BioC 3.4: CHECK report for DAPAR on morelia

Package: DAPAR

Version: 1.5.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.5.9.tar.gz

StartedAt: 2016-09-20 05:21:06 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 05:23:34 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 147.7 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_1.5.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/DAPAR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.5.9’
* 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 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 code objects:
  ‘wrapper.identifyMCAR_MNAR’ ‘wrapper.impute.slsa’
  ‘wrapper.imputeImp4p’
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
* 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-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	0.198	0.058	0.257
BuildColumnToProteinDataset	0.216	0.005	0.221
CountPep	0.120	0.053	0.174
GraphPepProt	0.445	0.012	0.456
MeanPeptides	0.088	0.038	0.127
SumPeptides	0.066	0.029	0.096
TopnPeptides	1.418	0.044	1.462
boxPlotD	0.040	0.007	0.048
compareNormalizationD	0.037	0.007	0.054
corrMatrixD	0.191	0.009	0.204
createMSnset	0.129	0.001	0.132
deleteLinesFromIndices	0.025	0.006	0.029
densityPlotD	0.037	0.006	0.060
diffAna	0.210	0.024	0.234
diffAnaComputeFDR	0.073	0.007	0.080
diffAnaGetSignificant	0.026	0.006	0.032
diffAnaLimma	0.029	0.007	0.036
diffAnaSave	0.036	0.008	0.043
diffAnaVolcanoplot	0.031	0.006	0.038
diffAnaWelch	0.025	0.005	0.031
getIndicesConditions	0.024	0.006	0.030
getIndicesOfLinesToRemove	0.036	0.007	0.042
getNumberOf	0.031	0.008	0.038
getNumberOfEmptyLines	0.028	0.007	0.035
getPaletteForLabels	0.029	0.007	0.035
getPaletteForReplicates	0.029	0.005	0.035
getPourcentageOfMV	0.035	0.006	0.041
getProcessingInfo	0.028	0.007	0.035
getProteinsStats	0.074	0.013	0.086
heatmap.DAPAR	0.405	0.018	0.544
heatmapD	0.214	0.024	0.251
limmaCompleteTest	0.071	0.010	0.081
mvFilter	0.058	0.008	0.066
mvFilterFromIndices	0.025	0.007	0.031
mvFilterGetIndices	0.029	0.010	0.039
mvHisto	0.049	0.011	0.071
mvImage	0.145	0.008	0.153
mvImputation	0.052	0.023	0.075
mvPerLinesHisto	0.048	0.012	0.062
mvPerLinesHistoPerCondition	0.042	0.009	0.052
mvTypePlot	0.081	0.011	0.092
normalizeD	0.047	0.024	0.071
pepAgregate	0.129	0.019	0.148
proportionConRev	0.075	0.009	0.087
removeLines	0.038	0.008	0.047
varianceDistD	0.028	0.008	0.036
violinPlotD	0.146	0.012	0.210
wrapper.boxPlotD	0.043	0.010	0.052
wrapper.compareNormalizationD	0.040	0.007	0.048
wrapper.corrMatrixD	0.171	0.007	0.181
wrapper.densityPlotD	0.041	0.008	0.049
wrapper.diffAnaLimma	0.024	0.006	0.031
wrapper.diffAnaWelch	0.024	0.007	0.032
wrapper.heatmapD	0.208	0.015	0.223
wrapper.mvHisto	0.069	0.009	0.088
wrapper.mvImage	0.188	0.005	0.193
wrapper.mvImputation	0.041	0.004	0.045
wrapper.mvPerLinesHisto	0.039	0.005	0.047
wrapper.mvPerLinesHistoPerCondition	0.028	0.004	0.033
wrapper.mvTypePlot	0.075	0.007	0.081
wrapper.normalizeD	0.043	0.005	0.048
wrapper.varianceDistD	0.249	0.007	0.258
wrapper.violinPlotD	0.157	0.007	0.164
wrapperCalibrationPlot	0.026	0.005	0.031
writeMSnsetToExcel	0.524	0.035	0.670