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This page was generated on 2025-08-12 12:07 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 903/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.13.0  (landing page)
Christian Arnold
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 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 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for GRaNIE on palomino8

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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings GRaNIE_1.13.0.tar.gz
StartedAt: 2025-08-12 02:56:03 -0400 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 03:05:12 -0400 (Tue, 12 Aug 2025)
EllapsedTime: 548.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRaNIE.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings GRaNIE_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* 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 whether package 'GRaNIE' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
See 'F:/biocbuild/bbs-3.22-bioc/meat/GRaNIE.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 ... 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           9.11   0.30   10.14
addConnections_TF_peak         6.14   1.98   11.44
addSNPData                     7.11   0.48    9.60
plotDiagnosticPlots_peakGene   6.03   0.11    6.56
visualizeGRN                   4.63   0.69    5.09
plotCommunitiesStats           4.65   0.18    5.32
plotPCA_all                    4.25   0.33    5.02
calculateCommunitiesEnrichment 4.00   0.30    5.67
getGRNConnections              3.62   0.11    5.53
* 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 WARNING, 1 NOTE
See
  'F:/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck/00check.log'
for details.


Installation output

GRaNIE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE'
** 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_peak 6.14 1.9811.44
addConnections_peak_gene3.530.104.25
addData000
addSNPData7.110.489.60
addTFBS000
add_TF_gene_correlation2.510.143.33
add_featureVariation000
build_eGRN_graph2.400.112.97
calculateCommunitiesEnrichment4.000.305.67
calculateCommunitiesStats3.640.284.56
calculateGeneralEnrichment2.450.173.27
calculateTFEnrichment2.860.093.89
changeOutputDirectory2.220.133.00
deleteIntermediateData2.250.113.05
filterConnectionsForPlotting2.230.173.46
filterData2.850.113.38
filterGRNAndConnectGenes2.350.123.86
generateStatsSummary 9.11 0.3010.14
getCounts2.540.093.17
getGRNConnections3.620.115.53
getGRNSummary3.340.244.17
getParameters3.520.154.19
getTopNodes2.160.162.74
initializeGRN0.040.000.04
loadExampleObject2.250.162.88
nGenes2.050.132.60
nPeaks2.200.112.83
nTFs2.140.092.68
overlapPeaksAndTFBS2.000.162.58
performAllNetworkAnalyses000
plotCommunitiesEnrichment3.710.254.42
plotCommunitiesStats4.650.185.32
plotCorrelations2.320.102.81
plotDiagnosticPlots_TFPeaks3.950.144.55
plotDiagnosticPlots_peakGene6.030.116.56
plotGeneralEnrichment2.160.152.73
plotGeneralGraphStats3.470.134.00
plotPCA_all4.250.335.02
plotTFEnrichment2.860.123.39
plot_stats_connectionSummary3.010.423.33
visualizeGRN4.630.695.09