Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-12 12:07 -0400 (Tue, 12 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 903/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.13.0 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings GRaNIE_1.13.0.tar.gz |
StartedAt: 2025-08-12 02:56:03 -0400 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 03:05:12 -0400 (Tue, 12 Aug 2025) |
EllapsedTime: 548.9 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GRaNIE.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings GRaNIE_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-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 '1.13.0' * 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 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 'F:/biocbuild/bbs-3.22-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 9.11 0.30 10.14 addConnections_TF_peak 6.14 1.98 11.44 addSNPData 7.11 0.48 9.60 plotDiagnosticPlots_peakGene 6.03 0.11 6.56 visualizeGRN 4.63 0.69 5.09 plotCommunitiesStats 4.65 0.18 5.32 plotPCA_all 4.25 0.33 5.02 calculateCommunitiesEnrichment 4.00 0.30 5.67 getGRNConnections 3.62 0.11 5.53 * 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 'F:/biocbuild/bbs-3.22-bioc/meat/GRaNIE.Rcheck/00check.log' for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 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 | 6.14 | 1.98 | 11.44 | |
addConnections_peak_gene | 3.53 | 0.10 | 4.25 | |
addData | 0 | 0 | 0 | |
addSNPData | 7.11 | 0.48 | 9.60 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 2.51 | 0.14 | 3.33 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 2.40 | 0.11 | 2.97 | |
calculateCommunitiesEnrichment | 4.00 | 0.30 | 5.67 | |
calculateCommunitiesStats | 3.64 | 0.28 | 4.56 | |
calculateGeneralEnrichment | 2.45 | 0.17 | 3.27 | |
calculateTFEnrichment | 2.86 | 0.09 | 3.89 | |
changeOutputDirectory | 2.22 | 0.13 | 3.00 | |
deleteIntermediateData | 2.25 | 0.11 | 3.05 | |
filterConnectionsForPlotting | 2.23 | 0.17 | 3.46 | |
filterData | 2.85 | 0.11 | 3.38 | |
filterGRNAndConnectGenes | 2.35 | 0.12 | 3.86 | |
generateStatsSummary | 9.11 | 0.30 | 10.14 | |
getCounts | 2.54 | 0.09 | 3.17 | |
getGRNConnections | 3.62 | 0.11 | 5.53 | |
getGRNSummary | 3.34 | 0.24 | 4.17 | |
getParameters | 3.52 | 0.15 | 4.19 | |
getTopNodes | 2.16 | 0.16 | 2.74 | |
initializeGRN | 0.04 | 0.00 | 0.04 | |
loadExampleObject | 2.25 | 0.16 | 2.88 | |
nGenes | 2.05 | 0.13 | 2.60 | |
nPeaks | 2.20 | 0.11 | 2.83 | |
nTFs | 2.14 | 0.09 | 2.68 | |
overlapPeaksAndTFBS | 2.00 | 0.16 | 2.58 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.71 | 0.25 | 4.42 | |
plotCommunitiesStats | 4.65 | 0.18 | 5.32 | |
plotCorrelations | 2.32 | 0.10 | 2.81 | |
plotDiagnosticPlots_TFPeaks | 3.95 | 0.14 | 4.55 | |
plotDiagnosticPlots_peakGene | 6.03 | 0.11 | 6.56 | |
plotGeneralEnrichment | 2.16 | 0.15 | 2.73 | |
plotGeneralGraphStats | 3.47 | 0.13 | 4.00 | |
plotPCA_all | 4.25 | 0.33 | 5.02 | |
plotTFEnrichment | 2.86 | 0.12 | 3.39 | |
plot_stats_connectionSummary | 3.01 | 0.42 | 3.33 | |
visualizeGRN | 4.63 | 0.69 | 5.09 | |