BioC 3.5: CHECK report for DAPAR on oaxaca

Package: DAPAR

Version: 1.7.7

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DAPAR_1.7.7.tar.gz

StartedAt: 2017-03-04 01:34:00 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:38:16 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 255.8 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_1.7.7.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 r72177)
* 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 ‘1.7.7’
* 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 ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'wrapper.dapar.impute.mi':
wrapper.dapar.impute.mi
  Code: function(obj, nb.iter = 3, nknn = 15, selec = 600, siz = 500,
                 weight = 1, ind.comp = 1, progress.bar = TRUE, x.min =
                 10, x.max = 35, x.step.mod = 300, x.step.pi = 300,
                 nb.rei = 100, method = 4, gridsize = 300, q = 0.95,
                 q.min = 0, q.norm = 3, eps = 2, methodi = "slsa",
                 lapala = TRUE)
  Docs: function(obj, nb.iter = 3, nknn = 15, selec = 600, siz = 500,
                 weight = 1, ind.comp = 1, progress.bar = TRUE, x.min =
                 20, x.max = 30, x.step.mod = 300, x.step.pi = 300,
                 nb.rei = 100, method = 4, gridsize = 300, q = 0.95,
                 q.min = 0, q.norm = 3, eps = 2, methodi = "slsa",
                 lapala = TRUE)
  Mismatches in argument default values:
    Name: 'x.min' Code: 10 Docs: 20
    Name: 'x.max' Code: 35 Docs: 30

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'wrapper.dapar.impute.mi'
  ‘nb.iter’ ‘nknn’ ‘siz’ ‘weight’ ‘ind.comp’ ‘progress.bar’ ‘x.min’
  ‘x.max’ ‘x.step.mod’ ‘x.step.pi’ ‘nb.rei’ ‘method’ ‘gridsize’ ‘q’
  ‘q.min’ ‘q.norm’ ‘eps’ ‘methodi’ ‘lapala’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 57.768   1.24  59.053
* 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
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	0.196	0.060	0.256
BuildColumnToProteinDataset	0.412	0.011	0.423
CountPep	0.152	0.054	0.207
GraphPepProt	0.059	0.005	0.063
MeanPeptides	0.059	0.022	0.080
SumPeptides	0.049	0.021	0.071
TopnPeptides	1.787	0.057	1.844
boxPlotD	0.050	0.005	0.055
compareNormalizationD	0.901	0.020	0.922
corrMatrixD	0.948	0.010	0.968
createMSnset	0.368	0.002	0.369
deleteLinesFromIndices	0.027	0.004	0.030
densityPlotD	0.038	0.004	0.042
diffAna	0.320	0.022	0.342
diffAnaComputeFDR	0.918	0.006	0.925
diffAnaGetSignificant	0.060	0.004	0.065
diffAnaLimma	0.026	0.003	0.030
diffAnaSave	0.059	0.003	0.062
diffAnaVolcanoplot	0.040	0.004	0.044
diffAnaWelch	0.032	0.003	0.036
getIndicesConditions	0.031	0.004	0.035
getIndicesOfLinesToRemove	0.038	0.004	0.042
getNumberOf	0.039	0.004	0.044
getNumberOfEmptyLines	0.044	0.005	0.049
getPaletteForLabels	0.039	0.004	0.044
getPaletteForReplicates	0.040	0.005	0.044
getPourcentageOfMV	0.045	0.005	0.050
getProcessingInfo	0.039	0.004	0.044
getProteinsStats	0.054	0.004	0.059
heatmap.DAPAR	0.236	0.020	0.256
heatmapD	0.891	0.025	0.927
limmaCompleteTest	0.145	0.004	0.150
mvFilter	0.124	0.004	0.128
mvFilterFromIndices	0.039	0.004	0.042
mvFilterGetIndices	0.044	0.006	0.050
mvHisto	0.062	0.007	0.079
mvImage	0.287	0.007	0.295
mvImputation	0.079	0.024	0.104
mvPerLinesHisto	0.048	0.005	0.055
mvPerLinesHistoPerCondition	0.039	0.004	0.044
mvTypePlot	0.134	0.005	0.139
normalizeD	0.124	0.024	0.149
pepAgregate	0.209	0.013	0.222
proportionConRev	0.076	0.004	0.082
removeLines	0.046	0.004	0.050
varianceDistD	0.036	0.003	0.041
violinPlotD	0.920	0.009	1.055
wrapper.boxPlotD	0.038	0.004	0.042
wrapper.compareNormalizationD	0.075	0.004	0.102
wrapper.corrMatrixD	1.640	0.006	1.648
wrapper.dapar.impute.mi	57.768	1.240	59.053
wrapper.densityPlotD	0.088	0.003	0.092
wrapper.diffAnaLimma	0.036	0.002	0.037
wrapper.diffAnaWelch	0.066	0.003	0.069
wrapper.heatmapD	0.155	0.018	0.173
wrapper.impute.pa	0.142	0.002	0.144
wrapper.mvHisto	0.084	0.006	0.101
wrapper.mvImage	0.399	0.007	0.406
wrapper.mvImputation	0.039	0.004	0.044
wrapper.mvPerLinesHisto	0.068	0.005	0.075
wrapper.mvPerLinesHistoPerCondition	0.082	0.004	0.086
wrapper.mvTypePlot	0.160	0.005	0.166
wrapper.normalizeD	0.051	0.004	0.056
wrapper.varianceDistD	0.308	0.007	0.317
wrapper.violinPlotD	0.178	0.005	0.183
wrapperCalibrationPlot	0.025	0.004	0.030
writeMSnsetToExcel	0.941	0.038	1.050