Samuel Wieczorek
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/DAPAR |
| Branch: RELEASE_3_6 |
| Last Commit: 6e078f3 |
| Last Changed Date: 2018-03-26 03:03:38 -0400 (Mon, 26 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:14:06 -0400 (Thu, 12 Apr 2018).
| Package 330/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DAPAR 1.10.4 Samuel Wieczorek
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DAPAR |
| Version: 1.10.4 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DAPAR_1.10.4.tar.gz |
| StartedAt: 2018-04-11 22:43:38 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:50:06 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 388.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DAPAR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DAPAR_1.10.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DAPAR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.4’
* 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 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.compareNormalizationD_HC 28.508 0.020 28.549
compareNormalizationD_HC 26.008 0.028 26.053
wrapper.dapar.impute.mi 25.444 0.032 25.502
enrich_GO 14.636 0.400 15.398
group_GO 10.832 0.184 11.265
* 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 ** 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/tests/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
Procedure of Benjamini-Hochberg is used. pi0 is fixed to 1.
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: 125 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
17.048 0.188 18.066
DAPAR.Rcheck/DAPAR-Ex.timings
| name | user | system | elapsed | |
| BuildAdjacencyMatrix | 1.200 | 0.052 | 1.264 | |
| BuildColumnToProteinDataset | 1.428 | 0.004 | 1.434 | |
| BuildColumnToProteinDataset_par | 1.208 | 0.304 | 0.940 | |
| CVDistD | 2.672 | 0.028 | 2.701 | |
| CVDistD_HC | 1.84 | 0.02 | 2.10 | |
| CountPep | 0.488 | 0.052 | 0.540 | |
| GraphPepProt | 0.756 | 0.020 | 0.774 | |
| MeanPeptides | 0.308 | 0.008 | 0.315 | |
| StringBasedFiltering | 0.880 | 0.004 | 0.888 | |
| SumPeptides | 0.256 | 0.016 | 0.275 | |
| TopnPeptides | 1.552 | 0.032 | 1.586 | |
| boxPlotD | 1.120 | 0.000 | 1.117 | |
| boxPlotD_HC | 1.576 | 0.012 | 1.596 | |
| compareNormalizationD | 0.332 | 0.012 | 0.344 | |
| compareNormalizationD_HC | 26.008 | 0.028 | 26.053 | |
| corrMatrixD | 1.504 | 0.004 | 1.507 | |
| corrMatrixD_HC | 0.272 | 0.008 | 0.279 | |
| createMSnset | 0.912 | 0.004 | 0.967 | |
| deleteLinesFromIndices | 0.292 | 0.004 | 0.296 | |
| densityPlotD | 0.292 | 0.000 | 0.295 | |
| densityPlotD_HC | 1.316 | 0.000 | 1.318 | |
| diffAna | 0.420 | 0.012 | 0.434 | |
| diffAnaComputeFDR | 1.352 | 0.000 | 1.354 | |
| diffAnaGetSignificant | 0.232 | 0.000 | 0.235 | |
| diffAnaLimma | 0.252 | 0.000 | 0.253 | |
| diffAnaSave | 0.268 | 0.004 | 0.276 | |
| diffAnaVolcanoplot_rCharts | 0.704 | 0.008 | 0.734 | |
| diffAnaWelch | 0.244 | 0.000 | 0.245 | |
| enrich_GO | 14.636 | 0.400 | 15.398 | |
| getIndicesConditions | 0.428 | 0.000 | 0.428 | |
| getIndicesOfLinesToRemove | 0.304 | 0.000 | 0.303 | |
| getNumberOf | 0.204 | 0.004 | 0.207 | |
| getNumberOfEmptyLines | 0.22 | 0.00 | 0.22 | |
| getPaletteForLabels | 0.192 | 0.000 | 0.193 | |
| getPaletteForLabels_HC | 0.196 | 0.000 | 0.196 | |
| getPaletteForReplicates | 0.708 | 0.004 | 0.713 | |
| getPaletteForReplicates_HC | 0.196 | 0.000 | 0.198 | |
| getPourcentageOfMV | 0.204 | 0.004 | 0.211 | |
| getProcessingInfo | 0.192 | 0.000 | 0.195 | |
| getProteinsStats | 0.228 | 0.004 | 0.234 | |
| getQuantile4Imp | 0.192 | 0.004 | 0.198 | |
| group_GO | 10.832 | 0.184 | 11.265 | |
| heatmap.DAPAR | 0.560 | 0.008 | 0.570 | |
| heatmapD | 0.924 | 0.016 | 0.943 | |
| impute.detQuant | 0.412 | 0.168 | 0.583 | |
| impute.pa2 | 0.276 | 0.000 | 0.277 | |
| limmaCompleteTest | 0.324 | 0.008 | 0.333 | |
| mvFilter | 0.260 | 0.000 | 0.258 | |
| mvFilterFromIndices | 0.220 | 0.004 | 0.225 | |
| mvFilterGetIndices | 0.232 | 0.040 | 0.272 | |
| mvHisto | 0.220 | 0.004 | 0.225 | |
| mvHisto_HC | 0.232 | 0.004 | 0.236 | |
| mvImage | 2.656 | 0.000 | 2.658 | |
| mvImputation | 0.200 | 0.004 | 0.207 | |
| mvPerLinesHisto | 0.280 | 0.004 | 0.286 | |
| mvPerLinesHistoPerCondition | 0.224 | 0.004 | 0.226 | |
| mvPerLinesHistoPerCondition_HC | 0.264 | 0.004 | 0.269 | |
| mvPerLinesHisto_HC | 0.244 | 0.016 | 0.262 | |
| mvTypePlot | 1.340 | 0.004 | 1.344 | |
| my_hc_ExportMenu | 0.112 | 0.004 | 0.118 | |
| my_hc_chart | 0.136 | 0.032 | 0.170 | |
| nonzero | 0.136 | 0.000 | 0.137 | |
| normalizeD | 0.256 | 0.012 | 0.268 | |
| normalizeD2 | 0.236 | 0.012 | 0.250 | |
| pepAgregate | 0.268 | 0.008 | 0.276 | |
| proportionConRev_HC | 0.036 | 0.004 | 0.041 | |
| removeLines | 0.2 | 0.0 | 0.2 | |
| translatedRandomBeta | 0.004 | 0.000 | 0.004 | |
| violinPlotD | 1.720 | 0.012 | 1.920 | |
| wrapper.CVDistD | 2.852 | 0.000 | 2.855 | |
| wrapper.CVDistD_HC | 2.252 | 0.004 | 2.261 | |
| wrapper.boxPlotD | 0.228 | 0.000 | 0.228 | |
| wrapper.boxPlotD_HC | 1.016 | 0.008 | 1.024 | |
| wrapper.compareNormalizationD | 0.356 | 0.004 | 0.359 | |
| wrapper.compareNormalizationD_HC | 28.508 | 0.020 | 28.549 | |
| wrapper.corrMatrixD | 1.712 | 0.004 | 1.720 | |
| wrapper.corrMatrixD_HC | 0.352 | 0.004 | 0.356 | |
| wrapper.dapar.impute.mi | 25.444 | 0.032 | 25.502 | |
| wrapper.densityPlotD | 0.272 | 0.004 | 0.277 | |
| wrapper.densityPlotD_HC | 1.292 | 0.012 | 1.305 | |
| wrapper.diffAnaLimma | 0.228 | 0.000 | 0.230 | |
| wrapper.diffAnaWelch | 0.240 | 0.000 | 0.239 | |
| wrapper.heatmapD | 1.188 | 0.004 | 1.193 | |
| wrapper.impute.detQuant | 0.228 | 0.000 | 0.230 | |
| wrapper.impute.pa | 0.324 | 0.000 | 0.323 | |
| wrapper.impute.pa2 | 0.264 | 0.004 | 0.265 | |
| wrapper.mvHisto | 0.240 | 0.004 | 0.247 | |
| wrapper.mvHisto_HC | 0.188 | 0.000 | 0.190 | |
| wrapper.mvImage | 2.412 | 0.012 | 2.426 | |
| wrapper.mvImputation | 0.328 | 0.000 | 0.326 | |
| wrapper.mvPerLinesHisto | 0.300 | 0.004 | 0.307 | |
| wrapper.mvPerLinesHistoPerCondition | 0.268 | 0.000 | 0.268 | |
| wrapper.mvPerLinesHistoPerCondition_HC | 0.244 | 0.000 | 0.244 | |
| wrapper.mvPerLinesHisto_HC | 0.248 | 0.000 | 0.245 | |
| wrapper.mvTypePlot | 1.620 | 0.012 | 1.634 | |
| wrapper.normalizeD | 0.228 | 0.000 | 0.227 | |
| wrapper.normalizeD2 | 0.272 | 0.008 | 0.277 | |
| wrapper.violinPlotD | 1.256 | 0.008 | 1.263 | |
| wrapperCalibrationPlot | 0.224 | 0.000 | 0.223 | |
| writeMSnsetToExcel | 0 | 0 | 0 | |