Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-08-14 11:42 -0400 (Thu, 14 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
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 913/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.12.0 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / 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. |
Package: GRaNIE |
Version: 1.12.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GRaNIE_1.12.0.tar.gz |
StartedAt: 2025-08-12 03:13:10 -0400 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 03:22:42 -0400 (Tue, 12 Aug 2025) |
EllapsedTime: 572.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GRaNIE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings GRaNIE_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'GRaNIE/DESCRIPTION' ... OK * this is package 'GRaNIE' version '1.12.0' * 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 whether package 'GRaNIE' can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE' See 'E:/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck/00install.out' for details. * 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 8.97 0.27 10.08 addConnections_TF_peak 5.55 1.63 8.98 addSNPData 6.36 0.51 9.46 plotDiagnosticPlots_peakGene 6.36 0.11 7.00 plotCommunitiesStats 4.97 0.25 5.77 plotPCA_all 4.53 0.25 5.34 plotCommunitiesEnrichment 4.49 0.28 6.15 visualizeGRN 4.36 0.30 5.10 plotDiagnosticPlots_TFPeaks 4.25 0.11 5.89 calculateCommunitiesEnrichment 3.82 0.36 5.62 * 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 WARNING, 1 NOTE See 'E:/biocbuild/bbs-3.21-bioc/meat/GRaNIE.Rcheck/00check.log' for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'GRaNIE' ... ** this is package 'GRaNIE' version '1.12.0' ** using staged installation ** R ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE' ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE' ** testing if installed package can be loaded from final location Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'GRaNIE' ** 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 | 5.55 | 1.63 | 8.98 | |
addConnections_peak_gene | 3.11 | 0.14 | 3.70 | |
addData | 0 | 0 | 0 | |
addSNPData | 6.36 | 0.51 | 9.46 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 2.14 | 0.11 | 2.70 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.07 | 0.06 | 2.56 | |
calculateCommunitiesEnrichment | 3.82 | 0.36 | 5.62 | |
calculateCommunitiesStats | 2.32 | 0.19 | 3.00 | |
calculateGeneralEnrichment | 2.86 | 0.16 | 3.96 | |
calculateTFEnrichment | 3.99 | 0.09 | 4.58 | |
changeOutputDirectory | 2.06 | 0.10 | 2.73 | |
deleteIntermediateData | 2.34 | 0.09 | 3.25 | |
filterConnectionsForPlotting | 2.27 | 0.12 | 3.88 | |
filterData | 2.74 | 0.13 | 3.48 | |
filterGRNAndConnectGenes | 2.23 | 0.09 | 3.11 | |
generateStatsSummary | 8.97 | 0.27 | 10.08 | |
getCounts | 2.48 | 0.15 | 3.52 | |
getGRNConnections | 3.57 | 0.19 | 4.31 | |
getGRNSummary | 3.39 | 0.39 | 4.72 | |
getParameters | 3.48 | 0.11 | 4.14 | |
getTopNodes | 2.36 | 0.16 | 3.33 | |
initializeGRN | 0.03 | 0.00 | 0.11 | |
loadExampleObject | 2.44 | 0.12 | 3.05 | |
nGenes | 2.31 | 0.16 | 4.00 | |
nPeaks | 2.19 | 0.12 | 2.84 | |
nTFs | 2.16 | 0.08 | 2.67 | |
overlapPeaksAndTFBS | 2.18 | 0.21 | 3.12 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 4.49 | 0.28 | 6.15 | |
plotCommunitiesStats | 4.97 | 0.25 | 5.77 | |
plotCorrelations | 2.50 | 0.15 | 3.28 | |
plotDiagnosticPlots_TFPeaks | 4.25 | 0.11 | 5.89 | |
plotDiagnosticPlots_peakGene | 6.36 | 0.11 | 7.00 | |
plotGeneralEnrichment | 2.37 | 0.21 | 3.20 | |
plotGeneralGraphStats | 3.52 | 0.10 | 4.14 | |
plotPCA_all | 4.53 | 0.25 | 5.34 | |
plotTFEnrichment | 2.95 | 0.08 | 3.61 | |
plot_stats_connectionSummary | 2.96 | 0.64 | 3.47 | |
visualizeGRN | 4.36 | 0.30 | 5.10 | |