Britta Velten
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/MOFA |
| Branch: RELEASE_3_12 |
| Last Commit: 0ae14cf |
| Last Changed Date: 2021-02-08 07:46:11 -0400 (Mon, 08 Feb 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:19 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the MOFA package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1133/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Britta Velten
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MOFA |
| Version: 1.6.2 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MOFA_1.6.2.tar.gz |
| StartedAt: 2021-05-06 04:46:15 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:55:01 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 525.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MOFA.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:MOFA.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings MOFA_1.6.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MOFA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MOFA' version '1.6.2'
* 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 ... 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 whether package 'MOFA' can be installed ... WARNING
Found the following significant warnings:
Warning: Please use MOFA2 instead of MOFA. Package 'MOFA' is deprecated and
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck/00install.out' for details.
* 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
compareModels 22.36 0.05 25.40
selectModel 20.25 0.11 23.38
compareFactors 18.43 0.48 51.94
predict 16.98 0.91 17.89
runEnrichmentAnalysis 16.22 0.79 17.04
regressCovariates 15.89 0.13 16.01
plotFactorScatters 9.25 0.47 9.72
plotEnrichmentDetailed 7.81 0.88 8.70
plotEnrichment 6.42 0.87 7.55
calculateVarianceExplained 6.22 0.77 8.98
plotEnrichmentHeatmap 5.92 0.62 6.55
plotWeightsHeatmap 6.01 0.48 6.50
plotEnrichmentBars 5.39 0.47 5.86
getTrainData 4.92 0.42 5.35
DataOptions 4.00 0.28 8.99
* 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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.12-bioc/meat/MOFA.Rcheck/00check.log'
for details.
MOFA.Rcheck/00install.out
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###
### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch MOFA
###
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* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
* installing *source* package 'MOFA' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MOFA'
finding HTML links ... done
DataOptions html
Dimensions html
Expectations html
FeatureIntercepts html
ImputedData html
InputData html
MOFA html
MOFAmodel html
ModelOptions html
Status html
TrainData html
TrainOptions html
TrainStats html
calculateVarianceExplained html
clusterSamples html
compareFactors html
compareModels html
createMOFAobject html
finding level-2 HTML links ... done
factorNames html
featureNames html
getCovariates html
getDefaultDataOptions html
getDefaultModelOptions html
getDefaultTrainOptions html
getDimensions html
getELBO html
getExpectations html
getFactors html
getImputedData html
getTrainData html
getWeights html
impute html
loadModel html
makeExampleData html
plotDataHeatmap html
plotDataOverview html
plotDataScatter html
plotEnrichment html
plotEnrichmentBars html
plotEnrichmentDetailed html
plotEnrichmentHeatmap html
plotFactorBeeswarm html
plotFactorCor html
plotFactorHist html
plotFactorScatter html
plotFactorScatters html
plotTopWeights html
plotVarianceExplained html
plotWeights html
plotWeightsHeatmap html
predict html
prepareMOFA html
qualityControl html
regressCovariates html
runEnrichmentAnalysis html
runMOFA html
sampleNames html
selectModel html
subsetFactors html
subsetSamples html
subsetViews html
trainCurveELBO html
trainCurveFactors html
viewNames html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Please use MOFA2 instead of MOFA. Package 'MOFA' is deprecated and
will be removed from Bioconductor version 3.13. Please see
replacement package MOFA2.
** testing if installed package can be loaded from final location
Warning: Please use MOFA2 instead of MOFA. Package 'MOFA' is deprecated and
will be removed from Bioconductor version 3.13. Please see
replacement package MOFA2.
** testing if installed package keeps a record of temporary installation path
* DONE (MOFA)
Making 'packages.html' ... done
MOFA.Rcheck/MOFA-Ex.timings
| name | user | system | elapsed | |
| DataOptions | 4.00 | 0.28 | 8.99 | |
| Dimensions | 2.25 | 0.32 | 2.56 | |
| Expectations | 1.92 | 0.17 | 2.09 | |
| FeatureIntercepts | 1.97 | 0.19 | 2.16 | |
| ImputedData | 2.57 | 0.23 | 2.80 | |
| InputData | 2.14 | 0.20 | 2.34 | |
| ModelOptions | 2.04 | 0.24 | 2.28 | |
| Status | 2.75 | 0.22 | 2.97 | |
| TrainData | 1.85 | 0.20 | 2.05 | |
| TrainOptions | 2.15 | 0.23 | 2.39 | |
| TrainStats | 2.00 | 0.22 | 2.22 | |
| calculateVarianceExplained | 6.22 | 0.77 | 8.98 | |
| clusterSamples | 3.85 | 0.56 | 4.41 | |
| compareFactors | 18.43 | 0.48 | 51.94 | |
| compareModels | 22.36 | 0.05 | 25.40 | |
| createMOFAobject | 1.78 | 0.11 | 3.40 | |
| factorNames | 1.27 | 0.24 | 1.50 | |
| featureNames | 0.57 | 0.12 | 0.70 | |
| getCovariates | 3.16 | 0.17 | 3.39 | |
| getDefaultDataOptions | 0.01 | 0.00 | 0.01 | |
| getDefaultModelOptions | 1.48 | 0.14 | 1.62 | |
| getDefaultTrainOptions | 0 | 0 | 0 | |
| getDimensions | 1.65 | 0.28 | 1.93 | |
| getELBO | 2.17 | 0.18 | 2.34 | |
| getExpectations | 2.13 | 0.25 | 2.38 | |
| getFactors | 2.24 | 0.45 | 2.69 | |
| getImputedData | 2.44 | 0.42 | 2.86 | |
| getTrainData | 4.92 | 0.42 | 5.35 | |
| getWeights | 2.72 | 0.50 | 3.22 | |
| impute | 3.19 | 0.69 | 3.88 | |
| loadModel | 1.98 | 0.31 | 2.30 | |
| makeExampleData | 0.05 | 0.00 | 0.04 | |
| plotDataHeatmap | 2.67 | 0.50 | 3.17 | |
| plotDataOverview | 3.55 | 0.75 | 4.30 | |
| plotDataScatter | 3.61 | 0.49 | 4.09 | |
| plotEnrichment | 6.42 | 0.87 | 7.55 | |
| plotEnrichmentBars | 5.39 | 0.47 | 5.86 | |
| plotEnrichmentDetailed | 7.81 | 0.88 | 8.70 | |
| plotEnrichmentHeatmap | 5.92 | 0.62 | 6.55 | |
| plotFactorBeeswarm | 4.43 | 0.34 | 4.78 | |
| plotFactorCor | 2.95 | 0.13 | 3.08 | |
| plotFactorHist | 3.35 | 0.39 | 3.74 | |
| plotFactorScatter | 3.64 | 0.50 | 4.14 | |
| plotFactorScatters | 9.25 | 0.47 | 9.72 | |
| plotTopWeights | 4.09 | 0.48 | 4.57 | |
| plotVarianceExplained | 4.41 | 0.36 | 4.77 | |
| plotWeights | 4.47 | 0.35 | 4.81 | |
| plotWeightsHeatmap | 6.01 | 0.48 | 6.50 | |
| predict | 16.98 | 0.91 | 17.89 | |
| prepareMOFA | 1.28 | 0.17 | 1.46 | |
| qualityControl | 2.12 | 0.42 | 2.54 | |
| regressCovariates | 15.89 | 0.13 | 16.01 | |
| runEnrichmentAnalysis | 16.22 | 0.79 | 17.04 | |
| runMOFA | 0.39 | 0.00 | 0.39 | |
| sampleNames | 0.66 | 0.00 | 0.66 | |
| selectModel | 20.25 | 0.11 | 23.38 | |
| subsetFactors | 1.56 | 0.11 | 1.67 | |
| subsetSamples | 2.39 | 0.22 | 2.61 | |
| subsetViews | 1.52 | 0.27 | 1.78 | |
| trainCurveELBO | 3.16 | 0.48 | 3.64 | |
| trainCurveFactors | 2.88 | 0.41 | 3.28 | |
| viewNames | 0.68 | 0.00 | 0.69 | |