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This page was generated on 2023-04-12 11:06:10 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for GRaNIE on lconway


To the developers/maintainers of the GRaNIE package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 852/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.2.7  (landing page)
Christian Arnold
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: RELEASE_3_16
git_last_commit: 97c6ab9
git_last_commit_date: 2023-04-06 05:31:33 -0400 (Thu, 06 Apr 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GRaNIE
Version: 1.2.7
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_1.2.7.tar.gz
StartedAt: 2023-04-10 20:31:51 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 20:38:27 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 396.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRaNIE.Rcheck
Warnings: 3

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_1.2.7.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/GRaNIE.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.2.7’
* 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 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 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 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
.getFinalListOfTFs: no visible binding for global variable
  ‘external_gene_name’
.getFinalListOfTFs: no visible binding for global variable
  ‘ensembl_gene_id’
.getFinalListOfTFs: no visible binding for global variable ‘SYMBOL’
.makeObjectCompatible: no visible binding for global variable ‘TF.name’
.performIHW: no visible binding for global variable ‘adj_pvalue’
.printGene: no visible binding for global variable ‘gene.ENSEMBL’
.printTF: no visible binding for global variable ‘TF.ID’
getGRNSummary: no visible binding for global variable ‘pval’
Undefined global functions or variables:
  SYMBOL TF.ID TF.name adj_pvalue ensembl_gene_id external_gene_name
  gene.ENSEMBL 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotCorrelations':
  ‘peak_gene_max_adjP’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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           9.251  0.321   9.791
addConnections_TF_peak         8.461  0.926  13.854
plotCommunitiesStats           6.627  0.356   9.081
calculateCommunitiesEnrichment 6.018  0.456   8.068
plotCommunitiesEnrichment      6.026  0.421   7.280
plotDiagnosticPlots_peakGene   6.148  0.254   6.605
add_TF_gene_correlation        5.866  0.434   8.512
getGRNSummary                  5.814  0.425   8.148
plotPCA_all                    5.455  0.333   5.991
plot_stats_connectionSummary   5.337  0.353   5.917
getTopNodes                    5.295  0.318   7.076
getParameters                  5.026  0.537   7.087
getGRNConnections              5.115  0.430   7.619
plotDiagnosticPlots_TFPeaks    5.218  0.322   5.738
nGenes                         4.956  0.581   6.990
loadExampleObject              5.191  0.295   6.900
build_eGRN_graph               4.928  0.388   6.581
plotTFEnrichment               4.810  0.346   5.393
calculateGeneralEnrichment     4.650  0.345   6.303
calculateCommunitiesStats      4.473  0.359   6.492
nPeaks                         4.383  0.440   5.993
calculateTFEnrichment          4.442  0.288   5.100
overlapPeaksAndTFBS            4.237  0.357   6.186
nTFs                           4.180  0.413   6.014
peaks-methods                  4.158  0.322   5.752
* 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
  ‘/Users/biocbuild/bbs-3.16-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/4.2/Resources/library’
* installing *source* package ‘GRaNIE’ ...
** 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_wrapper0.0000.0010.000
addConnections_TF_peak 8.461 0.92613.854
addConnections_peak_gene3.9820.2634.648
addData0.0000.0000.001
addTFBS000
add_TF_gene_correlation5.8660.4348.512
add_featureVariation0.0000.0000.001
build_eGRN_graph4.9280.3886.581
calculateCommunitiesEnrichment6.0180.4568.068
calculateCommunitiesStats4.4730.3596.492
calculateGeneralEnrichment4.6500.3456.303
calculateTFEnrichment4.4420.2885.100
changeOutputDirectory4.0300.3074.679
deleteIntermediateData3.9000.2334.355
filterData4.2740.2124.698
filterGRNAndConnectGenes3.9650.2334.408
generateStatsSummary9.2510.3219.791
genes-methods3.5280.1913.907
getCounts3.9220.2264.335
getGRNConnections5.1150.4307.619
getGRNSummary5.8140.4258.148
getParameters5.0260.5377.087
getTopNodes5.2950.3187.076
initializeGRN0.0240.0030.042
installSuggestedPackages000
loadExampleObject5.1910.2956.900
nGenes4.9560.5816.990
nPeaks4.3830.4405.993
nTFs4.1800.4136.014
overlapPeaksAndTFBS4.2370.3576.186
peaks-methods4.1580.3225.752
performAllNetworkAnalyses0.0000.0000.001
plotCommunitiesEnrichment6.0260.4217.280
plotCommunitiesStats6.6270.3569.081
plotCorrelations4.2670.2924.930
plotDiagnosticPlots_TFPeaks5.2180.3225.738
plotDiagnosticPlots_peakGene6.1480.2546.605
plotGeneralEnrichment4.2250.2284.648
plotGeneralGraphStats4.3640.2304.786
plotPCA_all5.4550.3335.991
plotTFEnrichment4.8100.3465.393
plot_stats_connectionSummary5.3370.3535.917
visualizeGRN4.0280.2604.509