.022
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.


Installation output

GRaNIE.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GRaNIE’ ...
** this is package ‘GRaNIE’ version ‘1.12.0’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GRaNIE)

Tests output


Example timings

GRaNIE.Rcheck/GRaNIE-Ex.timings

nameusersystemelapsed
AR_classification_wrapper0.0000.0010.001
addConnections_TF_peak 8.522 1.75613.711
addConnections_peak_gene3.9260.0994.602
addData0.0010.0010.001
addSNPData 8.002 0.74711.273
addTFBS0.0000.0010.000
add_TF_gene_correlation3.8820.0924.640
add_featureVariation0.0010.0000.001
build_eGRN_graph2.7050.0783.298
calculateCommunitiesEnrichment5.7090.2346.726
calculateCommunitiesStats2.8110.0693.424
calculateGeneralEnrichment3.2280.1123.799
calculateTFEnrichment3.5060.1044.182
changeOutputDirectory2.7480.0803.441
deleteIntermediateData2.8500.0813.409
filterConnectionsForPlotting2.8020.0703.333
filterData3.6220.0924.167
filterGRNAndConnectGenes2.9500.0703.489
generateStatsSummary12.978 0.20413.890
getCounts2.9220.0723.583
getGRNConnections2.8350.0823.449
getGRNSummary4.1780.1064.959
getParameters3.9140.0904.601
getTopNodes3.1780.0673.791
initializeGRN0.0380.0030.042
loadExampleObject2.7450.0683.375
nGenes2.9160.0753.548
nPeaks2.9560.0763.629
nTFs2.7870.0643.409
overlapPeaksAndTFBS2.8800.0723.529
performAllNetworkAnalyses0.0000.0010.000
plotCommunitiesEnrichment7.1300.1978.505
plotCommunitiesStats7.7700.1138.828
plotCorrelations3.8040.1024.703
plotDiagnosticPlots_TFPeaks7.1160.1508.375
plotDiagnosticPlots_peakGene8.2940.1589.689
plotGeneralEnrichment3.7050.0734.454
plotGeneralGraphStats6.0760.1256.949
plotPCA_all5.9260.1716.859
plotTFEnrichment4.6280.0915.365
plot_stats_connectionSummary4.2580.1085.022
visualizeGRN5.7320.1296.620