Back to Mac ARM64 build report for BioC 3.19 |
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This page was generated on 2024-05-07 11:32:35 -0400 (Tue, 07 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 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
| kjohnson3 | macOS 13.6.5 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: 1.8.0 |
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: 2024-05-06 22:01:21 -0400 (Mon, 06 May 2024) |
EndedAt: 2024-05-06 22:04:13 -0400 (Mon, 06 May 2024) |
EllapsedTime: 171.9 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-mac-arm64/meat/GRaNIE.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 13.6.5 * 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 * 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-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 | 1.633 | 0.195 | 2.983 | |
addConnections_peak_gene | 1.128 | 0.015 | 1.590 | |
addData | 0 | 0 | 0 | |
addSNPData | 1.740 | 0.059 | 3.593 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 0.658 | 0.012 | 1.149 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 0.730 | 0.016 | 1.200 | |
calculateCommunitiesEnrichment | 1.106 | 0.029 | 1.571 | |
calculateCommunitiesStats | 1.072 | 0.022 | 1.584 | |
calculateGeneralEnrichment | 0.787 | 0.015 | 1.224 | |
calculateTFEnrichment | 0.797 | 0.020 | 1.296 | |
changeOutputDirectory | 0.603 | 0.014 | 1.063 | |
deleteIntermediateData | 0.666 | 0.022 | 1.086 | |
filterConnectionsForPlotting | 0.659 | 0.014 | 1.113 | |
filterData | 0.852 | 0.018 | 1.295 | |
filterGRNAndConnectGenes | 0.734 | 0.022 | 1.240 | |
generateStatsSummary | 2.626 | 0.071 | 3.152 | |
getCounts | 0.720 | 0.026 | 1.323 | |
getGRNConnections | 1.105 | 0.028 | 1.584 | |
getGRNSummary | 0.840 | 0.023 | 1.302 | |
getParameters | 0.680 | 0.015 | 1.152 | |
getTopNodes | 0.676 | 0.027 | 1.139 | |
initializeGRN | 0.005 | 0.000 | 0.006 | |
loadExampleObject | 0.758 | 0.024 | 1.267 | |
nGenes | 0.670 | 0.015 | 1.121 | |
nPeaks | 1.062 | 0.028 | 1.620 | |
nTFs | 0.583 | 0.013 | 1.072 | |
overlapPeaksAndTFBS | 0.680 | 0.019 | 1.147 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 1.142 | 0.043 | 1.652 | |
plotCommunitiesStats | 1.511 | 0.037 | 2.101 | |
plotCorrelations | 0.746 | 0.024 | 1.289 | |
plotDiagnosticPlots_TFPeaks | 1.032 | 0.038 | 1.506 | |
plotDiagnosticPlots_peakGene | 1.437 | 0.049 | 1.944 | |
plotGeneralEnrichment | 0.772 | 0.015 | 1.217 | |
plotGeneralGraphStats | 0.972 | 0.020 | 1.401 | |
plotPCA_all | 1.510 | 0.062 | 2.023 | |
plotTFEnrichment | 0.840 | 0.023 | 1.272 | |
plot_stats_connectionSummary | 0.788 | 0.026 | 1.261 | |
visualizeGRN | 0.961 | 0.031 | 1.403 | |