Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-30 11:35:03 -0400 (Thu, 30 May 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" | 4753 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4518 |
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 | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GRaNIE_1.8.0.tar.gz |
StartedAt: 2024-05-29 23:05:40 -0400 (Wed, 29 May 2024) |
EndedAt: 2024-05-29 23:15:51 -0400 (Wed, 29 May 2024) |
EllapsedTime: 611.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GRaNIE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GRaNIE_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 9.724 0.434 12.491 plotDiagnosticPlots_peakGene 6.356 0.463 7.499 addSNPData 5.969 0.699 11.345 calculateCommunitiesEnrichment 5.327 0.536 6.809 getGRNSummary 5.107 0.543 6.601 deleteIntermediateData 4.209 0.418 6.010 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 | 0.001 | 0.000 | 0.001 | |
addConnections_TF_peak | 2.929 | 0.372 | 4.509 | |
addConnections_peak_gene | 2.586 | 0.308 | 3.319 | |
addData | 0 | 0 | 0 | |
addSNPData | 5.969 | 0.699 | 11.345 | |
addTFBS | 0.000 | 0.000 | 0.001 | |
add_TF_gene_correlation | 2.550 | 0.105 | 3.064 | |
add_featureVariation | 0.001 | 0.000 | 0.000 | |
build_eGRN_graph | 2.559 | 0.142 | 3.137 | |
calculateCommunitiesEnrichment | 5.327 | 0.536 | 6.809 | |
calculateCommunitiesStats | 2.452 | 0.148 | 3.070 | |
calculateGeneralEnrichment | 3.012 | 0.264 | 3.717 | |
calculateTFEnrichment | 3.574 | 0.248 | 4.280 | |
changeOutputDirectory | 2.061 | 0.088 | 2.613 | |
deleteIntermediateData | 4.209 | 0.418 | 6.010 | |
filterConnectionsForPlotting | 2.192 | 0.125 | 2.746 | |
filterData | 3.826 | 0.210 | 4.921 | |
filterGRNAndConnectGenes | 1.893 | 0.080 | 2.379 | |
generateStatsSummary | 9.724 | 0.434 | 12.491 | |
getCounts | 2.563 | 0.181 | 3.226 | |
getGRNConnections | 2.625 | 0.203 | 3.501 | |
getGRNSummary | 5.107 | 0.543 | 6.601 | |
getParameters | 2.129 | 0.088 | 2.689 | |
getTopNodes | 1.897 | 0.099 | 2.563 | |
initializeGRN | 0.024 | 0.008 | 0.032 | |
loadExampleObject | 2.826 | 0.224 | 4.366 | |
nGenes | 1.779 | 0.199 | 2.392 | |
nPeaks | 2.672 | 0.300 | 3.423 | |
nTFs | 1.646 | 0.076 | 2.110 | |
overlapPeaksAndTFBS | 1.664 | 0.060 | 2.188 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 2.875 | 0.200 | 3.506 | |
plotCommunitiesStats | 3.702 | 0.308 | 4.438 | |
plotCorrelations | 1.874 | 0.056 | 2.459 | |
plotDiagnosticPlots_TFPeaks | 2.814 | 0.160 | 3.361 | |
plotDiagnosticPlots_peakGene | 6.356 | 0.463 | 7.499 | |
plotGeneralEnrichment | 1.868 | 0.064 | 2.363 | |
plotGeneralGraphStats | 2.493 | 0.076 | 3.167 | |
plotPCA_all | 3.550 | 0.236 | 4.208 | |
plotTFEnrichment | 2.293 | 0.060 | 2.744 | |
plot_stats_connectionSummary | 2.351 | 0.055 | 2.815 | |
visualizeGRN | 2.436 | 0.044 | 2.916 | |