Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-03-27 11:36:48 -0400 (Wed, 27 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4698 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4436 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4461 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4376 |
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 892/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.7.2 (landing page) Christian Arnold
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.7.2 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GRaNIE_1.7.2.tar.gz |
StartedAt: 2024-03-26 23:03:11 -0400 (Tue, 26 Mar 2024) |
EndedAt: 2024-03-26 23:13:43 -0400 (Tue, 26 Mar 2024) |
EllapsedTime: 631.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GRaNIE_1.7.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck’ * using R Under development (unstable) (2024-03-18 r86148) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.7.2’ * 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 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 ... 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 addSNPData 9.471 0.939 14.929 generateStatsSummary 6.806 0.532 7.808 plotDiagnosticPlots_peakGene 6.290 0.840 7.592 calculateCommunitiesEnrichment 5.722 0.551 7.966 plotPCA_all 5.556 0.524 7.512 addConnections_TF_peak 5.348 0.661 7.322 plotGeneralGraphStats 5.454 0.395 6.311 addConnections_peak_gene 4.715 0.435 6.395 filterData 4.676 0.469 6.515 plotCommunitiesEnrichment 4.523 0.524 5.490 plotCommunitiesStats 4.505 0.351 6.542 add_TF_gene_correlation 3.411 0.218 5.030 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘GRaNIE’ ... ** 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 | 0.000 | 0.000 | 0.001 | |
addConnections_TF_peak | 5.348 | 0.661 | 7.322 | |
addConnections_peak_gene | 4.715 | 0.435 | 6.395 | |
addData | 0.001 | 0.000 | 0.000 | |
addSNPData | 9.471 | 0.939 | 14.929 | |
addTFBS | 0.000 | 0.001 | 0.000 | |
add_TF_gene_correlation | 3.411 | 0.218 | 5.030 | |
add_featureVariation | 0.000 | 0.001 | 0.000 | |
build_eGRN_graph | 2.393 | 0.113 | 3.172 | |
calculateCommunitiesEnrichment | 5.722 | 0.551 | 7.966 | |
calculateCommunitiesStats | 3.050 | 0.108 | 3.867 | |
calculateGeneralEnrichment | 3.246 | 0.215 | 4.034 | |
calculateTFEnrichment | 2.942 | 0.240 | 3.874 | |
changeOutputDirectory | 2.191 | 0.075 | 2.757 | |
deleteIntermediateData | 3.269 | 0.187 | 4.155 | |
filterConnectionsForPlotting | 1.991 | 0.184 | 2.680 | |
filterData | 4.676 | 0.469 | 6.515 | |
filterGRNAndConnectGenes | 1.854 | 0.108 | 2.411 | |
generateStatsSummary | 6.806 | 0.532 | 7.808 | |
getCounts | 1.766 | 0.064 | 2.278 | |
getGRNConnections | 2.714 | 0.208 | 3.395 | |
getGRNSummary | 2.169 | 0.076 | 2.687 | |
getParameters | 3.082 | 0.345 | 4.066 | |
getTopNodes | 3.068 | 0.147 | 3.959 | |
initializeGRN | 0.017 | 0.003 | 0.020 | |
loadExampleObject | 1.872 | 0.108 | 2.432 | |
nGenes | 1.861 | 0.065 | 2.405 | |
nPeaks | 1.969 | 0.104 | 2.522 | |
nTFs | 1.799 | 0.076 | 2.372 | |
overlapPeaksAndTFBS | 1.847 | 0.088 | 2.398 | |
performAllNetworkAnalyses | 0.001 | 0.000 | 0.000 | |
plotCommunitiesEnrichment | 4.523 | 0.524 | 5.490 | |
plotCommunitiesStats | 4.505 | 0.351 | 6.542 | |
plotCorrelations | 3.684 | 0.384 | 4.536 | |
plotDiagnosticPlots_TFPeaks | 3.122 | 0.228 | 3.812 | |
plotDiagnosticPlots_peakGene | 6.290 | 0.840 | 7.592 | |
plotGeneralEnrichment | 2.859 | 0.232 | 3.828 | |
plotGeneralGraphStats | 5.454 | 0.395 | 6.311 | |
plotPCA_all | 5.556 | 0.524 | 7.512 | |
plotTFEnrichment | 2.985 | 0.120 | 3.589 | |
plot_stats_connectionSummary | 2.246 | 0.136 | 2.848 | |
visualizeGRN | 2.590 | 0.152 | 3.229 | |