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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4541
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 905/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.13.0  (landing page)
Christian Arnold
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: devel
git_last_commit: a6d5f09
git_last_commit_date: 2025-04-15 12:51:24 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for GRaNIE on nebbiolo2

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: 1.13.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GRaNIE_1.13.0.tar.gz
StartedAt: 2025-08-29 23:19:53 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 23:30:09 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 615.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GRaNIE.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GRaNIE_1.13.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.13.0’
* 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 loading without being on the library search path ... 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           9.439  0.446  10.592
calculateCommunitiesEnrichment 5.552  0.509   6.732
addSNPData                     5.237  0.514   8.113
plotGeneralGraphStats          4.953  0.447   6.176
nPeaks                         4.525  0.612   5.591
plotDiagnosticPlots_TFPeaks    4.375  0.450   5.235
filterGRNAndConnectGenes       3.881  0.459   5.102
addConnections_TF_peak         3.251  0.345   6.248
* 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-3.22-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.


Installation output

GRaNIE.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GRaNIE’ ...
** this is package ‘GRaNIE’ version ‘1.13.0’
** 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_wrapper000
addConnections_TF_peak3.2510.3456.248
addConnections_peak_gene2.7060.2663.406
addData0.0000.0000.001
addSNPData5.2370.5148.113
addTFBS0.0000.0000.001
add_TF_gene_correlation2.0710.0432.631
add_featureVariation000
build_eGRN_graph2.9240.0414.137
calculateCommunitiesEnrichment5.5520.5096.732
calculateCommunitiesStats2.1930.1682.925
calculateGeneralEnrichment3.1610.2804.461
calculateTFEnrichment3.0530.1843.902
changeOutputDirectory2.8480.2043.483
deleteIntermediateData2.6490.1573.523
filterConnectionsForPlotting3.0140.1123.930
filterData3.6990.2554.942
filterGRNAndConnectGenes3.8810.4595.102
generateStatsSummary 9.439 0.44610.592
getCounts2.0800.1162.663
getGRNConnections3.2750.1653.937
getGRNSummary3.9880.4004.904
getParameters2.8790.1263.431
getTopNodes2.3430.4163.265
initializeGRN0.0160.0040.020
loadExampleObject2.9160.1663.533
nGenes2.4670.3113.198
nPeaks4.5250.6125.591
nTFs1.9590.0832.519
overlapPeaksAndTFBS1.7680.1062.300
performAllNetworkAnalyses000
plotCommunitiesEnrichment2.9640.2283.611
plotCommunitiesStats2.8380.1853.436
plotCorrelations2.1380.2212.774
plotDiagnosticPlots_TFPeaks4.3750.4505.235
plotDiagnosticPlots_peakGene3.6850.3164.419
plotGeneralEnrichment2.8800.1844.007
plotGeneralGraphStats4.9530.4476.176
plotPCA_all3.7620.4654.647
plotTFEnrichment2.4900.1133.014
plot_stats_connectionSummary2.3170.1942.916
visualizeGRN2.9140.2163.641