Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-23 11:38 -0400 (Tue, 23 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4280 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
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 884/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.9.3 (landing page) Christian Arnold
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | 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: 1.9.3 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GRaNIE_1.9.3.tar.gz |
StartedAt: 2024-07-22 23:58:16 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-23 00:08:47 -0400 (Tue, 23 Jul 2024) |
EllapsedTime: 631.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GRaNIE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GRaNIE.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GRaNIE_1.9.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GRaNIE.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘1.9.3’ * 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 ... 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 9.896 0.128 12.547 plotCommunitiesEnrichment 6.088 0.107 7.454 plotDiagnosticPlots_peakGene 5.389 0.072 5.941 getGRNSummary 5.175 0.216 6.882 addSNPData 5.075 0.240 13.617 filterData 4.636 0.068 6.365 plotCommunitiesStats 4.193 0.084 5.938 nGenes 4.059 0.152 5.839 plot_stats_connectionSummary 3.567 0.048 5.523 * 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-3.20-bioc/meat/GRaNIE.Rcheck/00check.log’ for details.
GRaNIE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GRaNIE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 | 0 | 0 | |
addConnections_TF_peak | 3.098 | 0.172 | 4.481 | |
addConnections_peak_gene | 2.674 | 0.044 | 3.089 | |
addData | 0 | 0 | 0 | |
addSNPData | 5.075 | 0.240 | 13.617 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.625 | 0.028 | 2.114 | |
add_featureVariation | 0 | 0 | 0 | |
build_eGRN_graph | 1.689 | 0.028 | 2.179 | |
calculateCommunitiesEnrichment | 3.856 | 0.104 | 4.424 | |
calculateCommunitiesStats | 1.698 | 0.020 | 2.148 | |
calculateGeneralEnrichment | 1.985 | 0.048 | 2.469 | |
calculateTFEnrichment | 2.100 | 0.068 | 2.605 | |
changeOutputDirectory | 1.646 | 0.016 | 2.099 | |
deleteIntermediateData | 1.673 | 0.012 | 2.146 | |
filterConnectionsForPlotting | 2.778 | 0.036 | 4.353 | |
filterData | 4.636 | 0.068 | 6.365 | |
filterGRNAndConnectGenes | 2.423 | 0.012 | 3.154 | |
generateStatsSummary | 9.896 | 0.128 | 12.547 | |
getCounts | 2.577 | 0.052 | 3.913 | |
getGRNConnections | 2.402 | 0.040 | 3.253 | |
getGRNSummary | 5.175 | 0.216 | 6.882 | |
getParameters | 2.890 | 0.044 | 3.585 | |
getTopNodes | 2.206 | 0.024 | 2.862 | |
initializeGRN | 0.015 | 0.004 | 0.019 | |
loadExampleObject | 3.014 | 0.056 | 4.308 | |
nGenes | 4.059 | 0.152 | 5.839 | |
nPeaks | 1.998 | 0.024 | 2.618 | |
nTFs | 2.820 | 0.056 | 4.807 | |
overlapPeaksAndTFBS | 1.999 | 0.020 | 2.500 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 6.088 | 0.107 | 7.454 | |
plotCommunitiesStats | 4.193 | 0.084 | 5.938 | |
plotCorrelations | 1.894 | 0.040 | 2.434 | |
plotDiagnosticPlots_TFPeaks | 2.980 | 0.048 | 3.453 | |
plotDiagnosticPlots_peakGene | 5.389 | 0.072 | 5.941 | |
plotGeneralEnrichment | 1.920 | 0.032 | 2.395 | |
plotGeneralGraphStats | 2.546 | 0.032 | 3.043 | |
plotPCA_all | 2.514 | 0.044 | 2.982 | |
plotTFEnrichment | 3.402 | 0.092 | 3.938 | |
plot_stats_connectionSummary | 3.567 | 0.048 | 5.523 | |
visualizeGRN | 2.608 | 0.032 | 3.149 | |