Britta Velten
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MOFA |
| Branch: RELEASE_3_9 |
| Last Commit: d66907c |
| Last Changed Date: 2019-05-02 11:54:15 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:04:38 -0400 (Wed, 16 Oct 2019).
| Package 1033/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MOFA 1.0.0 Britta Velten
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: MOFA |
| Version: 1.0.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MOFA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MOFA_1.0.0.tar.gz |
| StartedAt: 2019-10-16 04:46:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:59:38 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 769.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MOFA.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MOFA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MOFA_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MOFA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MOFA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOFA’ version ‘1.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MOFA’ 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 R 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 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
plotEnrichmentDetailed: no visible binding for global variable
‘pathway’
plotEnrichmentDetailed: no visible binding for global variable
‘feature.statistic’
Undefined global functions or variables:
feature.statistic pathway
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘PCGSE’
* 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 or elapsed time > 5s
user system elapsed
selectModel 57.008 0.313 61.564
compareFactors 48.135 2.448 53.342
compareModels 49.780 0.186 53.001
regressCovariates 32.098 0.911 33.363
predict 23.676 4.592 28.981
plotEnrichmentDetailed 11.876 3.612 15.488
plotFactorScatters 11.654 1.800 13.509
plotEnrichment 9.660 2.408 12.070
plotEnrichmentHeatmap 8.457 2.733 11.199
plotEnrichmentBars 8.458 2.601 11.060
runEnrichmentAnalysis 8.482 2.418 10.950
plotWeightsHeatmap 7.718 2.189 9.945
plotFactorBeeswarm 7.564 2.087 9.660
plotWeights 7.051 2.019 9.088
plotVarianceExplained 6.723 2.069 8.803
clusterSamples 7.196 1.333 8.532
plotTopWeights 6.104 2.151 8.280
trainCurveFactors 6.522 1.653 8.205
calculateVarianceExplained 6.839 1.321 8.188
plotFactorHist 5.701 2.064 7.802
plotFactorScatter 5.893 1.778 7.673
plotFactorCor 5.158 1.856 7.069
trainCurveELBO 5.368 1.425 6.794
plotDataOverview 5.132 1.231 6.362
getTrainData 5.019 1.122 6.140
impute 4.427 1.566 5.992
plotDataScatter 4.231 0.777 5.008
DataOptions 4.461 0.520 5.035
qualityControl 3.879 1.100 5.187
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/MOFA.Rcheck/00check.log’
for details.
MOFA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MOFA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘MOFA’ ... ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (MOFA)
MOFA.Rcheck/MOFA-Ex.timings
| name | user | system | elapsed | |
| DataOptions | 4.461 | 0.520 | 5.035 | |
| Dimensions | 2.758 | 0.508 | 3.267 | |
| Expectations | 2.736 | 0.455 | 3.192 | |
| FeatureIntercepts | 2.706 | 0.482 | 3.188 | |
| ImputedData | 3.455 | 0.599 | 4.054 | |
| InputData | 2.275 | 0.406 | 2.681 | |
| ModelOptions | 2.461 | 0.408 | 2.869 | |
| Status | 2.619 | 0.428 | 3.047 | |
| TrainData | 2.857 | 0.456 | 3.314 | |
| TrainOptions | 2.527 | 0.403 | 2.930 | |
| TrainStats | 2.812 | 0.454 | 3.267 | |
| calculateVarianceExplained | 6.839 | 1.321 | 8.188 | |
| clusterSamples | 7.196 | 1.333 | 8.532 | |
| compareFactors | 48.135 | 2.448 | 53.342 | |
| compareModels | 49.780 | 0.186 | 53.001 | |
| createMOFAobject | 2.754 | 0.313 | 3.071 | |
| factorNames | 2.483 | 0.414 | 2.896 | |
| featureNames | 1.052 | 0.152 | 1.205 | |
| getCovariates | 3.449 | 0.307 | 3.780 | |
| getDefaultDataOptions | 0.000 | 0.000 | 0.001 | |
| getDefaultModelOptions | 1.444 | 0.354 | 1.799 | |
| getDefaultTrainOptions | 0.000 | 0.000 | 0.002 | |
| getDimensions | 2.388 | 0.635 | 3.025 | |
| getELBO | 2.688 | 0.559 | 3.248 | |
| getExpectations | 2.626 | 0.746 | 3.372 | |
| getFactors | 2.904 | 0.825 | 3.729 | |
| getImputedData | 2.873 | 1.322 | 4.195 | |
| getTrainData | 5.019 | 1.122 | 6.140 | |
| getWeights | 3.091 | 1.295 | 4.386 | |
| impute | 4.427 | 1.566 | 5.992 | |
| loadModel | 2.428 | 0.753 | 3.181 | |
| makeExampleData | 0.028 | 0.002 | 0.029 | |
| plotDataHeatmap | 3.514 | 1.019 | 4.535 | |
| plotDataOverview | 5.132 | 1.231 | 6.362 | |
| plotDataScatter | 4.231 | 0.777 | 5.008 | |
| plotEnrichment | 9.660 | 2.408 | 12.070 | |
| plotEnrichmentBars | 8.458 | 2.601 | 11.060 | |
| plotEnrichmentDetailed | 11.876 | 3.612 | 15.488 | |
| plotEnrichmentHeatmap | 8.457 | 2.733 | 11.199 | |
| plotFactorBeeswarm | 7.564 | 2.087 | 9.660 | |
| plotFactorCor | 5.158 | 1.856 | 7.069 | |
| plotFactorHist | 5.701 | 2.064 | 7.802 | |
| plotFactorScatter | 5.893 | 1.778 | 7.673 | |
| plotFactorScatters | 11.654 | 1.800 | 13.509 | |
| plotTopWeights | 6.104 | 2.151 | 8.280 | |
| plotVarianceExplained | 6.723 | 2.069 | 8.803 | |
| plotWeights | 7.051 | 2.019 | 9.088 | |
| plotWeightsHeatmap | 7.718 | 2.189 | 9.945 | |
| predict | 23.676 | 4.592 | 28.981 | |
| prepareMOFA | 2.616 | 0.650 | 3.348 | |
| qualityControl | 3.879 | 1.100 | 5.187 | |
| regressCovariates | 32.098 | 0.911 | 33.363 | |
| runEnrichmentAnalysis | 8.482 | 2.418 | 10.950 | |
| runMOFA | 0.493 | 0.012 | 0.505 | |
| sampleNames | 0.941 | 0.144 | 1.084 | |
| selectModel | 57.008 | 0.313 | 61.564 | |
| subsetFactors | 2.226 | 0.824 | 3.049 | |
| subsetSamples | 2.474 | 0.902 | 3.375 | |
| subsetViews | 2.341 | 0.885 | 3.250 | |
| trainCurveELBO | 5.368 | 1.425 | 6.794 | |
| trainCurveFactors | 6.522 | 1.653 | 8.205 | |
| viewNames | 1.034 | 0.147 | 1.182 | |