Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-05-30 12:36:55 -0400 (Thu, 30 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4404 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4431 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4384 |
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 876/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.9.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | 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 | ERROR | skipped | skipped | |||||||||
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: 1.9.0 |
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_1.9.0.tar.gz |
StartedAt: 2024-05-30 01:52:30 -0400 (Thu, 30 May 2024) |
EndedAt: 2024-05-30 02:08:39 -0400 (Thu, 30 May 2024) |
EllapsedTime: 969.0 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_1.9.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GRaNIE.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 ‘1.9.0’ * 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 12.732 0.261 15.233 addSNPData 9.341 0.412 14.278 addConnections_TF_peak 8.190 1.389 16.604 plotDiagnosticPlots_peakGene 7.833 0.170 9.449 plotCommunitiesStats 6.563 0.157 7.829 plotDiagnosticPlots_TFPeaks 6.519 0.134 7.761 visualizeGRN 6.318 0.173 7.819 plotGeneralGraphStats 6.300 0.106 7.658 plotCommunitiesEnrichment 6.149 0.187 7.593 plotPCA_all 5.846 0.192 6.800 calculateCommunitiesEnrichment 4.974 0.162 6.385 calculateTFEnrichment 4.885 0.105 6.141 plot_stats_connectionSummary 4.390 0.129 5.646 plotTFEnrichment 4.351 0.084 5.523 getGRNSummary 4.232 0.123 5.373 addConnections_peak_gene 4.039 0.094 5.471 getParameters 3.970 0.115 5.274 * 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-3.20-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 | 0.001 | 0.001 | |
addConnections_TF_peak | 8.190 | 1.389 | 16.604 | |
addConnections_peak_gene | 4.039 | 0.094 | 5.471 | |
addData | 0.000 | 0.000 | 0.001 | |
addSNPData | 9.341 | 0.412 | 14.278 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 3.009 | 0.094 | 3.989 | |
add_featureVariation | 0.000 | 0.000 | 0.001 | |
build_eGRN_graph | 3.077 | 0.090 | 4.117 | |
calculateCommunitiesEnrichment | 4.974 | 0.162 | 6.385 | |
calculateCommunitiesStats | 2.981 | 0.134 | 3.982 | |
calculateGeneralEnrichment | 3.678 | 0.082 | 4.583 | |
calculateTFEnrichment | 4.885 | 0.105 | 6.141 | |
changeOutputDirectory | 2.791 | 0.073 | 3.675 | |
deleteIntermediateData | 2.867 | 0.075 | 3.658 | |
filterConnectionsForPlotting | 2.928 | 0.071 | 3.794 | |
filterData | 3.520 | 0.106 | 4.426 | |
filterGRNAndConnectGenes | 2.906 | 0.083 | 3.800 | |
generateStatsSummary | 12.732 | 0.261 | 15.233 | |
getCounts | 3.053 | 0.094 | 4.061 | |
getGRNConnections | 2.890 | 0.090 | 3.674 | |
getGRNSummary | 4.232 | 0.123 | 5.373 | |
getParameters | 3.970 | 0.115 | 5.274 | |
getTopNodes | 2.970 | 0.077 | 3.848 | |
initializeGRN | 0.040 | 0.004 | 0.052 | |
loadExampleObject | 2.958 | 0.080 | 3.904 | |
nGenes | 2.925 | 0.080 | 3.789 | |
nPeaks | 2.856 | 0.073 | 3.793 | |
nTFs | 2.853 | 0.073 | 3.724 | |
overlapPeaksAndTFBS | 2.852 | 0.088 | 3.679 | |
performAllNetworkAnalyses | 0.000 | 0.001 | 0.000 | |
plotCommunitiesEnrichment | 6.149 | 0.187 | 7.593 | |
plotCommunitiesStats | 6.563 | 0.157 | 7.829 | |
plotCorrelations | 3.563 | 0.186 | 4.420 | |
plotDiagnosticPlots_TFPeaks | 6.519 | 0.134 | 7.761 | |
plotDiagnosticPlots_peakGene | 7.833 | 0.170 | 9.449 | |
plotGeneralEnrichment | 3.492 | 0.085 | 4.472 | |
plotGeneralGraphStats | 6.300 | 0.106 | 7.658 | |
plotPCA_all | 5.846 | 0.192 | 6.800 | |
plotTFEnrichment | 4.351 | 0.084 | 5.523 | |
plot_stats_connectionSummary | 4.390 | 0.129 | 5.646 | |
visualizeGRN | 6.318 | 0.173 | 7.819 | |