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This page was generated on 2023-09-23 11:35:49 -0400 (Sat, 23 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 873/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.4.1  (landing page)
Christian Arnold
Snapshot Date: 2023-09-22 14:00:14 -0400 (Fri, 22 Sep 2023)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: RELEASE_3_17
git_last_commit: d3d7da1
git_last_commit_date: 2023-06-19 10:19:10 -0400 (Mon, 19 Jun 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for GRaNIE on palomino3


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: 1.4.1
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GRaNIE_1.4.1.tar.gz
StartedAt: 2023-09-23 02:56:29 -0400 (Sat, 23 Sep 2023)
EndedAt: 2023-09-23 03:04:57 -0400 (Sat, 23 Sep 2023)
EllapsedTime: 508.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRaNIE.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GRaNIE_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* 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 '1.4.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... 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 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-3.17-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 R 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 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'
getGRNSummary: no visible binding for global variable 'pval'
Undefined global functions or variables:
  adj_pvalue pval
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated name 'nGenes':
  'genes-methods.Rd' 'nGenes.Rd'
Rd files with duplicated name 'nPeaks':
  'nPeaks.Rd' 'peaks-methods.Rd'
Rd files with duplicated alias 'genes':
  'genes-methods.Rd' 'nGenes.Rd'
Rd files with duplicated alias 'nGenes':
  'genes-methods.Rd' 'nGenes.Rd'
Rd files with duplicated alias 'nPeaks':
  'nPeaks.Rd' 'peaks-methods.Rd'
Rd files with duplicated alias 'peaks':
  'nPeaks.Rd' 'peaks-methods.Rd'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'installSuggestedPackages' but not in code:
  'installSuggestedPackages'

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
generateStatsSummary         7.55   0.30    8.31
addConnections_TF_peak       5.71   1.61    9.13
plotCommunitiesStats         5.08   0.24    5.78
plotDiagnosticPlots_peakGene 5.07   0.25    5.98
plotGeneralGraphStats        5.00   0.13    5.64
visualizeGRN                 4.57   0.12    5.30
plotCommunitiesEnrichment    4.11   0.20    5.06
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc/meat/GRaNIE.Rcheck/00check.log'
for details.



Installation output

GRaNIE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'GRaNIE' ...
** 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_peak5.711.619.13
addConnections_peak_gene3.300.084.11
addData000
addTFBS000
add_TF_gene_correlation1.630.092.20
add_featureVariation000
build_eGRN_graph2.110.132.69
calculateCommunitiesEnrichment4.170.114.75
calculateCommunitiesStats2.090.113.32
calculateGeneralEnrichment2.390.132.99
calculateTFEnrichment3.030.073.66
changeOutputDirectory1.710.162.34
deleteIntermediateData1.530.082.20
filterData3.120.063.63
filterGRNAndConnectGenes1.860.082.39
generateStatsSummary7.550.308.31
genes-methods1.610.072.16
getCounts2.550.053.06
getGRNConnections1.650.112.22
getGRNSummary2.160.142.79
getParameters1.540.112.11
getTopNodes1.720.032.19
initializeGRN0.030.000.03
installSuggestedPackages000
loadExampleObject2.500.053.02
nGenes1.540.052.03
nPeaks1.530.092.08
nTFs1.470.082.04
overlapPeaksAndTFBS2.000.092.60
peaks-methods2.060.082.85
performAllNetworkAnalyses000
plotCommunitiesEnrichment4.110.205.06
plotCommunitiesStats5.080.245.78
plotCorrelations2.610.043.91
plotDiagnosticPlots_TFPeaks3.930.194.78
plotDiagnosticPlots_peakGene5.070.255.98
plotGeneralEnrichment2.450.093.24
plotGeneralGraphStats5.000.135.64
plotPCA_all3.170.274.39
plotTFEnrichment3.410.124.26
plot_stats_connectionSummary2.970.164.24
visualizeGRN4.570.125.30