Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-11 12:03 -0400 (Sat, 11 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
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 913/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.13.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | 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: 1.13.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GRaNIE_1.13.0.tar.gz |
StartedAt: 2025-10-11 00:41:10 -0400 (Sat, 11 Oct 2025) |
EndedAt: 2025-10-11 00:51:48 -0400 (Sat, 11 Oct 2025) |
EllapsedTime: 637.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GRaNIE_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.13.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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 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 8.068 0.061 8.952 plotDiagnosticPlots_peakGene 5.064 0.242 5.746 addSNPData 4.985 0.271 6.399 plotCommunitiesEnrichment 5.077 0.055 6.062 plotPCA_all 4.881 0.103 6.179 filterGRNAndConnectGenes 4.497 0.021 5.205 getCounts 4.032 0.153 5.484 addConnections_TF_peak 3.685 0.218 6.666 calculateGeneralEnrichment 3.769 0.108 5.039 * 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 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘GRaNIE’ ... ** this is package ‘GRaNIE’ version ‘1.13.0’ ** 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 | 3.685 | 0.218 | 6.666 | |
addConnections_peak_gene | 2.647 | 0.099 | 3.148 | |
addData | 0 | 0 | 0 | |
addSNPData | 4.985 | 0.271 | 6.399 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.838 | 0.035 | 2.274 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 1.851 | 0.023 | 2.245 | |
calculateCommunitiesEnrichment | 3.592 | 0.133 | 4.104 | |
calculateCommunitiesStats | 3.138 | 0.043 | 4.701 | |
calculateGeneralEnrichment | 3.769 | 0.108 | 5.039 | |
calculateTFEnrichment | 2.591 | 0.024 | 3.337 | |
changeOutputDirectory | 2.481 | 0.024 | 2.926 | |
deleteIntermediateData | 2.784 | 0.032 | 3.242 | |
filterConnectionsForPlotting | 2.165 | 0.019 | 2.660 | |
filterData | 3.394 | 0.030 | 4.181 | |
filterGRNAndConnectGenes | 4.497 | 0.021 | 5.205 | |
generateStatsSummary | 8.068 | 0.061 | 8.952 | |
getCounts | 4.032 | 0.153 | 5.484 | |
getGRNConnections | 2.491 | 0.032 | 3.272 | |
getGRNSummary | 3.172 | 0.056 | 3.786 | |
getParameters | 3.064 | 0.037 | 4.221 | |
getTopNodes | 4.421 | 0.047 | 4.926 | |
initializeGRN | 0.033 | 0.002 | 0.035 | |
loadExampleObject | 2.727 | 0.016 | 3.612 | |
nGenes | 1.814 | 0.013 | 2.216 | |
nPeaks | 2.604 | 0.018 | 3.019 | |
nTFs | 2.600 | 0.024 | 3.252 | |
overlapPeaksAndTFBS | 1.822 | 0.030 | 2.288 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 5.077 | 0.055 | 6.062 | |
plotCommunitiesStats | 4.067 | 0.018 | 4.464 | |
plotCorrelations | 2.180 | 0.045 | 2.690 | |
plotDiagnosticPlots_TFPeaks | 3.446 | 0.011 | 3.834 | |
plotDiagnosticPlots_peakGene | 5.064 | 0.242 | 5.746 | |
plotGeneralEnrichment | 3.307 | 0.051 | 3.737 | |
plotGeneralGraphStats | 4.272 | 0.027 | 4.704 | |
plotPCA_all | 4.881 | 0.103 | 6.179 | |
plotTFEnrichment | 2.449 | 0.011 | 2.842 | |
plot_stats_connectionSummary | 2.198 | 0.025 | 2.604 | |
visualizeGRN | 2.620 | 0.038 | 3.040 | |