Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:12 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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
| kjohnson1 | macOS 13.6.6 Ventura / 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: 1.9.0 |
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: 2024-05-19 15:15:43 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 15:24:21 -0400 (Sun, 19 May 2024) |
EllapsedTime: 517.7 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-mac-arm64/meat/GRaNIE.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * 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 8.172 0.231 8.910 addConnections_TF_peak 7.086 0.693 8.302 addSNPData 7.300 0.287 8.932 visualizeGRN 5.303 0.116 5.824 plotPCA_all 5.226 0.156 5.795 plotCommunitiesStats 5.240 0.089 5.709 plotGeneralGraphStats 5.117 0.068 5.574 plotDiagnosticPlots_peakGene 4.783 0.131 5.377 * 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-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/4.4-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 | 7.086 | 0.693 | 8.302 | |
addConnections_peak_gene | 4.121 | 0.067 | 4.606 | |
addData | 0 | 0 | 0 | |
addSNPData | 7.300 | 0.287 | 8.932 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 2.984 | 0.064 | 3.495 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.908 | 0.062 | 3.342 | |
calculateCommunitiesEnrichment | 4.075 | 0.100 | 4.540 | |
calculateCommunitiesStats | 2.669 | 0.070 | 3.135 | |
calculateGeneralEnrichment | 3.089 | 0.055 | 3.494 | |
calculateTFEnrichment | 4.091 | 0.065 | 4.578 | |
changeOutputDirectory | 2.465 | 0.050 | 2.888 | |
deleteIntermediateData | 2.597 | 0.062 | 3.055 | |
filterConnectionsForPlotting | 2.575 | 0.058 | 3.034 | |
filterData | 3.142 | 0.088 | 3.638 | |
filterGRNAndConnectGenes | 2.612 | 0.068 | 3.103 | |
generateStatsSummary | 8.172 | 0.231 | 8.910 | |
getCounts | 2.685 | 0.072 | 3.144 | |
getGRNConnections | 2.621 | 0.067 | 3.009 | |
getGRNSummary | 3.209 | 0.074 | 3.673 | |
getParameters | 3.857 | 0.066 | 4.364 | |
getTopNodes | 2.607 | 0.058 | 3.033 | |
initializeGRN | 0.018 | 0.003 | 0.020 | |
loadExampleObject | 2.687 | 0.059 | 3.160 | |
nGenes | 2.688 | 0.059 | 3.184 | |
nPeaks | 2.628 | 0.061 | 3.020 | |
nTFs | 2.547 | 0.049 | 3.022 | |
overlapPeaksAndTFBS | 2.552 | 0.064 | 3.063 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 4.151 | 0.121 | 4.663 | |
plotCommunitiesStats | 5.240 | 0.089 | 5.709 | |
plotCorrelations | 2.953 | 0.102 | 3.481 | |
plotDiagnosticPlots_TFPeaks | 4.086 | 0.087 | 4.569 | |
plotDiagnosticPlots_peakGene | 4.783 | 0.131 | 5.377 | |
plotGeneralEnrichment | 2.912 | 0.061 | 3.396 | |
plotGeneralGraphStats | 5.117 | 0.068 | 5.574 | |
plotPCA_all | 5.226 | 0.156 | 5.795 | |
plotTFEnrichment | 3.293 | 0.065 | 3.760 | |
plot_stats_connectionSummary | 3.312 | 0.089 | 3.834 | |
visualizeGRN | 5.303 | 0.116 | 5.824 | |