Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-12 11:44 -0500 (Thu, 12 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4752 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4464 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4415 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4370 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4279 |
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 891/2273 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.11.0 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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: 1.11.0 |
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_1.11.0.tar.gz |
StartedAt: 2024-12-11 21:54:32 -0500 (Wed, 11 Dec 2024) |
EndedAt: 2024-12-11 22:03:57 -0500 (Wed, 11 Dec 2024) |
EllapsedTime: 564.7 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_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck’ * using R Under development (unstable) (2024-11-20 r87352) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.11.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' INFO Imports includes 37 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ... 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 4.468 0.135 5.070 addConnections_TF_peak 3.208 0.595 11.392 addSNPData 3.055 0.210 13.611 * 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 NOTE See ‘/Users/biocbuild/bbs-3.21-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/4.5-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 | 3.208 | 0.595 | 11.392 | |
addConnections_peak_gene | 1.811 | 0.031 | 2.394 | |
addData | 0.001 | 0.000 | 0.000 | |
addSNPData | 3.055 | 0.210 | 13.611 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.980 | 0.054 | 2.520 | |
add_featureVariation | 0.001 | 0.000 | 0.000 | |
build_eGRN_graph | 1.149 | 0.029 | 1.699 | |
calculateCommunitiesEnrichment | 1.849 | 0.107 | 2.420 | |
calculateCommunitiesStats | 1.912 | 0.040 | 2.470 | |
calculateGeneralEnrichment | 1.416 | 0.032 | 2.038 | |
calculateTFEnrichment | 1.436 | 0.041 | 2.144 | |
changeOutputDirectory | 1.166 | 0.030 | 1.731 | |
deleteIntermediateData | 1.204 | 0.031 | 1.750 | |
filterConnectionsForPlotting | 1.293 | 0.037 | 1.853 | |
filterData | 2.300 | 0.041 | 2.846 | |
filterGRNAndConnectGenes | 1.235 | 0.030 | 1.741 | |
generateStatsSummary | 4.468 | 0.135 | 5.070 | |
getCounts | 2.118 | 0.076 | 2.674 | |
getGRNConnections | 1.263 | 0.028 | 1.773 | |
getGRNSummary | 2.320 | 0.076 | 2.852 | |
getParameters | 1.253 | 0.037 | 1.759 | |
getTopNodes | 1.241 | 0.030 | 1.738 | |
initializeGRN | 0.012 | 0.001 | 0.014 | |
loadExampleObject | 1.267 | 0.044 | 1.740 | |
nGenes | 1.194 | 0.036 | 1.652 | |
nPeaks | 1.161 | 0.033 | 1.633 | |
nTFs | 1.206 | 0.032 | 1.682 | |
overlapPeaksAndTFBS | 1.934 | 0.047 | 2.417 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 2.259 | 0.071 | 2.924 | |
plotCommunitiesStats | 2.204 | 0.042 | 2.692 | |
plotCorrelations | 2.254 | 0.061 | 2.762 | |
plotDiagnosticPlots_TFPeaks | 2.279 | 0.080 | 2.831 | |
plotDiagnosticPlots_peakGene | 4.194 | 0.115 | 4.772 | |
plotGeneralEnrichment | 1.384 | 0.041 | 1.959 | |
plotGeneralGraphStats | 1.963 | 0.044 | 2.589 | |
plotPCA_all | 2.616 | 0.084 | 3.274 | |
plotTFEnrichment | 1.784 | 0.069 | 2.365 | |
plot_stats_connectionSummary | 1.695 | 0.055 | 2.211 | |
visualizeGRN | 1.904 | 0.068 | 2.413 | |