Britta Velten
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/MOFA |
| Branch: master |
| Last Commit: 35c639d |
| Last Changed Date: 2019-10-30 03:29:44 -0500 (Wed, 30 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:53:47 -0500 (Thu, 16 Jan 2020).
| Package 1075/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MOFA 1.3.1 Britta Velten
| malbec2 | Linux (Ubuntu 18.04.3 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: 1.3.1 |
| 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_1.3.1.tar.gz |
| StartedAt: 2020-01-16 06:39:26 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 06:53:18 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 831.4 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_1.3.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MOFA.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.3.1’
* 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 (user + system) or elapsed time > 5s
user system elapsed
compareFactors 60.844 2.766 66.781
selectModel 60.997 0.269 64.387
compareModels 49.431 0.258 52.708
regressCovariates 32.966 0.829 36.292
predict 20.488 3.572 24.072
plotFactorScatters 12.278 1.819 14.444
plotEnrichmentDetailed 10.410 3.532 13.940
plotEnrichment 10.363 2.616 12.978
runEnrichmentAnalysis 9.205 2.245 11.483
plotEnrichmentBars 8.384 2.460 10.842
plotEnrichmentHeatmap 7.781 2.534 10.315
plotWeightsHeatmap 8.591 1.687 10.280
plotVarianceExplained 7.461 2.127 9.587
plotWeights 6.834 1.859 8.693
clusterSamples 7.435 1.208 8.646
plotFactorBeeswarm 6.754 1.794 8.550
plotTopWeights 6.703 1.692 8.455
plotFactorHist 6.217 1.952 8.170
plotFactorScatter 6.310 1.710 8.064
trainCurveELBO 6.443 1.571 8.015
plotDataOverview 6.206 1.649 7.856
calculateVarianceExplained 6.304 1.433 7.771
plotFactorCor 5.799 1.612 7.413
trainCurveFactors 5.341 1.635 6.979
impute 5.266 1.593 6.859
qualityControl 4.897 1.355 6.644
getTrainData 5.128 0.998 6.125
getImputedData 3.893 1.483 5.375
plotDataScatter 4.379 0.909 5.289
DataOptions 4.812 0.466 5.311
* 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-3.11-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/4.0/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 | 4.812 | 0.466 | 5.311 | |
| Dimensions | 2.871 | 0.445 | 3.315 | |
| Expectations | 2.921 | 0.467 | 3.389 | |
| FeatureIntercepts | 2.917 | 0.380 | 3.297 | |
| ImputedData | 3.597 | 0.660 | 4.256 | |
| InputData | 3.687 | 0.369 | 4.055 | |
| ModelOptions | 3.224 | 0.487 | 3.711 | |
| Status | 3.103 | 0.419 | 3.522 | |
| TrainData | 3.002 | 0.390 | 3.397 | |
| TrainOptions | 3.007 | 0.490 | 3.497 | |
| TrainStats | 3.017 | 0.404 | 3.423 | |
| calculateVarianceExplained | 6.304 | 1.433 | 7.771 | |
| clusterSamples | 7.435 | 1.208 | 8.646 | |
| compareFactors | 60.844 | 2.766 | 66.781 | |
| compareModels | 49.431 | 0.258 | 52.708 | |
| createMOFAobject | 3.408 | 0.745 | 4.157 | |
| factorNames | 3.154 | 0.710 | 3.863 | |
| featureNames | 1.197 | 0.185 | 1.382 | |
| getCovariates | 4.518 | 0.320 | 4.841 | |
| getDefaultDataOptions | 0.001 | 0.000 | 0.001 | |
| getDefaultModelOptions | 1.598 | 0.363 | 1.961 | |
| getDefaultTrainOptions | 0 | 0 | 0 | |
| getDimensions | 3.341 | 0.752 | 4.092 | |
| getELBO | 2.713 | 0.511 | 3.224 | |
| getExpectations | 3.261 | 0.895 | 4.155 | |
| getFactors | 2.572 | 0.715 | 3.286 | |
| getImputedData | 3.893 | 1.483 | 5.375 | |
| getTrainData | 5.128 | 0.998 | 6.125 | |
| getWeights | 3.516 | 1.119 | 4.635 | |
| impute | 5.266 | 1.593 | 6.859 | |
| loadModel | 3.391 | 0.974 | 4.364 | |
| makeExampleData | 0.025 | 0.001 | 0.026 | |
| plotDataHeatmap | 3.492 | 1.188 | 4.683 | |
| plotDataOverview | 6.206 | 1.649 | 7.856 | |
| plotDataScatter | 4.379 | 0.909 | 5.289 | |
| plotEnrichment | 10.363 | 2.616 | 12.978 | |
| plotEnrichmentBars | 8.384 | 2.460 | 10.842 | |
| plotEnrichmentDetailed | 10.410 | 3.532 | 13.940 | |
| plotEnrichmentHeatmap | 7.781 | 2.534 | 10.315 | |
| plotFactorBeeswarm | 6.754 | 1.794 | 8.550 | |
| plotFactorCor | 5.799 | 1.612 | 7.413 | |
| plotFactorHist | 6.217 | 1.952 | 8.170 | |
| plotFactorScatter | 6.310 | 1.710 | 8.064 | |
| plotFactorScatters | 12.278 | 1.819 | 14.444 | |
| plotTopWeights | 6.703 | 1.692 | 8.455 | |
| plotVarianceExplained | 7.461 | 2.127 | 9.587 | |
| plotWeights | 6.834 | 1.859 | 8.693 | |
| plotWeightsHeatmap | 8.591 | 1.687 | 10.280 | |
| predict | 20.488 | 3.572 | 24.072 | |
| prepareMOFA | 2.127 | 0.610 | 2.737 | |
| qualityControl | 4.897 | 1.355 | 6.644 | |
| regressCovariates | 32.966 | 0.829 | 36.292 | |
| runEnrichmentAnalysis | 9.205 | 2.245 | 11.483 | |
| runMOFA | 0.67 | 0.01 | 0.68 | |
| sampleNames | 1.059 | 0.112 | 1.172 | |
| selectModel | 60.997 | 0.269 | 64.387 | |
| subsetFactors | 2.529 | 0.853 | 3.382 | |
| subsetSamples | 2.538 | 0.940 | 3.480 | |
| subsetViews | 2.494 | 0.855 | 3.348 | |
| trainCurveELBO | 6.443 | 1.571 | 8.015 | |
| trainCurveFactors | 5.341 | 1.635 | 6.979 | |
| viewNames | 1.056 | 0.157 | 1.213 | |