BioC 3.5: CHECK report for DAPAR on veracruz2

Package: DAPAR

Version: 1.8.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.8.7.tar.gz

StartedAt: 2017-08-16 01:45:19 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:49:58 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 279.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DAPAR.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.8.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DAPAR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DAPAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DAPAR’ version ‘1.8.7’
* 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 ‘DAPAR’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  ‘testWithoutNA’ ‘test’ ‘UPSpep25’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
wrapper.dapar.impute.mi 21.862  0.457  23.119
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/DAPAR.Rcheck/00check.log’
for details.

* installing *source* package ‘DAPAR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DAPAR)

name	user	system	elapsed
BuildAdjacencyMatrix	0.906	0.095	1.017
BuildColumnToProteinDataset	1.305	0.027	1.357
CVDistD	2.969	0.037	3.069
CountPep	0.391	0.083	0.488
GraphPepProt	0.660	0.017	0.707
MeanPeptides	0.343	0.035	0.389
SumPeptides	0.344	0.033	0.397
TopnPeptides	2.009	0.041	2.099
boxPlotD	0.984	0.016	1.035
compareNormalizationD	0.363	0.017	0.391
corrMatrixD	1.357	0.025	1.419
createMSnset	1.397	0.023	1.488
deleteLinesFromIndices	0.334	0.007	0.345
densityPlotD	0.351	0.005	0.368
diffAna	0.626	0.021	0.700
diffAnaComputeFDR	1.186	0.009	1.221
diffAnaGetSignificant	0.257	0.005	0.271
diffAnaLimma	0.303	0.005	0.321
diffAnaSave	0.307	0.003	0.314
diffAnaVolcanoplot	0.290	0.004	0.304
diffAnaVolcanoplot_rCharts	1.285	0.029	1.358
diffAnaWelch	0.267	0.004	0.273
getIndicesConditions	0.233	0.003	0.246
getIndicesOfLinesToRemove	0.237	0.004	0.246
getNumberOf	0.235	0.003	0.240
getNumberOfEmptyLines	0.319	0.005	0.337
getPaletteForLabels	0.230	0.002	0.244
getPaletteForReplicates	0.249	0.002	0.254
getPourcentageOfMV	0.574	0.008	0.596
getProcessingInfo	0.231	0.004	0.240
getProteinsStats	0.289	0.010	0.304
heatmap.DAPAR	0.489	0.016	0.516
heatmapD	0.903	0.028	0.960
impute.pa2	0.363	0.004	0.373
limmaCompleteTest	0.355	0.007	0.368
mvFilter	0.350	0.007	0.370
mvFilterFromIndices	0.621	0.010	0.648
mvFilterGetIndices	0.314	0.061	0.388
mvHisto	0.286	0.008	0.296
mvImage	2.927	0.020	3.050
mvImputation	0.249	0.007	0.265
mvPerLinesHisto	0.330	0.015	0.353
mvPerLinesHistoPerCondition	0.253	0.006	0.268
mvTypePlot	0.952	0.022	1.002
normalizeD	0.360	0.021	0.384
normalizeD2	0.304	0.025	0.344
pepAgregate	0.423	0.011	0.479
proportionConRev	0.794	0.011	0.873
removeLines	0.246	0.003	0.269
translatedRandomBeta	0.003	0.004	0.007
violinPlotD	1.754	0.010	1.826
wrapper.CVDistD	2.958	0.015	3.092
wrapper.boxPlotD	0.271	0.007	0.284
wrapper.compareNormalizationD	0.434	0.018	0.463
wrapper.corrMatrixD	1.687	0.020	1.760
wrapper.dapar.impute.mi	21.862	0.457	23.119
wrapper.densityPlotD	0.311	0.005	0.332
wrapper.diffAnaLimma	0.245	0.004	0.271
wrapper.diffAnaWelch	0.270	0.004	0.282
wrapper.heatmapD	1.439	0.028	1.531
wrapper.impute.pa	0.334	0.003	0.346
wrapper.impute.pa2	0.328	0.005	0.347
wrapper.mvHisto	0.301	0.006	0.315
wrapper.mvImage	2.553	0.026	2.667
wrapper.mvImputation	0.275	0.004	0.301
wrapper.mvPerLinesHisto	0.337	0.019	0.381
wrapper.mvPerLinesHistoPerCondition	0.271	0.005	0.283
wrapper.mvTypePlot	1.006	0.022	1.055
wrapper.normalizeD	0.274	0.004	0.285
wrapper.normalizeD2	0.283	0.003	0.295
wrapper.violinPlotD	1.689	0.021	1.761
wrapperCalibrationPlot	0.275	0.003	0.291
writeMSnsetToExcel	1.044	0.028	1.098