Back to Mac ARM64 build report for BioC 3.17 |
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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
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 873/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.4.1 (landing page) Christian Arnold
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | ||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * 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)
GRaNIE.Rcheck/GRaNIE-Ex.timings
name | user | system | elapsed | |
AR_classification_wrapper | 0 | 0 | 0 | |
addConnections_TF_peak | 9.647 | 1.589 | 17.446 | |
addConnections_peak_gene | 4.872 | 0.223 | 7.697 | |
addData | 0.000 | 0.000 | 0.001 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 6.518 | 0.251 | 9.847 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 4.714 | 0.204 | 7.528 | |
calculateCommunitiesEnrichment | 5.746 | 0.250 | 9.125 | |
calculateCommunitiesStats | 4.197 | 0.204 | 6.868 | |
calculateGeneralEnrichment | 5.334 | 0.205 | 8.427 | |
calculateTFEnrichment | 5.480 | 0.212 | 8.641 | |
changeOutputDirectory | 5.029 | 0.212 | 8.205 | |
deleteIntermediateData | 5.026 | 0.221 | 8.206 | |
filterData | 5.523 | 0.223 | 9.121 | |
filterGRNAndConnectGenes | 5.164 | 0.213 | 9.731 | |
generateStatsSummary | 11.799 | 0.299 | 20.230 | |
genes-methods | 5.081 | 0.189 | 8.215 | |
getCounts | 5.077 | 0.213 | 8.216 | |
getGRNConnections | 5.131 | 0.207 | 8.273 | |
getGRNSummary | 5.699 | 0.215 | 9.222 | |
getParameters | 5.174 | 0.210 | 9.537 | |
getTopNodes | 4.888 | 0.220 | 9.244 | |
initializeGRN | 0.022 | 0.003 | 0.048 | |
installSuggestedPackages | 0 | 0 | 0 | |
loadExampleObject | 4.220 | 0.214 | 6.045 | |
nGenes | 4.977 | 0.201 | 7.543 | |
nPeaks | 5.023 | 0.202 | 7.989 | |
nTFs | 5.008 | 0.209 | 8.692 | |
overlapPeaksAndTFBS | 5.039 | 0.217 | 9.507 | |
peaks-methods | 4.934 | 0.207 | 9.323 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 6.808 | 0.303 | 11.446 | |
plotCommunitiesStats | 6.422 | 0.275 | 10.184 | |
plotCorrelations | 4.659 | 0.236 | 6.754 | |
plotDiagnosticPlots_TFPeaks | 6.754 | 0.298 | 10.015 | |
plotDiagnosticPlots_peakGene | 8.835 | 0.290 | 14.177 | |
plotGeneralEnrichment | 5.470 | 0.211 | 8.759 | |
plotGeneralGraphStats | 6.428 | 0.213 | 10.301 | |
plotPCA_all | 6.136 | 0.236 | 9.979 | |
plotTFEnrichment | 6.478 | 0.224 | 10.419 | |
plot_stats_connectionSummary | 6.028 | 0.247 | 9.889 | |
visualizeGRN | 6.291 | 0.228 | 10.125 | |