Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:41 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
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 906/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.8.0 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: GRaNIE |
Version: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2024-07-08 05:37:34 -0400 (Mon, 08 Jul 2024) |
EndedAt: 2024-07-08 05:53:18 -0400 (Mon, 08 Jul 2024) |
EllapsedTime: 944.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GRaNIE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.8.0’ * 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 code 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 whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING Missing or unexported object: 'AnnotationHub::getAnnotationHub' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .getAnnotationHub: no visible global function definition for 'is' .performIHW: no visible binding for global variable 'adj_pvalue' .retrieveAnnotationData: no visible global function definition for 'is' Undefined global functions or variables: adj_pvalue is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ * 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 13.602 0.237 16.496 addSNPData 9.327 0.393 31.850 plotDiagnosticPlots_peakGene 9.363 0.196 11.718 addConnections_TF_peak 7.289 1.407 10.842 plotDiagnosticPlots_TFPeaks 6.630 0.160 8.142 visualizeGRN 6.525 0.173 7.903 plotCommunitiesEnrichment 6.153 0.239 7.831 calculateCommunitiesEnrichment 5.948 0.176 7.440 plotPCA_all 5.942 0.179 7.564 getGRNSummary 5.688 0.131 7.110 plotCommunitiesStats 5.576 0.098 6.934 plotGeneralGraphStats 5.228 0.113 6.805 plotCorrelations 4.932 0.151 6.159 plotTFEnrichment 4.539 0.104 5.606 plot_stats_connectionSummary 4.482 0.117 6.474 changeOutputDirectory 4.266 0.109 5.913 nGenes 4.184 0.102 5.371 addConnections_peak_gene 4.175 0.097 5.353 calculateTFEnrichment 4.100 0.109 5.910 calculateGeneralEnrichment 3.822 0.145 5.498 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/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/4.4-x86_64/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 | 0.000 | 0.000 | 0.001 | |
addConnections_TF_peak | 7.289 | 1.407 | 10.842 | |
addConnections_peak_gene | 4.175 | 0.097 | 5.353 | |
addData | 0.000 | 0.000 | 0.001 | |
addSNPData | 9.327 | 0.393 | 31.850 | |
addTFBS | 0.001 | 0.000 | 0.001 | |
add_TF_gene_correlation | 2.911 | 0.089 | 3.816 | |
add_featureVariation | 0.001 | 0.000 | 0.000 | |
build_eGRN_graph | 2.968 | 0.098 | 3.920 | |
calculateCommunitiesEnrichment | 5.948 | 0.176 | 7.440 | |
calculateCommunitiesStats | 3.021 | 0.136 | 4.121 | |
calculateGeneralEnrichment | 3.822 | 0.145 | 5.498 | |
calculateTFEnrichment | 4.100 | 0.109 | 5.910 | |
changeOutputDirectory | 4.266 | 0.109 | 5.913 | |
deleteIntermediateData | 2.923 | 0.077 | 3.936 | |
filterConnectionsForPlotting | 3.092 | 0.089 | 3.949 | |
filterData | 3.704 | 0.103 | 4.734 | |
filterGRNAndConnectGenes | 3.018 | 0.083 | 3.882 | |
generateStatsSummary | 13.602 | 0.237 | 16.496 | |
getCounts | 3.192 | 0.092 | 4.183 | |
getGRNConnections | 3.022 | 0.085 | 3.961 | |
getGRNSummary | 5.688 | 0.131 | 7.110 | |
getParameters | 2.910 | 0.072 | 3.796 | |
getTopNodes | 3.132 | 0.078 | 4.023 | |
initializeGRN | 0.044 | 0.005 | 0.054 | |
loadExampleObject | 3.038 | 0.101 | 4.105 | |
nGenes | 4.184 | 0.102 | 5.371 | |
nPeaks | 2.936 | 0.074 | 3.863 | |
nTFs | 3.018 | 0.088 | 3.868 | |
overlapPeaksAndTFBS | 2.944 | 0.079 | 3.936 | |
performAllNetworkAnalyses | 0.000 | 0.000 | 0.001 | |
plotCommunitiesEnrichment | 6.153 | 0.239 | 7.831 | |
plotCommunitiesStats | 5.576 | 0.098 | 6.934 | |
plotCorrelations | 4.932 | 0.151 | 6.159 | |
plotDiagnosticPlots_TFPeaks | 6.630 | 0.160 | 8.142 | |
plotDiagnosticPlots_peakGene | 9.363 | 0.196 | 11.718 | |
plotGeneralEnrichment | 3.546 | 0.095 | 4.760 | |
plotGeneralGraphStats | 5.228 | 0.113 | 6.805 | |
plotPCA_all | 5.942 | 0.179 | 7.564 | |
plotTFEnrichment | 4.539 | 0.104 | 5.606 | |
plot_stats_connectionSummary | 4.482 | 0.117 | 6.474 | |
visualizeGRN | 6.525 | 0.173 | 7.903 | |