Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
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 906/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.8.0 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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: 1.8.0 |
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GRaNIE_1.8.0.tar.gz |
StartedAt: 2024-06-13 04:38:07 -0400 (Thu, 13 Jun 2024) |
EndedAt: 2024-06-13 04:50:30 -0400 (Thu, 13 Jun 2024) |
EllapsedTime: 743.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GRaNIE.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GRaNIE.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GRaNIE_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck' * using R version 4.4.0 (2024-04-24 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * 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 '1.8.0' * 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 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-3.19-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 ... WARNING Missing or unexported object: 'AnnotationHub::getAnnotationHub' * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .getAnnotationHub: no visible global function definition for 'is' .performIHW: no visible binding for global variable 'adj_pvalue' .retrieveAnnotationData: no visible global function definition for 'is' Undefined global functions or variables: adj_pvalue is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ checkRd: (-1) addData.Rd:36: Lost braces; missing escapes or markup? 36 | The required format must be {chr}:{start}-{end}", with {chr} denoting the abbreviated chromosome name, and {start} and {end} the begin and end | ^ * 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 8.83 0.42 9.72 addConnections_TF_peak 5.33 3.60 10.70 addSNPData 6.64 1.01 10.81 plotDiagnosticPlots_peakGene 6.11 0.85 7.39 calculateCommunitiesEnrichment 4.43 0.39 5.52 * 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: 2 WARNINGs, 2 NOTEs See 'F:/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log' for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'GRaNIE' ... ** 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 | 5.33 | 3.60 | 10.70 | |
addConnections_peak_gene | 2.42 | 0.17 | 3.06 | |
addData | 0 | 0 | 0 | |
addSNPData | 6.64 | 1.01 | 10.81 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.97 | 0.20 | 3.33 | |
add_featureVariation | 0.00 | 0.02 | 0.01 | |
build_eGRN_graph | 1.59 | 0.11 | 2.17 | |
calculateCommunitiesEnrichment | 4.43 | 0.39 | 5.52 | |
calculateCommunitiesStats | 2.01 | 0.15 | 2.66 | |
calculateGeneralEnrichment | 2.77 | 0.27 | 3.45 | |
calculateTFEnrichment | 2.18 | 0.25 | 2.95 | |
changeOutputDirectory | 3.05 | 0.22 | 3.74 | |
deleteIntermediateData | 2.17 | 0.26 | 3.06 | |
filterConnectionsForPlotting | 2.14 | 0.19 | 2.73 | |
filterData | 2.96 | 0.16 | 3.60 | |
filterGRNAndConnectGenes | 1.90 | 0.25 | 2.74 | |
generateStatsSummary | 8.83 | 0.42 | 9.72 | |
getCounts | 2.41 | 0.27 | 3.22 | |
getGRNConnections | 1.84 | 0.28 | 2.67 | |
getGRNSummary | 3.06 | 0.34 | 3.89 | |
getParameters | 3.08 | 0.27 | 3.97 | |
getTopNodes | 2.10 | 0.17 | 2.70 | |
initializeGRN | 0.03 | 0.00 | 0.03 | |
loadExampleObject | 1.97 | 0.19 | 2.52 | |
nGenes | 2.84 | 0.17 | 3.47 | |
nPeaks | 1.86 | 0.14 | 2.42 | |
nTFs | 1.83 | 0.11 | 2.39 | |
overlapPeaksAndTFBS | 1.84 | 0.14 | 2.47 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.56 | 0.70 | 4.86 | |
plotCommunitiesStats | 3.17 | 0.19 | 3.78 | |
plotCorrelations | 3.22 | 0.34 | 4.06 | |
plotDiagnosticPlots_TFPeaks | 3.86 | 0.39 | 4.69 | |
plotDiagnosticPlots_peakGene | 6.11 | 0.85 | 7.39 | |
plotGeneralEnrichment | 2.38 | 0.15 | 2.90 | |
plotGeneralGraphStats | 3.08 | 0.19 | 3.66 | |
plotPCA_all | 4.08 | 0.33 | 4.81 | |
plotTFEnrichment | 2.47 | 0.23 | 3.09 | |
plot_stats_connectionSummary | 2.87 | 0.72 | 3.42 | |
visualizeGRN | 4.12 | 0.67 | 4.69 | |