Samuel Wieczorek
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/DAPAR |
| Branch: RELEASE_3_7 |
| Last Commit: 9f6641c |
| Last Changed Date: 2018-07-12 04:11:20 -0400 (Thu, 12 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:41:09 -0400 (Wed, 17 Oct 2018).
| Package 345/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DAPAR 1.12.11 Samuel Wieczorek
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DAPAR |
| Version: 1.12.11 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DAPAR_1.12.11.tar.gz |
| StartedAt: 2018-10-17 01:27:49 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:38:14 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 624.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DAPAR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings DAPAR_1.12.11.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/DAPAR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.12.11'
* 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
diffAnaVolcanoplot_rCharts: no visible binding for global variable 'x'
diffAnaVolcanoplot_rCharts: no visible binding for global variable 'y'
diffAnaVolcanoplot_rCharts: no visible binding for global variable 'g'
getTextForGOAnalysis: no visible binding for global variable
'textGOParams'
getTextForGOAnalysis: no visible binding for global variable 'input'
Undefined global functions or variables:
g input textGOParams x y
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wrapper.compareNormalizationD_HC 37.74 0.24 38.25
wrapper.dapar.impute.mi 11.71 0.03 11.74
wrapper.CVDistD 7.08 0.00 7.08
BuildColumnToProteinDataset_par 0.95 0.11 12.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wrapper.compareNormalizationD_HC 39.01 0.14 39.16
wrapper.dapar.impute.mi 16.44 0.05 16.52
CVDistD 5.50 0.04 5.55
wrapper.CVDistD 5.39 0.00 5.39
BuildColumnToProteinDataset_par 0.91 0.07 12.36
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/DAPAR.Rcheck/00check.log'
for details.
DAPAR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/DAPAR_1.12.11.tar.gz && rm -rf DAPAR.buildbin-libdir && mkdir DAPAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAPAR.buildbin-libdir DAPAR_1.12.11.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL DAPAR_1.12.11.zip && rm DAPAR_1.12.11.tar.gz DAPAR_1.12.11.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1454k 100 1454k 0 0 19.9M 0 --:--:-- --:--:-- --:--:-- 21.8M
install for i386
* installing *source* package 'DAPAR' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DAPAR'
finding HTML links ... done
BuildAdjacencyMatrix html
BuildColumnToProteinDataset html
BuildColumnToProteinDataset_par html
CVDistD html
CVDistD_HC html
CountPep html
GOAnalysisSave html
finding level-2 HTML links ... done
GraphPepProt html
LH0 html
LH0.lm html
LH1 html
LH1.lm html
MeanPeptides html
StringBasedFiltering html
StringBasedFiltering2 html
SumPeptides html
TopnPeptides html
addOriginOfValue html
barplotEnrichGO_HC html
barplotGroupGO_HC html
boxPlotD html
boxPlotD_HC html
buildLogText html
check.conditions html
check.design html
compareNormalizationD html
compareNormalizationD_HC html
compute.t.tests html
corrMatrixD html
corrMatrixD_HC html
createMSnset html
deleteLinesFromIndices html
densityPlotD html
densityPlotD_HC html
diffAnaComputeFDR html
diffAnaGetSignificant html
diffAnaSave html
diffAnaVolcanoplot html
diffAnaVolcanoplot_rCharts html
enrich_GO html
findMECBlock html
formatLimmaResult html
fudge2LRT html
getIndicesConditions html
getIndicesOfLinesToRemove html
getListNbValuesInLines html
getNumberOf html
getNumberOfEmptyLines html
getPaletteForLabels html
getPaletteForLabels_HC html
getPaletteForReplicates html
getPaletteForReplicates_HC html
getPourcentageOfMV html
getProcessingInfo html
getProteinsStats html
getQuantile4Imp html
getTextForAggregation html
getTextForAnaDiff html
getTextForFiltering html
getTextForGOAnalysis html
getTextForImputation html
getTextForNewDataset html
getTextForNormalization html
group_GO html
hc_FC_DensityPlot html
hc_mvTypePlot2 html
heatmap.DAPAR html
heatmapD html
impute.detQuant html
impute.pa2 html
is.MV html
is.OfType html
limmaCompleteTest html
listSheets html
make.contrast html
make.design.1 html
make.design.2 html
make.design.3 html
make.design html
mvFilter html
mvFilterFromIndices html
mvFilterGetIndices html
mvHisto html
mvHisto_HC html
mvImage html
mvImputation html
mvPerLinesHisto html
mvPerLinesHistoPerCondition html
mvPerLinesHistoPerCondition_HC html
mvPerLinesHisto_HC html
mvTypePlot html
my_hc_ExportMenu html
my_hc_chart html
nonzero html
normalizeD html
pepAgregate html
pepa.test html
proportionConRev_HC html
rbindMSnset html
reIntroduceMEC html
readExcel html
removeLines html
samLRT html
saveParameters html
scatterplotEnrichGO_HC html
setMEC html
test.design html
translatedRandomBeta html
univ_AnnotDbPkg html
violinPlotD html
wrapper.CVDistD html
wrapper.CVDistD_HC html
wrapper.boxPlotD html
wrapper.boxPlotD_HC html
wrapper.compareNormalizationD html
wrapper.compareNormalizationD_HC html
wrapper.corrMatrixD html
wrapper.corrMatrixD_HC html
wrapper.dapar.impute.mi html
wrapper.densityPlotD html
wrapper.densityPlotD_HC html
wrapper.hc_mvTypePlot2 html
wrapper.heatmapD html
wrapper.impute.KNN html
wrapper.impute.detQuant html
wrapper.impute.fixedValue html
wrapper.impute.pa html
wrapper.impute.pa2 html
wrapper.impute.slsa html
wrapper.mvHisto html
wrapper.mvHisto_HC html
wrapper.mvImage html
wrapper.mvImputation html
wrapper.mvPerLinesHisto html
wrapper.mvPerLinesHistoPerCondition html
wrapper.mvPerLinesHistoPerCondition_HC
html
wrapper.mvPerLinesHisto_HC html
wrapper.mvTypePlot html
wrapper.normalizeD html
wrapper.t_test_Complete html
wrapper.violinPlotD html
wrapperCalibrationPlot html
writeMSnsetToCSV html
writeMSnsetToExcel html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'DAPAR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DAPAR' as DAPAR_1.12.11.zip
* DONE (DAPAR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'DAPAR' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
DAPAR.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(DAPAR)
>
> test_check("DAPAR")
1 2 3 4 5
5 2 2 4 1 0
1 2 3 4 5
5 2 2 4 1 0
1 2 3 4 5
5 2 2 4 1 0
== testthat results ===========================================================
OK: 41 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
15.39 1.15 16.95
|
DAPAR.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(DAPAR)
>
> test_check("DAPAR")
1 2 3 4 5
5 2 2 4 1 0
1 2 3 4 5
5 2 2 4 1 0
1 2 3 4 5
5 2 2 4 1 0
== testthat results ===========================================================
OK: 41 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
12.29 0.56 13.01
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DAPAR.Rcheck/examples_i386/DAPAR-Ex.timings
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DAPAR.Rcheck/examples_x64/DAPAR-Ex.timings
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