Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:27 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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 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 | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 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: 2024-06-05 20:47:57 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 20:56:21 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 504.2 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 4.4.0 (2024-04-24) * 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 12.7.1 * 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 7.058 0.183 7.689 addConnections_TF_peak 6.086 1.138 8.556 addSNPData 5.876 0.265 10.722 plotDiagnosticPlots_peakGene 4.492 0.136 5.132 * 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 | 0 | 0 | |
addConnections_TF_peak | 6.086 | 1.138 | 8.556 | |
addConnections_peak_gene | 2.943 | 0.060 | 3.451 | |
addData | 0 | 0 | 0 | |
addSNPData | 5.876 | 0.265 | 10.722 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.906 | 0.054 | 2.427 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.064 | 0.066 | 2.592 | |
calculateCommunitiesEnrichment | 3.004 | 0.103 | 3.579 | |
calculateCommunitiesStats | 1.898 | 0.071 | 2.383 | |
calculateGeneralEnrichment | 2.365 | 0.055 | 2.886 | |
calculateTFEnrichment | 3.106 | 0.075 | 3.628 | |
changeOutputDirectory | 1.704 | 0.045 | 2.204 | |
deleteIntermediateData | 1.734 | 0.051 | 2.247 | |
filterConnectionsForPlotting | 1.901 | 0.049 | 2.373 | |
filterData | 2.221 | 0.099 | 2.780 | |
filterGRNAndConnectGenes | 1.895 | 0.053 | 2.424 | |
generateStatsSummary | 7.058 | 0.183 | 7.689 | |
getCounts | 1.795 | 0.067 | 2.296 | |
getGRNConnections | 1.877 | 0.081 | 2.416 | |
getGRNSummary | 2.666 | 0.079 | 3.236 | |
getParameters | 2.938 | 0.088 | 3.477 | |
getTopNodes | 1.808 | 0.045 | 2.329 | |
initializeGRN | 0.019 | 0.002 | 0.022 | |
loadExampleObject | 1.953 | 0.056 | 2.445 | |
nGenes | 1.898 | 0.062 | 2.381 | |
nPeaks | 1.684 | 0.044 | 2.153 | |
nTFs | 1.840 | 0.050 | 2.308 | |
overlapPeaksAndTFBS | 1.840 | 0.064 | 2.375 | |
performAllNetworkAnalyses | 0.001 | 0.000 | 0.000 | |
plotCommunitiesEnrichment | 3.303 | 0.141 | 3.885 | |
plotCommunitiesStats | 4.032 | 0.096 | 4.588 | |
plotCorrelations | 2.176 | 0.093 | 2.708 | |
plotDiagnosticPlots_TFPeaks | 3.378 | 0.096 | 3.899 | |
plotDiagnosticPlots_peakGene | 4.492 | 0.136 | 5.132 | |
plotGeneralEnrichment | 2.139 | 0.059 | 2.675 | |
plotGeneralGraphStats | 3.862 | 0.057 | 4.392 | |
plotPCA_all | 4.037 | 0.179 | 4.690 | |
plotTFEnrichment | 2.462 | 0.058 | 2.986 | |
plot_stats_connectionSummary | 2.663 | 0.089 | 3.207 | |
visualizeGRN | 4.353 | 0.146 | 4.938 | |