Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-27 12:24 -0400 (Fri, 27 Sep 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4451 |
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4417 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4456 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4489 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4436 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4435 |
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 889/2262 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GRaNIE 1.9.7 (landing page) Christian Arnold
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 22.04.3 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 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.9.7 |
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_1.9.7.tar.gz |
StartedAt: 2024-09-27 02:14:41 -0400 (Fri, 27 Sep 2024) |
EndedAt: 2024-09-27 02:22:33 -0400 (Fri, 27 Sep 2024) |
EllapsedTime: 471.6 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_1.9.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/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 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘GRaNIE/DESCRIPTION’ ... OK * this is package ‘GRaNIE’ version ‘1.9.7’ * 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 addSNPData 3.635 0.186 22.505 * 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 ‘/media/volume/teran2_disk/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 ‘/media/volume/teran2_disk/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 | 2.309 | 0.123 | 3.308 | |
addConnections_peak_gene | 2.059 | 0.035 | 2.616 | |
addData | 0 | 0 | 0 | |
addSNPData | 3.635 | 0.186 | 22.505 | |
addTFBS | 0 | 0 | 0 | |
add_TF_gene_correlation | 1.127 | 0.030 | 1.590 | |
add_featureVariation | 0.000 | 0.000 | 0.001 | |
build_eGRN_graph | 1.160 | 0.028 | 1.656 | |
calculateCommunitiesEnrichment | 1.716 | 0.018 | 2.186 | |
calculateCommunitiesStats | 2.238 | 0.013 | 2.691 | |
calculateGeneralEnrichment | 1.215 | 0.020 | 1.712 | |
calculateTFEnrichment | 1.298 | 0.023 | 1.795 | |
changeOutputDirectory | 1.148 | 0.013 | 1.602 | |
deleteIntermediateData | 1.114 | 0.016 | 1.577 | |
filterConnectionsForPlotting | 1.029 | 0.012 | 1.514 | |
filterData | 1.346 | 0.013 | 1.829 | |
filterGRNAndConnectGenes | 2.086 | 0.010 | 2.530 | |
generateStatsSummary | 3.919 | 0.014 | 4.406 | |
getCounts | 1.204 | 0.035 | 2.370 | |
getGRNConnections | 1.026 | 0.013 | 1.643 | |
getGRNSummary | 1.513 | 0.043 | 2.627 | |
getParameters | 2.380 | 0.022 | 3.901 | |
getTopNodes | 1.179 | 0.020 | 1.791 | |
initializeGRN | 0.012 | 0.002 | 0.029 | |
loadExampleObject | 1.424 | 0.023 | 3.071 | |
nGenes | 1.131 | 0.019 | 2.004 | |
nPeaks | 1.186 | 0.016 | 2.645 | |
nTFs | 1.201 | 0.016 | 1.766 | |
overlapPeaksAndTFBS | 1.150 | 0.015 | 1.681 | |
performAllNetworkAnalyses | 0 | 0 | 0 | |
plotCommunitiesEnrichment | 3.100 | 0.018 | 3.677 | |
plotCommunitiesStats | 1.873 | 0.083 | 2.471 | |
plotCorrelations | 2.719 | 0.041 | 3.252 | |
plotDiagnosticPlots_TFPeaks | 2.437 | 0.059 | 3.150 | |
plotDiagnosticPlots_peakGene | 3.624 | 0.105 | 4.224 | |
plotGeneralEnrichment | 1.360 | 0.153 | 1.948 | |
plotGeneralGraphStats | 1.644 | 0.048 | 2.173 | |
plotPCA_all | 1.742 | 0.049 | 2.311 | |
plotTFEnrichment | 1.710 | 0.010 | 2.179 | |
plot_stats_connectionSummary | 1.439 | 0.016 | 1.907 | |
visualizeGRN | 2.983 | 0.033 | 3.518 | |