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 08:28:04 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DAPAR_1.12.11.tar.gz |
| StartedAt: 2018-10-15 23:38:46 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:43:53 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 306.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DAPAR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings DAPAR_1.12.11.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/DAPAR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.12.11’
* 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 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wrapper.compareNormalizationD_HC 39.400 1.780 41.180
wrapper.dapar.impute.mi 10.180 0.156 10.378
wrapper.CVDistD 6.016 0.284 6.358
* 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 NOTE
See
‘/home/biocbuild/bbs-3.7-bioc/meat/DAPAR.Rcheck/00check.log’
for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’ * installing *source* package ‘DAPAR’ ... ** R ** inst ** byte-compile and prepare 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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")
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
9.972 0.260 10.731
DAPAR.Rcheck/DAPAR-Ex.timings
| name | user | system | elapsed | |
| BuildAdjacencyMatrix | 0.932 | 0.048 | 0.986 | |
| BuildColumnToProteinDataset | 0.680 | 0.012 | 0.693 | |
| BuildColumnToProteinDataset_par | 1.160 | 0.480 | 0.902 | |
| CVDistD | 4.228 | 0.064 | 4.292 | |
| CVDistD_HC | 3.024 | 0.068 | 3.240 | |
| CountPep | 0.404 | 0.044 | 0.448 | |
| GraphPepProt | 0.308 | 0.020 | 0.327 | |
| MeanPeptides | 0.308 | 0.008 | 0.315 | |
| StringBasedFiltering | 0.408 | 0.008 | 0.414 | |
| StringBasedFiltering2 | 0.308 | 0.004 | 0.311 | |
| SumPeptides | 0.308 | 0.012 | 0.320 | |
| TopnPeptides | 1.864 | 0.020 | 1.889 | |
| addOriginOfValue | 0.220 | 0.000 | 0.223 | |
| boxPlotD | 0.244 | 0.000 | 0.247 | |
| boxPlotD_HC | 1.072 | 0.012 | 1.085 | |
| buildLogText | 0.004 | 0.000 | 0.002 | |
| check.conditions | 0.352 | 0.004 | 0.357 | |
| check.design | 0.236 | 0.000 | 0.237 | |
| compareNormalizationD | 0.376 | 0.000 | 0.378 | |
| compareNormalizationD_HC | 2.328 | 0.004 | 2.334 | |
| compute.t.tests | 0.536 | 0.004 | 0.543 | |
| corrMatrixD | 0.640 | 0.004 | 0.646 | |
| corrMatrixD_HC | 0.312 | 0.004 | 0.315 | |
| createMSnset | 0.628 | 0.004 | 0.667 | |
| deleteLinesFromIndices | 0.268 | 0.000 | 0.265 | |
| densityPlotD | 0.284 | 0.000 | 0.282 | |
| densityPlotD_HC | 1.428 | 0.008 | 1.439 | |
| diffAnaComputeFDR | 0.260 | 0.000 | 0.261 | |
| diffAnaGetSignificant | 0.496 | 0.000 | 0.494 | |
| diffAnaSave | 0.920 | 0.000 | 0.922 | |
| diffAnaVolcanoplot | 0.248 | 0.000 | 0.249 | |
| diffAnaVolcanoplot_rCharts | 0 | 0 | 0 | |
| enrich_GO | 0 | 0 | 0 | |
| findMECBlock | 0.224 | 0.000 | 0.225 | |
| formatLimmaResult | 0.312 | 0.000 | 0.311 | |
| getIndicesConditions | 0.232 | 0.000 | 0.230 | |
| getIndicesOfLinesToRemove | 0.232 | 0.004 | 0.235 | |
| getListNbValuesInLines | 0.232 | 0.004 | 0.234 | |
| getNumberOf | 0.228 | 0.004 | 0.231 | |
| getNumberOfEmptyLines | 0.232 | 0.004 | 0.237 | |
| getPaletteForLabels | 0.208 | 0.000 | 0.209 | |
| getPaletteForLabels_HC | 0.208 | 0.004 | 0.212 | |
| getPaletteForReplicates | 0.212 | 0.000 | 0.212 | |
| getPaletteForReplicates_HC | 0.208 | 0.000 | 0.208 | |
| getPourcentageOfMV | 0.232 | 0.012 | 0.243 | |
| getProcessingInfo | 0.208 | 0.000 | 0.211 | |
| getProteinsStats | 0.248 | 0.012 | 0.264 | |
| getQuantile4Imp | 0.208 | 0.004 | 0.212 | |
| getTextForAggregation | 0.000 | 0.000 | 0.001 | |
| getTextForAnaDiff | 0.004 | 0.000 | 0.002 | |
| getTextForFiltering | 0.000 | 0.000 | 0.001 | |
| getTextForGOAnalysis | 0 | 0 | 0 | |
| getTextForImputation | 0.004 | 0.000 | 0.003 | |
| getTextForNewDataset | 0.000 | 0.000 | 0.001 | |
| getTextForNormalization | 0.004 | 0.000 | 0.002 | |
| group_GO | 0.000 | 0.000 | 0.001 | |
| hc_FC_DensityPlot | 0.452 | 0.000 | 0.451 | |
| hc_mvTypePlot2 | 2.372 | 0.004 | 2.376 | |
| heatmap.DAPAR | 0.440 | 0.004 | 0.443 | |
| heatmapD | 0.740 | 0.004 | 0.742 | |
| impute.detQuant | 0.380 | 0.168 | 0.549 | |
| impute.pa2 | 0.344 | 0.004 | 0.351 | |
| is.MV | 0.360 | 0.148 | 0.511 | |
| is.OfType | 0.336 | 0.176 | 0.514 | |
| limmaCompleteTest | 0.312 | 0.000 | 0.313 | |
| make.contrast | 0.220 | 0.000 | 0.223 | |
| make.design.1 | 0.232 | 0.004 | 0.237 | |
| make.design.2 | 0 | 0 | 0 | |
| make.design.3 | 0.000 | 0.000 | 0.001 | |
| make.design | 0.244 | 0.000 | 0.241 | |
| mvFilter | 0.308 | 0.000 | 0.307 | |
| mvFilterFromIndices | 0.240 | 0.000 | 0.241 | |
| mvFilterGetIndices | 0.272 | 0.044 | 0.317 | |
| mvHisto | 0.260 | 0.004 | 0.264 | |
| mvHisto_HC | 0.252 | 0.000 | 0.252 | |
| mvImage | 2.392 | 0.012 | 2.408 | |
| mvImputation | 0.212 | 0.008 | 0.220 | |
| mvPerLinesHisto | 0.296 | 0.008 | 0.302 | |
| mvPerLinesHistoPerCondition | 0.236 | 0.000 | 0.236 | |
| mvPerLinesHistoPerCondition_HC | 0.296 | 0.004 | 0.297 | |
| mvPerLinesHisto_HC | 0.252 | 0.008 | 0.260 | |
| mvTypePlot | 1.196 | 0.004 | 1.200 | |
| my_hc_ExportMenu | 0.084 | 0.012 | 0.108 | |
| my_hc_chart | 0.092 | 0.004 | 0.097 | |
| nonzero | 0.016 | 0.000 | 0.015 | |
| normalizeD | 0.252 | 0.016 | 0.271 | |
| pepAgregate | 0.320 | 0.000 | 0.323 | |
| proportionConRev_HC | 0.032 | 0.004 | 0.037 | |
| rbindMSnset | 0.244 | 0.000 | 0.264 | |
| reIntroduceMEC | 0.396 | 0.000 | 0.397 | |
| removeLines | 0.224 | 0.004 | 0.226 | |
| saveParameters | 0.232 | 0.000 | 0.234 | |
| setMEC | 0.336 | 0.004 | 0.344 | |
| test.design | 0.224 | 0.000 | 0.225 | |
| translatedRandomBeta | 0.000 | 0.004 | 0.003 | |
| violinPlotD | 1.204 | 0.008 | 1.222 | |
| wrapper.CVDistD | 6.016 | 0.284 | 6.358 | |
| wrapper.CVDistD_HC | 3.124 | 0.152 | 3.283 | |
| wrapper.boxPlotD | 0.272 | 0.004 | 0.276 | |
| wrapper.boxPlotD_HC | 1.220 | 0.072 | 1.293 | |
| wrapper.compareNormalizationD | 0.340 | 0.008 | 0.348 | |
| wrapper.compareNormalizationD_HC | 39.40 | 1.78 | 41.18 | |
| wrapper.corrMatrixD | 0.624 | 0.040 | 0.671 | |
| wrapper.corrMatrixD_HC | 0.484 | 0.008 | 0.495 | |
| wrapper.dapar.impute.mi | 10.180 | 0.156 | 10.378 | |
| wrapper.densityPlotD | 0.252 | 0.000 | 0.252 | |
| wrapper.densityPlotD_HC | 1.376 | 0.068 | 1.436 | |
| wrapper.hc_mvTypePlot2 | 2.000 | 0.120 | 2.109 | |
| wrapper.heatmapD | 0.740 | 0.024 | 0.763 | |
| wrapper.impute.KNN | 0.356 | 0.000 | 0.355 | |
| wrapper.impute.detQuant | 0.276 | 0.000 | 0.276 | |
| wrapper.impute.fixedValue | 0.240 | 0.004 | 0.241 | |
| wrapper.impute.pa | 0.348 | 0.012 | 0.366 | |
| wrapper.impute.pa2 | 0.356 | 0.008 | 0.362 | |
| wrapper.impute.slsa | 1.720 | 0.044 | 1.760 | |
| wrapper.mvHisto | 0.248 | 0.004 | 0.251 | |
| wrapper.mvHisto_HC | 0.212 | 0.000 | 0.210 | |
| wrapper.mvImage | 2.832 | 0.116 | 2.965 | |
| wrapper.mvImputation | 0.244 | 0.000 | 0.243 | |
| wrapper.mvPerLinesHisto | 0.288 | 0.008 | 0.296 | |
| wrapper.mvPerLinesHistoPerCondition | 0.252 | 0.004 | 0.256 | |
| wrapper.mvPerLinesHistoPerCondition_HC | 0.284 | 0.000 | 0.285 | |
| wrapper.mvPerLinesHisto_HC | 0.240 | 0.004 | 0.244 | |
| wrapper.mvTypePlot | 1.356 | 0.028 | 1.390 | |
| wrapper.normalizeD | 0.272 | 0.004 | 0.276 | |
| wrapper.t_test_Complete | 0.360 | 0.000 | 0.359 | |
| wrapper.violinPlotD | 1.088 | 0.012 | 1.101 | |
| wrapperCalibrationPlot | 0.276 | 0.012 | 0.287 | |
| writeMSnsetToCSV | 0.000 | 0.000 | 0.001 | |
| writeMSnsetToExcel | 0 | 0 | 0 | |