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This page was generated on 2024-02-22 11:35:59 -0500 (Thu, 22 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4691
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4444
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4465
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 894/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.6.1  (landing page)
Christian Arnold
Snapshot Date: 2024-02-21 14:05:05 -0500 (Wed, 21 Feb 2024)
git_url: https://git.bioconductor.org/packages/GRaNIE
git_branch: RELEASE_3_18
git_last_commit: 35f2aa9
git_last_commit_date: 2023-10-26 11:47:33 -0500 (Thu, 26 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 1.6.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GRaNIE_1.6.1.tar.gz
StartedAt: 2024-02-21 22:53:49 -0500 (Wed, 21 Feb 2024)
EndedAt: 2024-02-21 23:04:00 -0500 (Wed, 21 Feb 2024)
EllapsedTime: 611.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GRaNIE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GRaNIE_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GRaNIE/DESCRIPTION’ ... OK
* this is package ‘GRaNIE’ version ‘1.6.1’
* 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 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 loading without being on the library search path ... 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'
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
addSNPData                   6.777  0.651  18.535
plotPCA_all                  5.937  0.828   7.236
plotDiagnosticPlots_TFPeaks  6.182  0.503   8.037
generateStatsSummary         5.641  0.332   6.453
plotDiagnosticPlots_peakGene 5.072  0.452   6.577
plotCommunitiesEnrichment    4.936  0.391   5.815
calculateCommunitiesStats    4.403  0.528   5.743
plot_stats_connectionSummary 4.423  0.284   5.480
plotGeneralGraphStats        4.341  0.300   5.182
plotCommunitiesStats         4.309  0.256   6.224
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GRaNIE_packageDetails.Rmd’ using ‘UTF-8’... OK
  ‘GRaNIE_singleCell_eGRNs.Rmd’ using ‘UTF-8’... OK
  ‘GRaNIE_workflow.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck/00check.log’
for details.



Installation output

GRaNIE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GRaNIE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘GRaNIE’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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_wrapper0.0010.0000.000
addConnections_TF_peak2.9930.3244.739
addConnections_peak_gene2.5330.2603.277
addData000
addSNPData 6.777 0.65118.535
addTFBS000
add_TF_gene_correlation2.0010.0652.642
add_featureVariation000
build_eGRN_graph2.2490.1322.881
calculateCommunitiesEnrichment3.4120.2234.438
calculateCommunitiesStats4.4030.5285.743
calculateGeneralEnrichment2.0680.1082.642
calculateTFEnrichment2.0710.1202.619
changeOutputDirectory1.8020.1122.390
deleteIntermediateData2.6960.3303.476
filterConnectionsForPlotting1.6550.0572.185
filterData2.2110.0962.754
filterGRNAndConnectGenes1.7460.0402.242
generateStatsSummary5.6410.3326.453
getCounts2.8770.2563.628
getGRNConnections1.6200.0282.149
getGRNSummary2.1280.1322.720
getParameters1.6250.0162.119
getTopNodes1.7880.0482.292
initializeGRN0.0180.0000.019
loadExampleObject1.5860.0282.076
nGenes1.6510.0682.168
nPeaks2.7500.1673.378
nTFs2.5440.0603.681
overlapPeaksAndTFBS1.7600.0482.291
performAllNetworkAnalyses000
plotCommunitiesEnrichment4.9360.3915.815
plotCommunitiesStats4.3090.2566.224
plotCorrelations2.5560.1763.356
plotDiagnosticPlots_TFPeaks6.1820.5038.037
plotDiagnosticPlots_peakGene5.0720.4526.577
plotGeneralEnrichment2.4240.1353.388
plotGeneralGraphStats4.3410.3005.182
plotPCA_all5.9370.8287.236
plotTFEnrichment3.3760.2114.039
plot_stats_connectionSummary4.4230.2845.480
visualizeGRN3.5510.1244.950