BioC 3.5: CHECK report for DAPAR on toluca2

Package: DAPAR

Version: 1.7.23

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.7.23.tar.gz

StartedAt: 2017-04-23 02:40:38 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 02:45:57 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 318.5 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_1.7.23.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DAPAR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.23’
* 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 20.028  0.573  21.261
* 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	0.588	0.086	0.679
BuildColumnToProteinDataset	1.026	0.045	1.073
CVDistD	3.679	0.050	3.779
CountPep	0.472	0.091	0.565
GraphPepProt	0.664	0.019	0.689
MeanPeptides	0.348	0.031	0.380
SumPeptides	0.348	0.034	0.400
TopnPeptides	2.251	0.050	2.355
boxPlotD	1.165	0.019	1.193
compareNormalizationD	0.438	0.019	0.488
corrMatrixD	1.556	0.022	1.741
createMSnset	1.866	0.026	1.955
deleteLinesFromIndices	0.399	0.008	0.409
densityPlotD	0.635	0.011	0.669
diffAna	0.632	0.023	0.659
diffAnaComputeFDR	1.414	0.008	1.444
diffAnaGetSignificant	0.314	0.003	0.318
diffAnaLimma	0.339	0.004	0.347
diffAnaSave	0.349	0.004	0.354
diffAnaVolcanoplot	0.314	0.004	0.320
diffAnaVolcanoplot_rCharts	1.309	0.032	1.368
diffAnaWelch	0.326	0.003	0.329
getIndicesConditions	0.280	0.003	0.284
getIndicesOfLinesToRemove	0.277	0.002	0.280
getNumberOf	0.276	0.004	0.282
getNumberOfEmptyLines	0.333	0.006	0.339
getPaletteForLabels	0.274	0.003	0.282
getPaletteForReplicates	0.279	0.004	0.287
getPourcentageOfMV	0.313	0.006	0.320
getProcessingInfo	0.277	0.003	0.283
getProteinsStats	0.370	0.016	0.387
heatmap.DAPAR	0.858	0.017	0.905
heatmapD	1.365	0.030	1.483
impute.pa2	0.415	0.004	0.421
limmaCompleteTest	0.388	0.005	0.394
mvFilter	0.404	0.010	0.416
mvFilterFromIndices	0.326	0.004	0.332
mvFilterGetIndices	0.392	0.064	0.458
mvHisto	0.322	0.009	0.336
mvImage	3.723	0.030	3.804
mvImputation	0.282	0.009	0.292
mvPerLinesHisto	0.362	0.013	0.381
mvPerLinesHistoPerCondition	0.305	0.004	0.317
mvTypePlot	1.120	0.028	1.161
normalizeD	0.437	0.026	0.467
normalizeD2	0.334	0.020	0.356
pepAgregate	0.505	0.012	0.523
proportionConRev	0.849	0.008	0.872
removeLines	0.258	0.002	0.261
translatedRandomBeta	0.002	0.002	0.004
violinPlotD	1.863	0.029	1.895
wrapper.CVDistD	3.834	0.014	3.874
wrapper.boxPlotD	0.271	0.008	0.280
wrapper.compareNormalizationD	0.475	0.019	0.496
wrapper.corrMatrixD	2.158	0.025	2.357
wrapper.dapar.impute.mi	20.028	0.573	21.261
wrapper.densityPlotD	0.336	0.005	0.344
wrapper.diffAnaLimma	0.300	0.007	0.307
wrapper.diffAnaWelch	0.313	0.003	0.317
wrapper.heatmapD	1.693	0.027	1.734
wrapper.impute.pa	0.449	0.011	0.463
wrapper.impute.pa2	0.371	0.006	0.378
wrapper.mvHisto	0.337	0.007	0.349
wrapper.mvImage	3.472	0.027	3.509
wrapper.mvImputation	0.314	0.003	0.319
wrapper.mvPerLinesHisto	0.396	0.013	0.413
wrapper.mvPerLinesHistoPerCondition	0.353	0.005	0.371
wrapper.mvTypePlot	1.246	0.027	1.289
wrapper.normalizeD	0.322	0.005	0.330
wrapper.normalizeD2	0.400	0.009	0.410
wrapper.violinPlotD	2.206	0.029	2.265
wrapperCalibrationPlot	0.318	0.002	0.324
writeMSnsetToExcel	1.299	0.035	1.421