Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-27 11:35:54 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4667 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4403 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4426 |
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 894/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.6.1 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 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: 1.6.1 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GRaNIE_1.6.1.tar.gz |
StartedAt: 2024-03-25 22:53:54 -0400 (Mon, 25 Mar 2024) |
EndedAt: 2024-03-25 23:04:08 -0400 (Mon, 25 Mar 2024) |
EllapsedTime: 613.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GRaNIE_1.6.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘1.6.1’ * 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 R 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 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 ... OK * 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 7.549 0.100 8.113 plotPCA_all 6.120 0.464 7.498 plotDiagnosticPlots_peakGene 6.065 0.343 7.421 plotCommunitiesStats 5.864 0.060 8.389 addSNPData 5.614 0.303 16.930 plotDiagnosticPlots_TFPeaks 4.833 0.331 6.139 getGRNSummary 4.701 0.091 5.479 plotCommunitiesEnrichment 4.365 0.140 6.005 addConnections_TF_peak 3.925 0.203 5.367 plotGeneralEnrichment 3.505 0.136 5.348 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘GRaNIE_packageDetails.Rmd’ using ‘UTF-8’... OK ‘GRaNIE_singleCell_eGRNs.Rmd’ using ‘UTF-8’... OK ‘GRaNIE_workflow.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.18-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘GRaNIE’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 | 3.925 | 0.203 | 5.367 | |
addConnections_peak_gene | 3.241 | 0.092 | 3.921 | |
addData | 0 | 0 | 0 | |
addSNPData | 5.614 | 0.303 | 16.930 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.604 | 0.028 | 2.073 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 1.671 | 0.021 | 2.153 | |
calculateCommunitiesEnrichment | 2.437 | 0.027 | 2.909 | |
calculateCommunitiesStats | 2.578 | 0.060 | 3.097 | |
calculateGeneralEnrichment | 1.844 | 0.028 | 2.326 | |
calculateTFEnrichment | 2.030 | 0.060 | 2.562 | |
changeOutputDirectory | 1.646 | 0.012 | 2.115 | |
deleteIntermediateData | 1.692 | 0.044 | 2.173 | |
filterConnectionsForPlotting | 1.670 | 0.024 | 2.146 | |
filterData | 3.142 | 0.172 | 3.766 | |
filterGRNAndConnectGenes | 1.656 | 0.012 | 2.132 | |
generateStatsSummary | 7.549 | 0.100 | 8.113 | |
getCounts | 2.621 | 0.060 | 3.143 | |
getGRNConnections | 2.775 | 0.056 | 3.444 | |
getGRNSummary | 4.701 | 0.091 | 5.479 | |
getParameters | 2.610 | 0.032 | 3.695 | |
getTopNodes | 2.322 | 0.064 | 2.883 | |
initializeGRN | 0.039 | 0.004 | 0.043 | |
loadExampleObject | 2.991 | 0.108 | 4.039 | |
nGenes | 2.400 | 0.028 | 3.434 | |
nPeaks | 3.545 | 0.176 | 4.563 | |
nTFs | 2.741 | 0.036 | 4.612 | |
overlapPeaksAndTFBS | 1.949 | 0.032 | 2.531 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 4.365 | 0.140 | 6.005 | |
plotCommunitiesStats | 5.864 | 0.060 | 8.389 | |
plotCorrelations | 2.609 | 0.228 | 3.617 | |
plotDiagnosticPlots_TFPeaks | 4.833 | 0.331 | 6.139 | |
plotDiagnosticPlots_peakGene | 6.065 | 0.343 | 7.421 | |
plotGeneralEnrichment | 3.505 | 0.136 | 5.348 | |
plotGeneralGraphStats | 4.013 | 0.244 | 4.743 | |
plotPCA_all | 6.120 | 0.464 | 7.498 | |
plotTFEnrichment | 2.383 | 0.044 | 2.832 | |
plot_stats_connectionSummary | 2.331 | 0.120 | 2.865 | |
visualizeGRN | 3.938 | 0.436 | 4.877 | |