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BioC 3.4: CHECK report for DAPAR on malbec1

This page was generated on 2017-04-15 16:13:15 -0400 (Sat, 15 Apr 2017).

Package 296/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DAPAR 1.6.0
Samuel Wieczorek
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/DAPAR
Last Changed Rev: 122844 / Revision: 128728
Last Changed Date: 2016-10-19 13:54:49 -0400 (Wed, 19 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: DAPAR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DAPAR_1.6.0.tar.gz
StartedAt: 2017-04-14 21:57:24 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:00:00 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 156.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DAPAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings DAPAR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/DAPAR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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 ... 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 ... 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: OK

DAPAR.Rcheck/00install.out:

* 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)

DAPAR.Rcheck/DAPAR-Ex.timings:

nameusersystemelapsed
BuildAdjacencyMatrix0.4280.0280.455
BuildColumnToProteinDataset0.2320.0000.231
CountPep0.1240.0360.157
GraphPepProt0.3200.0000.321
MeanPeptides0.0520.0160.066
SumPeptides0.0560.0040.059
TopnPeptides1.4760.0281.507
boxPlotD0.0360.0040.041
compareNormalizationD0.0440.0000.044
corrMatrixD0.2240.0040.228
createMSnset0.1160.0000.117
deleteLinesFromIndices0.0280.0000.029
densityPlotD0.0440.0040.045
diffAna0.1560.0080.166
diffAnaComputeFDR0.0760.0000.077
diffAnaGetSignificant0.0280.0000.029
diffAnaLimma0.0320.0000.029
diffAnaSave0.0280.0000.029
diffAnaVolcanoplot0.0320.0040.035
diffAnaWelch0.0240.0040.029
getIndicesConditions0.0280.0000.028
getIndicesOfLinesToRemove0.0280.0000.029
getNumberOf0.0320.0000.029
getNumberOfEmptyLines0.0280.0000.030
getPaletteForLabels0.0320.0000.029
getPaletteForReplicates0.0280.0000.028
getPourcentageOfMV0.0320.0000.032
getProcessingInfo0.0240.0000.027
getProteinsStats0.0440.0000.047
heatmap.DAPAR0.2320.0040.235
heatmapD0.5400.0040.544
limmaCompleteTest0.0520.0000.052
mvFilter0.0520.0000.054
mvFilterFromIndices0.0280.0000.027
mvFilterGetIndices0.0280.0040.033
mvHisto0.0520.0040.059
mvImage0.1520.0000.149
mvImputation0.0480.0120.060
mvPerLinesHisto0.0400.0000.039
mvPerLinesHistoPerCondition0.0320.0000.030
mvTypePlot0.0840.0000.082
normalizeD0.0400.0040.046
pepAgregate0.0880.0000.089
proportionConRev0.0640.0000.066
removeLines0.0280.0040.030
varianceDistD0.0320.0000.031
violinPlotD0.1120.0000.111
wrapper.boxPlotD0.0360.0000.033
wrapper.compareNormalizationD0.0360.0040.041
wrapper.corrMatrixD0.1880.0000.191
wrapper.densityPlotD0.0520.0000.049
wrapper.diffAnaLimma0.0240.0000.026
wrapper.diffAnaWelch0.0240.0000.027
wrapper.heatmapD0.2120.0000.212
wrapper.mvHisto0.0520.0040.056
wrapper.mvImage0.1480.0000.150
wrapper.mvImputation0.0440.0000.044
wrapper.mvPerLinesHisto0.0360.0000.038
wrapper.mvPerLinesHistoPerCondition0.0320.0000.031
wrapper.mvTypePlot0.0880.0040.090
wrapper.normalizeD0.0320.0000.031
wrapper.varianceDistD0.1520.0000.153
wrapper.violinPlotD0.1280.0040.132
wrapperCalibrationPlot0.0280.0000.030
writeMSnsetToExcel0.3160.0120.329