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This page was generated on 2024-03-04 11:37:25 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 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 lconway


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: /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_1.6.1.tar.gz
StartedAt: 2024-03-03 21:00:15 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 21:10:38 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 623.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GRaNIE.Rcheck
Warnings: 0

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_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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           12.480  0.600  13.442
addConnections_TF_peak         11.276  1.560  14.529
addSNPData                      7.017  0.649  10.238
plotCommunitiesEnrichment       6.770  0.430   7.440
plotDiagnosticPlots_peakGene    6.676  0.340   7.257
plotGeneralGraphStats           6.457  0.389   7.077
visualizeGRN                    6.426  0.386   7.038
plotCommunitiesStats            6.308  0.338   6.856
plotTFEnrichment                6.187  0.369   6.752
plot_stats_connectionSummary    6.106  0.309   6.599
add_TF_gene_correlation         5.770  0.411   6.451
getGRNSummary                   5.713  0.312   6.220
plotCorrelations                5.658  0.366   6.230
filterData                      5.594  0.353   6.210
plotDiagnosticPlots_TFPeaks     5.582  0.343   6.144
calculateGeneralEnrichment      5.338  0.372   5.987
nPeaks                          5.365  0.344   5.926
calculateTFEnrichment           5.375  0.323   5.916
getTopNodes                     5.364  0.324   5.917
filterGRNAndConnectGenes        5.171  0.349   5.791
overlapPeaksAndTFBS             5.153  0.321   5.705
getGRNConnections               5.199  0.270   5.660
nGenes                          5.139  0.323   5.695
loadExampleObject               5.132  0.294   5.661
addConnections_peak_gene        5.056  0.356   5.652
calculateCommunitiesEnrichment  5.019  0.388   5.711
nTFs                            5.092  0.315   5.632
deleteIntermediateData          5.089  0.309   5.608
filterConnectionsForPlotting    5.083  0.313   5.612
calculateCommunitiesStats       5.015  0.334   5.610
plotPCA_all                     5.002  0.325   5.518
getParameters                   5.020  0.296   5.515
changeOutputDirectory           4.990  0.314   5.502
plotGeneralEnrichment           4.705  0.276   5.183
build_eGRN_graph                4.584  0.366   5.212
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/Resources/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_wrapper000
addConnections_TF_peak11.276 1.56014.529
addConnections_peak_gene5.0560.3565.652
addData0.0000.0000.001
addSNPData 7.017 0.64910.238
addTFBS000
add_TF_gene_correlation5.7700.4116.451
add_featureVariation0.0000.0010.000
build_eGRN_graph4.5840.3665.212
calculateCommunitiesEnrichment5.0190.3885.711
calculateCommunitiesStats5.0150.3345.610
calculateGeneralEnrichment5.3380.3725.987
calculateTFEnrichment5.3750.3235.916
changeOutputDirectory4.9900.3145.502
deleteIntermediateData5.0890.3095.608
filterConnectionsForPlotting5.0830.3135.612
filterData5.5940.3536.210
filterGRNAndConnectGenes5.1710.3495.791
generateStatsSummary12.480 0.60013.442
getCounts4.2260.3534.797
getGRNConnections5.1990.2705.660
getGRNSummary5.7130.3126.220
getParameters5.0200.2965.515
getTopNodes5.3640.3245.917
initializeGRN0.0210.0020.024
loadExampleObject5.1320.2945.661
nGenes5.1390.3235.695
nPeaks5.3650.3445.926
nTFs5.0920.3155.632
overlapPeaksAndTFBS5.1530.3215.705
performAllNetworkAnalyses000
plotCommunitiesEnrichment6.770.437.44
plotCommunitiesStats6.3080.3386.856
plotCorrelations5.6580.3666.230
plotDiagnosticPlots_TFPeaks5.5820.3436.144
plotDiagnosticPlots_peakGene6.6760.3407.257
plotGeneralEnrichment4.7050.2765.183
plotGeneralGraphStats6.4570.3897.077
plotPCA_all5.0020.3255.518
plotTFEnrichment6.1870.3696.752
plot_stats_connectionSummary6.1060.3096.599
visualizeGRN6.4260.3867.038