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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 873/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRaNIE 1.4.1  (landing page)
Christian Arnold
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for GRaNIE on kjohnson2


To the developers/maintainers of the GRaNIE package:
- 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: /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_1.4.1.tar.gz
StartedAt: 2023-10-17 23:23:15 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 23:37:08 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 833.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GRaNIE.Rcheck
Warnings: 2

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_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GRaNIE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* 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 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'
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           11.799  0.299  20.230
addConnections_TF_peak          9.647  1.589  17.446
plotDiagnosticPlots_peakGene    8.835  0.290  14.177
plotCommunitiesEnrichment       6.808  0.303  11.446
plotDiagnosticPlots_TFPeaks     6.754  0.298  10.015
add_TF_gene_correlation         6.518  0.251   9.847
plotTFEnrichment                6.478  0.224  10.419
plotCommunitiesStats            6.422  0.275  10.184
plotGeneralGraphStats           6.428  0.213  10.301
visualizeGRN                    6.291  0.228  10.125
plotPCA_all                     6.136  0.236   9.979
plot_stats_connectionSummary    6.028  0.247   9.889
calculateCommunitiesEnrichment  5.746  0.250   9.125
getGRNSummary                   5.699  0.215   9.222
filterData                      5.523  0.223   9.121
calculateTFEnrichment           5.480  0.212   8.641
plotGeneralEnrichment           5.470  0.211   8.759
calculateGeneralEnrichment      5.334  0.205   8.427
getParameters                   5.174  0.210   9.537
filterGRNAndConnectGenes        5.164  0.213   9.731
getGRNConnections               5.131  0.207   8.273
getCounts                       5.077  0.213   8.216
genes-methods                   5.081  0.189   8.215
overlapPeaksAndTFBS             5.039  0.217   9.507
deleteIntermediateData          5.026  0.221   8.206
changeOutputDirectory           5.029  0.212   8.205
nPeaks                          5.023  0.202   7.989
nTFs                            5.008  0.209   8.692
nGenes                          4.977  0.201   7.543
peaks-methods                   4.934  0.207   9.323
getTopNodes                     4.888  0.220   9.244
addConnections_peak_gene        4.872  0.223   7.697
build_eGRN_graph                4.714  0.204   7.528
plotCorrelations                4.659  0.236   6.754
loadExampleObject               4.220  0.214   6.045
calculateCommunitiesStats       4.197  0.204   6.868
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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_wrapper000
addConnections_TF_peak 9.647 1.58917.446
addConnections_peak_gene4.8720.2237.697
addData0.0000.0000.001
addTFBS000
add_TF_gene_correlation6.5180.2519.847
add_featureVariation000
build_eGRN_graph4.7140.2047.528
calculateCommunitiesEnrichment5.7460.2509.125
calculateCommunitiesStats4.1970.2046.868
calculateGeneralEnrichment5.3340.2058.427
calculateTFEnrichment5.4800.2128.641
changeOutputDirectory5.0290.2128.205
deleteIntermediateData5.0260.2218.206
filterData5.5230.2239.121
filterGRNAndConnectGenes5.1640.2139.731
generateStatsSummary11.799 0.29920.230
genes-methods5.0810.1898.215
getCounts5.0770.2138.216
getGRNConnections5.1310.2078.273
getGRNSummary5.6990.2159.222
getParameters5.1740.2109.537
getTopNodes4.8880.2209.244
initializeGRN0.0220.0030.048
installSuggestedPackages000
loadExampleObject4.2200.2146.045
nGenes4.9770.2017.543
nPeaks5.0230.2027.989
nTFs5.0080.2098.692
overlapPeaksAndTFBS5.0390.2179.507
peaks-methods4.9340.2079.323
performAllNetworkAnalyses000
plotCommunitiesEnrichment 6.808 0.30311.446
plotCommunitiesStats 6.422 0.27510.184
plotCorrelations4.6590.2366.754
plotDiagnosticPlots_TFPeaks 6.754 0.29810.015
plotDiagnosticPlots_peakGene 8.835 0.29014.177
plotGeneralEnrichment5.4700.2118.759
plotGeneralGraphStats 6.428 0.21310.301
plotPCA_all6.1360.2369.979
plotTFEnrichment 6.478 0.22410.419
plot_stats_connectionSummary6.0280.2479.889
visualizeGRN 6.291 0.22810.125