Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 897/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.10.0 (landing page) Christian Arnold
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: GRaNIE |
Version: 1.10.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GRaNIE_1.10.0.tar.gz |
StartedAt: 2024-11-20 08:32:20 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 08:41:44 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 564.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings GRaNIE_1.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GRaNIE.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.10.0’ * 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 ... 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 7.319 0.063 8.019 addSNPData 6.262 0.309 10.288 plotDiagnosticPlots_peakGene 5.702 0.202 7.179 plotCommunitiesStats 4.361 0.179 5.275 plotPCA_all 4.365 0.036 5.048 addConnections_TF_peak 3.504 0.151 6.052 plotGeneralEnrichment 2.124 0.035 7.037 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 | 0 | 0 | |
addConnections_TF_peak | 3.504 | 0.151 | 6.052 | |
addConnections_peak_gene | 3.058 | 0.071 | 4.340 | |
addData | 0 | 0 | 0 | |
addSNPData | 6.262 | 0.309 | 10.288 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.785 | 0.044 | 2.924 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 1.789 | 0.019 | 2.482 | |
calculateCommunitiesEnrichment | 3.914 | 0.088 | 4.688 | |
calculateCommunitiesStats | 1.723 | 0.020 | 2.460 | |
calculateGeneralEnrichment | 2.131 | 0.056 | 3.446 | |
calculateTFEnrichment | 2.322 | 0.020 | 3.041 | |
changeOutputDirectory | 1.701 | 0.016 | 2.414 | |
deleteIntermediateData | 1.756 | 0.024 | 2.481 | |
filterConnectionsForPlotting | 1.804 | 0.020 | 2.530 | |
filterData | 3.587 | 0.092 | 4.874 | |
filterGRNAndConnectGenes | 1.740 | 0.024 | 2.431 | |
generateStatsSummary | 7.319 | 0.063 | 8.019 | |
getCounts | 2.003 | 0.044 | 2.735 | |
getGRNConnections | 2.939 | 0.088 | 4.242 | |
getGRNSummary | 2.462 | 0.087 | 4.272 | |
getParameters | 1.746 | 0.050 | 3.176 | |
getTopNodes | 1.871 | 0.052 | 2.589 | |
initializeGRN | 0.025 | 0.000 | 0.026 | |
loadExampleObject | 1.858 | 0.078 | 3.154 | |
nGenes | 2.993 | 0.070 | 3.784 | |
nPeaks | 1.850 | 0.055 | 2.627 | |
nTFs | 1.748 | 0.046 | 2.999 | |
overlapPeaksAndTFBS | 1.734 | 0.042 | 2.450 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.566 | 0.120 | 4.456 | |
plotCommunitiesStats | 4.361 | 0.179 | 5.275 | |
plotCorrelations | 2.197 | 0.085 | 3.026 | |
plotDiagnosticPlots_TFPeaks | 3.835 | 0.074 | 4.660 | |
plotDiagnosticPlots_peakGene | 5.702 | 0.202 | 7.179 | |
plotGeneralEnrichment | 2.124 | 0.035 | 7.037 | |
plotGeneralGraphStats | 3.029 | 0.068 | 3.784 | |
plotPCA_all | 4.365 | 0.036 | 5.048 | |
plotTFEnrichment | 2.683 | 0.016 | 3.399 | |
plot_stats_connectionSummary | 3.733 | 0.016 | 4.416 | |
visualizeGRN | 3.266 | 0.024 | 4.483 | |