BioC 3.6: CHECK report for DAPAR on veracruz1

Package: DAPAR

Version: 1.9.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.9.5.tar.gz

StartedAt: 2017-08-16 01:58:51 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:03:51 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 299.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DAPAR.Rcheck

Warnings: 2

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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_1.9.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.9.5’
* 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 ... NOTE
boxPlotD_HC: no visible binding for global variable ‘iris’
corrMatrixD_HC: no visible global function definition for ‘tbl_df’
corrMatrixD_HC: no visible global function definition for ‘gather’
corrMatrixD_HC: no visible global function definition for ‘mutate’
corrMatrixD_HC: no visible global function definition for ‘left_join’
corrMatrixD_HC: no visible global function definition for ‘data_frame’
corrMatrixD_HC: no visible global function definition for ‘select_’
fudge2LRT: no visible binding for global variable ‘mad’
mvTypePlot_HC: no visible global function definition for ‘str’
Undefined global functions or variables:
  data_frame gather iris left_join mad mutate select_ str tbl_df
Consider adding
  importFrom("datasets", "iris")
  importFrom("stats", "mad")
  importFrom("utils", "str")
to your NAMESPACE file.
* checking Rd files ... WARNING
fudge2LRT.Rd: non-ASCII input and no declared encoding
problem found in ‘fudge2LRT.Rd’
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘CVDistD_HC’ ‘boxPlotD_HC’ ‘compareNormalizationD_HC’
  ‘corrMatrixD_HC’ ‘densityPlotD_HC’ ‘getPaletteForLabels_HC’
  ‘getPaletteForReplicates_HC’ ‘mvTypePlot_HC’ ‘proportionConRev_HC’
  ‘wrapper.CVDistD_HC’ ‘wrapper.boxPlotD_HC’
  ‘wrapper.compareNormalizationD_HC’ ‘wrapper.corrMatrixD_HC’
  ‘wrapper.densityPlotD_HC’ ‘wrapper.mvTypePlot_HC’
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 22.089   0.35  23.273
* 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.6-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	0.965	0.086	1.129
BuildColumnToProteinDataset	0.961	0.026	1.034
CVDistD	3.147	0.029	3.241
CountPep	0.398	0.084	0.491
GraphPepProt	0.673	0.013	0.706
MeanPeptides	0.352	0.035	0.416
SumPeptides	0.361	0.037	0.413
TopnPeptides	1.713	0.044	1.827
boxPlotD	0.912	0.012	0.963
compareNormalizationD	0.299	0.010	0.319
corrMatrixD	1.171	0.022	1.202
createMSnset	1.057	0.013	1.091
deleteLinesFromIndices	0.329	0.005	0.354
densityPlotD	0.318	0.009	0.346
diffAna	0.548	0.016	0.573
diffAnaComputeFDR	1.393	0.008	1.443
diffAnaGetSignificant	0.294	0.003	0.302
diffAnaLimma	0.289	0.003	0.302
diffAnaSave	0.326	0.004	0.336
diffAnaVolcanoplot	0.285	0.003	0.292
diffAnaVolcanoplot_rCharts	1.299	0.031	1.375
diffAnaWelch	0.333	0.003	0.341
getIndicesConditions	0.274	0.004	0.279
getIndicesOfLinesToRemove	0.297	0.006	0.305
getNumberOf	0.277	0.003	0.285
getNumberOfEmptyLines	0.295	0.004	0.310
getPaletteForLabels	0.225	0.004	0.230
getPaletteForReplicates	0.276	0.004	0.285
getPourcentageOfMV	0.294	0.005	0.302
getProcessingInfo	0.282	0.007	0.295
getProteinsStats	0.348	0.012	0.371
heatmap.DAPAR	0.829	0.017	0.886
heatmapD	0.901	0.025	0.972
impute.pa2	0.329	0.005	0.339
limmaCompleteTest	0.308	0.005	0.315
mvFilter	0.313	0.003	0.320
mvFilterFromIndices	0.267	0.003	0.276
mvFilterGetIndices	0.619	0.052	0.689
mvHisto	0.267	0.008	0.284
mvHisto_HC	0.260	0.003	0.278
mvImage	2.750	0.017	2.839
mvImputation	0.248	0.006	0.260
mvPerLinesHisto	0.306	0.010	0.328
mvPerLinesHistoPerCondition	0.275	0.005	0.288
mvPerLinesHistoPerCondition_HC	0.307	0.005	0.325
mvPerLinesHisto_HC	0.674	0.008	0.706
mvTypePlot	0.920	0.017	0.960
normalizeD	0.379	0.022	0.405
normalizeD2	0.289	0.023	0.317
pepAgregate	0.406	0.010	0.422
proportionConRev	0.780	0.008	0.801
removeLines	0.609	0.004	0.627
translatedRandomBeta	0.002	0.002	0.004
violinPlotD	1.830	0.011	1.896
wrapper.CVDistD	2.964	0.010	3.128
wrapper.boxPlotD	0.264	0.008	0.281
wrapper.compareNormalizationD	0.404	0.015	0.423
wrapper.corrMatrixD	1.757	0.017	1.843
wrapper.dapar.impute.mi	22.089	0.350	23.273
wrapper.densityPlotD	0.319	0.006	0.337
wrapper.diffAnaLimma	0.288	0.004	0.293
wrapper.diffAnaWelch	0.283	0.003	0.295
wrapper.heatmapD	1.806	0.030	1.879
wrapper.impute.pa	0.354	0.005	0.367
wrapper.impute.pa2	0.322	0.005	0.336
wrapper.mvHisto	0.268	0.006	0.281
wrapper.mvHisto_HC	0.241	0.004	0.249
wrapper.mvImage	2.679	0.019	2.848
wrapper.mvImputation	0.295	0.003	0.313
wrapper.mvPerLinesHisto	0.326	0.010	0.354
wrapper.mvPerLinesHistoPerCondition	0.284	0.006	0.295
wrapper.mvPerLinesHistoPerCondition_HC	0.262	0.004	0.273
wrapper.mvPerLinesHisto_HC	0.274	0.006	0.290
wrapper.mvTypePlot	0.968	0.020	1.023
wrapper.normalizeD	0.278	0.004	0.288
wrapper.normalizeD2	0.350	0.003	0.357
wrapper.violinPlotD	1.683	0.018	1.772
wrapperCalibrationPlot	0.313	0.005	0.330
writeMSnsetToExcel	1.335	0.029	1.410