BioC 3.6: CHECK report for DAPAR on tokay1

Package: DAPAR

Version: 1.9.5

Command: rm -rf DAPAR.buildbin-libdir DAPAR.Rcheck && mkdir DAPAR.buildbin-libdir DAPAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DAPAR.buildbin-libdir DAPAR_1.9.5.tar.gz >DAPAR.Rcheck\00install.out 2>&1 && cp DAPAR.Rcheck\00install.out DAPAR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DAPAR.buildbin-libdir --install="check:DAPAR-install.out" --force-multiarch --no-vignettes --timings DAPAR_1.9.5.tar.gz

StartedAt: 2017-08-15 22:49:55 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:57:57 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 482.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DAPAR.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DAPAR.buildbin-libdir DAPAR.Rcheck && mkdir DAPAR.buildbin-libdir DAPAR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=DAPAR.buildbin-libdir DAPAR_1.9.5.tar.gz >DAPAR.Rcheck\00install.out 2>&1 && cp DAPAR.Rcheck\00install.out DAPAR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=DAPAR.buildbin-libdir --install="check:DAPAR-install.out" --force-multiarch --no-vignettes --timings DAPAR_1.9.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/DAPAR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
wrapper.dapar.impute.mi    17.81   0.00   17.81
diffAnaVolcanoplot_rCharts  1.08   0.03    5.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
wrapper.dapar.impute.mi 40.72      0   40.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/DAPAR.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'DAPAR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DAPAR' as DAPAR_1.9.5.zip
* DONE (DAPAR)

name	user	system	elapsed
BuildAdjacencyMatrix	0.72	0.11	1.15
BuildColumnToProteinDataset	1.14	0.03	1.17
CVDistD	1.82	0.03	1.84
CountPep	0.29	0.08	0.38
GraphPepProt	0.53	0.03	0.56
MeanPeptides	0.28	0.01	0.30
SumPeptides	0.29	0.05	0.33
TopnPeptides	1.45	0.05	1.50
boxPlotD	0.72	0.03	0.75
compareNormalizationD	0.53	0.00	0.53
corrMatrixD	1.25	0.02	1.26
createMSnset	0.76	0.03	0.99
deleteLinesFromIndices	0.32	0.01	0.32
densityPlotD	0.29	0.00	0.30
diffAna	0.43	0.00	0.42
diffAnaComputeFDR	0.86	0.00	0.86
diffAnaGetSignificant	0.25	0.02	0.27
diffAnaLimma	0.27	0.01	0.29
diffAnaSave	0.27	0.00	0.27
diffAnaVolcanoplot	0.27	0.02	0.28
diffAnaVolcanoplot_rCharts	1.08	0.03	5.64
diffAnaWelch	0.25	0.00	0.25
getIndicesConditions	0.22	0.00	0.22
getIndicesOfLinesToRemove	0.21	0.00	0.22
getNumberOf	0.24	0.02	0.25
getNumberOfEmptyLines	0.26	0.00	0.27
getPaletteForLabels	0.22	0.01	0.23
getPaletteForReplicates	0.21	0.02	0.22
getPourcentageOfMV	0.24	0.01	0.25
getProcessingInfo	0.22	0.00	0.21
getProteinsStats	0.29	0.02	0.32
heatmap.DAPAR	0.60	0.00	0.59
heatmapD	1.21	0.08	1.30
impute.pa2	0.30	0.00	0.29
limmaCompleteTest	0.27	0.01	0.29
mvFilter	0.29	0.00	0.29
mvFilterFromIndices	0.24	0.02	0.25
mvFilterGetIndices	0.30	0.03	0.33
mvHisto	0.25	0.01	0.27
mvHisto_HC	0.26	0.00	0.26
mvImage	2.16	0.00	2.16
mvImputation	0.23	0.00	0.23
mvPerLinesHisto	0.33	0.02	0.35
mvPerLinesHistoPerCondition	0.23	0.02	0.25
mvPerLinesHistoPerCondition_HC	0.28	0.00	0.28
mvPerLinesHisto_HC	0.28	0.01	0.30
mvTypePlot	1.05	0.00	1.05
normalizeD	0.33	0.02	0.34
normalizeD2	0.28	0.00	0.28
pepAgregate	0.60	0.00	0.59
proportionConRev	0.84	0.03	0.88
removeLines	0.20	0.01	0.22
translatedRandomBeta	0.02	0.00	0.01
violinPlotD	1.14	0.00	1.14
wrapper.CVDistD	1.92	0.02	1.94
wrapper.boxPlotD	0.28	0.00	0.28
wrapper.compareNormalizationD	0.57	0.02	0.58
wrapper.corrMatrixD	1.78	0.00	1.78
wrapper.dapar.impute.mi	17.81	0.00	17.81
wrapper.densityPlotD	0.31	0.00	0.31
wrapper.diffAnaLimma	0.25	0.00	0.25
wrapper.diffAnaWelch	0.27	0.00	0.27
wrapper.heatmapD	1.20	0.01	1.22
wrapper.impute.pa	0.58	0.00	0.58
wrapper.impute.pa2	0.28	0.02	0.29
wrapper.mvHisto	0.25	0.01	0.27
wrapper.mvHisto_HC	0.22	0.02	0.23
wrapper.mvImage	1.86	0.01	1.88
wrapper.mvImputation	0.25	0.00	0.25
wrapper.mvPerLinesHisto	0.33	0.02	0.34
wrapper.mvPerLinesHistoPerCondition	0.23	0.01	0.25
wrapper.mvPerLinesHistoPerCondition_HC	0.27	0.00	0.27
wrapper.mvPerLinesHisto_HC	0.23	0.04	0.26
wrapper.mvTypePlot	1.02	0.03	1.05
wrapper.normalizeD	0.25	0.00	0.25
wrapper.normalizeD2	0.31	0.00	0.31
wrapper.violinPlotD	1.37	0.01	1.39
wrapperCalibrationPlot	0.25	0.02	0.27
writeMSnsetToExcel	1.18	0.05	1.41

name	user	system	elapsed
BuildAdjacencyMatrix	0.84	0.03	0.88
BuildColumnToProteinDataset	1.26	0.02	1.29
CVDistD	2.37	0.00	2.38
CountPep	0.32	0.05	0.36
GraphPepProt	0.70	0.01	0.72
MeanPeptides	0.24	0.05	0.28
SumPeptides	0.26	0.03	0.30
TopnPeptides	1.52	0.00	1.51
boxPlotD	0.81	0.00	0.82
compareNormalizationD	0.86	0.02	0.87
corrMatrixD	1.11	0.01	1.13
createMSnset	0.94	0.00	0.93
deleteLinesFromIndices	0.30	0.02	0.31
densityPlotD	0.33	0.00	0.33
diffAna	0.45	0.00	0.45
diffAnaComputeFDR	1.14	0.00	1.14
diffAnaGetSignificant	0.25	0.01	0.27
diffAnaLimma	0.28	0.00	0.28
diffAnaSave	0.28	0.02	0.29
diffAnaVolcanoplot	0.27	0.00	0.27
diffAnaVolcanoplot_rCharts	1.90	0.03	1.97
diffAnaWelch	0.26	0.00	0.27
getIndicesConditions	0.25	0.00	0.25
getIndicesOfLinesToRemove	0.22	0.00	0.22
getNumberOf	0.35	0.01	0.36
getNumberOfEmptyLines	0.23	0.00	0.23
getPaletteForLabels	0.2	0.0	0.2
getPaletteForReplicates	0.21	0.00	0.21
getPourcentageOfMV	0.26	0.00	0.26
getProcessingInfo	0.22	0.00	0.22
getProteinsStats	0.30	0.02	0.31
heatmap.DAPAR	1.19	0.05	1.24
heatmapD	0.83	0.01	0.85
impute.pa2	0.45	0.00	0.45
limmaCompleteTest	0.53	0.02	0.55
mvFilter	0.49	0.00	0.48
mvFilterFromIndices	0.40	0.01	0.40
mvFilterGetIndices	0.25	0.04	0.29
mvHisto	0.25	0.00	0.25
mvHisto_HC	0.23	0.00	0.23
mvImage	2.58	0.04	2.63
mvImputation	0.22	0.00	0.22
mvPerLinesHisto	0.28	0.03	0.31
mvPerLinesHistoPerCondition	0.25	0.00	0.25
mvPerLinesHistoPerCondition_HC	0.25	0.00	0.25
mvPerLinesHisto_HC	0.23	0.02	0.25
mvTypePlot	1.22	0.00	1.22
normalizeD	0.36	0.00	0.36
normalizeD2	0.25	0.01	0.26
pepAgregate	0.33	0.00	0.33
proportionConRev	0.77	0.04	0.80
removeLines	0.18	0.00	0.18
translatedRandomBeta	0	0	0
violinPlotD	1.22	0.01	1.23
wrapper.CVDistD	3.70	0.00	3.71
wrapper.boxPlotD	0.41	0.00	0.40
wrapper.compareNormalizationD	0.64	0.02	0.66
wrapper.corrMatrixD	2.03	0.01	2.04
wrapper.dapar.impute.mi	40.72	0.00	40.74
wrapper.densityPlotD	0.27	0.00	0.26
wrapper.diffAnaLimma	0.3	0.0	0.3
wrapper.diffAnaWelch	0.39	0.00	0.39
wrapper.heatmapD	2.04	0.00	2.05
wrapper.impute.pa	0.41	0.00	0.40
wrapper.impute.pa2	0.48	0.02	0.50
wrapper.mvHisto	0.43	0.01	0.44
wrapper.mvHisto_HC	0.39	0.00	0.39
wrapper.mvImage	2.85	0.02	2.86
wrapper.mvImputation	0.20	0.02	0.21
wrapper.mvPerLinesHisto	0.3	0.0	0.3
wrapper.mvPerLinesHistoPerCondition	0.24	0.00	0.23
wrapper.mvPerLinesHistoPerCondition_HC	0.21	0.01	0.24
wrapper.mvPerLinesHisto_HC	0.24	0.00	0.23
wrapper.mvTypePlot	1.00	0.02	1.01
wrapper.normalizeD	0.24	0.01	0.25
wrapper.normalizeD2	0.28	0.00	0.28
wrapper.violinPlotD	1.39	0.02	1.41
wrapperCalibrationPlot	0.27	0.00	0.26
writeMSnsetToExcel	1.28	0.00	1.38