Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-27 11:39:31 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4436 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4461 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4376 |
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 892/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.7.2 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.7.2 |
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_1.7.2.tar.gz |
StartedAt: 2024-03-26 21:01:24 -0400 (Tue, 26 Mar 2024) |
EndedAt: 2024-03-26 21:11:07 -0400 (Tue, 26 Mar 2024) |
EllapsedTime: 582.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.7.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * 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 ‘1.7.2’ * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .performIHW: no visible binding for global variable 'adj_pvalue' Undefined global functions or variables: adj_pvalue * 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 8.152 0.199 8.985 plotDiagnosticPlots_peakGene 6.295 0.168 6.939 addSNPData 6.032 0.314 51.098 addConnections_TF_peak 5.078 1.134 7.712 getTopNodes 2.107 0.066 5.246 * 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: 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 | 5.078 | 1.134 | 7.712 | |
addConnections_peak_gene | 3.443 | 0.100 | 4.470 | |
addData | 0 | 0 | 0 | |
addSNPData | 6.032 | 0.314 | 51.098 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.946 | 0.070 | 2.613 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.062 | 0.080 | 2.681 | |
calculateCommunitiesEnrichment | 4.036 | 0.131 | 4.770 | |
calculateCommunitiesStats | 2.020 | 0.078 | 2.582 | |
calculateGeneralEnrichment | 2.435 | 0.087 | 3.047 | |
calculateTFEnrichment | 2.612 | 0.075 | 3.168 | |
changeOutputDirectory | 3.112 | 0.090 | 3.688 | |
deleteIntermediateData | 2.063 | 0.074 | 2.639 | |
filterConnectionsForPlotting | 1.990 | 0.060 | 2.568 | |
filterData | 2.537 | 0.095 | 3.066 | |
filterGRNAndConnectGenes | 2.074 | 0.070 | 2.650 | |
generateStatsSummary | 8.152 | 0.199 | 8.985 | |
getCounts | 2.174 | 0.082 | 2.738 | |
getGRNConnections | 2.031 | 0.092 | 2.572 | |
getGRNSummary | 3.842 | 0.110 | 4.461 | |
getParameters | 1.927 | 0.058 | 2.484 | |
getTopNodes | 2.107 | 0.066 | 5.246 | |
initializeGRN | 0.023 | 0.003 | 0.026 | |
loadExampleObject | 2.145 | 0.086 | 2.750 | |
nGenes | 3.127 | 0.082 | 3.759 | |
nPeaks | 1.937 | 0.065 | 2.610 | |
nTFs | 2.104 | 0.071 | 2.682 | |
overlapPeaksAndTFBS | 1.921 | 0.052 | 2.409 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.945 | 0.199 | 4.613 | |
plotCommunitiesStats | 3.423 | 0.099 | 4.043 | |
plotCorrelations | 3.833 | 0.133 | 4.440 | |
plotDiagnosticPlots_TFPeaks | 4.104 | 0.137 | 4.870 | |
plotDiagnosticPlots_peakGene | 6.295 | 0.168 | 6.939 | |
plotGeneralEnrichment | 2.643 | 0.075 | 3.255 | |
plotGeneralGraphStats | 3.798 | 0.070 | 4.360 | |
plotPCA_all | 4.318 | 0.188 | 4.981 | |
plotTFEnrichment | 3.042 | 0.082 | 3.618 | |
plot_stats_connectionSummary | 2.842 | 0.105 | 3.453 | |
visualizeGRN | 4.347 | 0.137 | 4.996 | |