Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:04 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 905/2320 | 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 | OK | ERROR | ||||||||||
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: 2025-08-29 23:19:53 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 23:30:09 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 615.8 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 (2025-06-13) * 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 9.439 0.446 10.592 calculateCommunitiesEnrichment 5.552 0.509 6.732 addSNPData 5.237 0.514 8.113 plotGeneralGraphStats 4.953 0.447 6.176 nPeaks 4.525 0.612 5.591 plotDiagnosticPlots_TFPeaks 4.375 0.450 5.235 filterGRNAndConnectGenes 3.881 0.459 5.102 addConnections_TF_peak 3.251 0.345 6.248 * 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 | 3.251 | 0.345 | 6.248 | |
addConnections_peak_gene | 2.706 | 0.266 | 3.406 | |
addData | 0.000 | 0.000 | 0.001 | |
addSNPData | 5.237 | 0.514 | 8.113 | |
addTFBS | 0.000 | 0.000 | 0.001 | |
add_TF_gene_correlation | 2.071 | 0.043 | 2.631 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.924 | 0.041 | 4.137 | |
calculateCommunitiesEnrichment | 5.552 | 0.509 | 6.732 | |
calculateCommunitiesStats | 2.193 | 0.168 | 2.925 | |
calculateGeneralEnrichment | 3.161 | 0.280 | 4.461 | |
calculateTFEnrichment | 3.053 | 0.184 | 3.902 | |
changeOutputDirectory | 2.848 | 0.204 | 3.483 | |
deleteIntermediateData | 2.649 | 0.157 | 3.523 | |
filterConnectionsForPlotting | 3.014 | 0.112 | 3.930 | |
filterData | 3.699 | 0.255 | 4.942 | |
filterGRNAndConnectGenes | 3.881 | 0.459 | 5.102 | |
generateStatsSummary | 9.439 | 0.446 | 10.592 | |
getCounts | 2.080 | 0.116 | 2.663 | |
getGRNConnections | 3.275 | 0.165 | 3.937 | |
getGRNSummary | 3.988 | 0.400 | 4.904 | |
getParameters | 2.879 | 0.126 | 3.431 | |
getTopNodes | 2.343 | 0.416 | 3.265 | |
initializeGRN | 0.016 | 0.004 | 0.020 | |
loadExampleObject | 2.916 | 0.166 | 3.533 | |
nGenes | 2.467 | 0.311 | 3.198 | |
nPeaks | 4.525 | 0.612 | 5.591 | |
nTFs | 1.959 | 0.083 | 2.519 | |
overlapPeaksAndTFBS | 1.768 | 0.106 | 2.300 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 2.964 | 0.228 | 3.611 | |
plotCommunitiesStats | 2.838 | 0.185 | 3.436 | |
plotCorrelations | 2.138 | 0.221 | 2.774 | |
plotDiagnosticPlots_TFPeaks | 4.375 | 0.450 | 5.235 | |
plotDiagnosticPlots_peakGene | 3.685 | 0.316 | 4.419 | |
plotGeneralEnrichment | 2.880 | 0.184 | 4.007 | |
plotGeneralGraphStats | 4.953 | 0.447 | 6.176 | |
plotPCA_all | 3.762 | 0.465 | 4.647 | |
plotTFEnrichment | 2.490 | 0.113 | 3.014 | |
plot_stats_connectionSummary | 2.317 | 0.194 | 2.916 | |
visualizeGRN | 2.914 | 0.216 | 3.641 | |