Samuel Wieczorek
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/DAPAR |
| Branch: RELEASE_3_10 |
| Last Commit: c9ebdff |
| Last Changed Date: 2020-01-24 02:48:40 -0400 (Fri, 24 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:42:30 -0400 (Wed, 15 Apr 2020).
| Package 406/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DAPAR 1.18.5 Samuel Wieczorek
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: DAPAR |
| Version: 1.18.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DAPAR_1.18.5.tar.gz |
| StartedAt: 2020-04-15 01:36:52 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:48:06 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 673.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DAPAR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DAPAR_1.18.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/DAPAR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.18.5’
* 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 ... NOTE
Package in Depends field not imported from: ‘igraph’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
boxPlotD: warning in axis(side = 1, at = 1:ncol(qData), label =
legend): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = labCol, las = 2, line =
-0.5 + offsetCol, tick = 0, cex.axis = cexCol, hadj = NA, padj = 0):
partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(1, 1:nc, label = rep("", nc), las = 2,
tick = 0): partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = labRow, las = 5, line =
-0.5 + offsetRow, tick = 0, cex.axis = cexRow, hadj = 0, padj = NA):
partial argument match of 'label' to 'labels'
heatmap.DAPAR: warning in axis(4, iy, label = rep("", nr), las = 2,
line = -0.5, tick = 0): partial argument match of 'label' to 'labels'
violinPlotD: warning in axis(side = 1, at = 1:ncol(qData), label = if
(is.vector(legend)) {: partial argument match of 'label' to 'labels'
violinPlotD: warning in legend: partial argument match of 'label' to
'labels'
violinPlotD: warning in } else {: partial argument match of 'label' to
'labels'
violinPlotD: warning in legend[, i]: partial argument match of 'label'
to 'labels'
violinPlotD: warning in }, line = 2 * i - 1): partial argument match of
'label' to 'labels'
aggregateIterParallel: no visible binding for global variable ‘cond’
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’
display.CC.visNet: no visible binding for global variable
‘layout_nicely’
getTextForGOAnalysis: no visible binding for global variable
‘textGOParams’
getTextForGOAnalysis: no visible binding for global variable ‘input’
Undefined global functions or variables:
cond g input layout_nicely textGOParams x y
* checking Rd files ... NOTE
prepare_Rd: plotJitter_rCharts.Rd:20-23: Dropping empty section \examples
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
wrapper.compareNormalizationD_HC 147.125 31.986 175.819
wrapper.dapar.impute.mi 14.177 1.281 15.375
compareNormalizationD_HC 10.827 2.302 12.850
CVDistD 7.243 5.239 11.824
wrapper.CVDistD 7.084 5.093 11.536
wrapper.CVDistD_HC 5.489 2.977 8.104
wrapper.hc_mvTypePlot2 6.998 1.360 8.213
CVDistD_HC 5.355 2.767 7.882
hc_mvTypePlot2 6.676 1.308 7.837
buildGraph 6.143 1.273 7.457
densityPlotD_HC 5.811 1.244 6.922
display.CC.visNet 4.660 1.100 5.795
boxPlotD_HC 4.429 0.948 5.290
aggregateIterParallel 3.582 1.697 4.162
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/DAPAR.Rcheck/00check.log’
for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘DAPAR’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (DAPAR)
DAPAR.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Loading required package: foreach
Loading required package: parallel
Loading required package: doParallel
Loading required package: iterators
Loading required package: igraph
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
>
> test_check("DAPAR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
14.625 1.187 16.103
DAPAR.Rcheck/DAPAR-Ex.timings
| name | user | system | elapsed | |
| BuildAdjacencyMatrix | 1.246 | 0.188 | 1.435 | |
| BuildColumnToProteinDataset | 3.309 | 0.392 | 3.703 | |
| BuildColumnToProteinDataset_par | 0.001 | 0.000 | 0.001 | |
| CVDistD | 7.243 | 5.239 | 11.824 | |
| CVDistD_HC | 5.355 | 2.767 | 7.882 | |
| CountPep | 0.607 | 0.169 | 0.778 | |
| GetDetailedNbPeptides | 0.986 | 0.039 | 1.031 | |
| Get_AllComparisons | 0.668 | 0.041 | 0.710 | |
| GraphPepProt | 0.483 | 0.041 | 0.528 | |
| NumericalFiltering | 0.419 | 0.027 | 0.446 | |
| NumericalgetIndicesOfLinesToRemove | 0.326 | 0.004 | 0.335 | |
| StringBasedFiltering | 0.541 | 0.058 | 0.602 | |
| StringBasedFiltering2 | 0.405 | 0.018 | 0.425 | |
| addOriginOfValue | 0.265 | 0.004 | 0.269 | |
| aggregateIter | 3.866 | 0.310 | 4.223 | |
| aggregateIterParallel | 3.582 | 1.697 | 4.162 | |
| aggregateMean | 0.637 | 0.041 | 0.689 | |
| aggregateSum | 1.089 | 0.025 | 1.128 | |
| aggregateTopn | 2.618 | 0.205 | 2.828 | |
| boxPlotD | 0.325 | 0.014 | 0.340 | |
| boxPlotD_HC | 4.429 | 0.948 | 5.290 | |
| buildGraph | 6.143 | 1.273 | 7.457 | |
| check.conditions | 0.288 | 0.003 | 0.294 | |
| check.design | 0.313 | 0.003 | 0.320 | |
| compareNormalizationD | 0.432 | 0.024 | 0.458 | |
| compareNormalizationD_HC | 10.827 | 2.302 | 12.850 | |
| compute.t.tests | 1.874 | 0.311 | 2.149 | |
| corrMatrixD | 0.805 | 0.048 | 0.857 | |
| corrMatrixD_HC | 0.550 | 0.079 | 0.639 | |
| createMSnset | 1.285 | 0.083 | 1.376 | |
| deleteLinesFromIndices | 0.385 | 0.013 | 0.397 | |
| densityPlotD | 0.310 | 0.008 | 0.322 | |
| densityPlotD_HC | 5.811 | 1.244 | 6.922 | |
| diffAnaComputeFDR | 0.383 | 0.012 | 0.396 | |
| diffAnaGetSignificant | 0.713 | 0.039 | 0.754 | |
| diffAnaSave | 0.664 | 0.040 | 0.701 | |
| diffAnaVolcanoplot | 0.415 | 0.014 | 0.429 | |
| diffAnaVolcanoplot_rCharts | 0.000 | 0.000 | 0.001 | |
| display.CC.visNet | 4.660 | 1.100 | 5.795 | |
| enrich_GO | 0.000 | 0.000 | 0.001 | |
| findMECBlock | 0.748 | 0.148 | 0.878 | |
| formatLimmaResult | 0.417 | 0.015 | 0.431 | |
| get.pep.prot.cc | 1.186 | 0.048 | 1.236 | |
| getIndicesConditions | 0.286 | 0.003 | 0.289 | |
| getIndicesOfLinesToRemove | 0.319 | 0.003 | 0.323 | |
| getListNbValuesInLines | 0.368 | 0.010 | 0.377 | |
| getNumberOf | 0.272 | 0.004 | 0.280 | |
| getNumberOfEmptyLines | 0.332 | 0.008 | 0.340 | |
| getPourcentageOfMV | 0.323 | 0.008 | 0.331 | |
| getProcessingInfo | 0.283 | 0.003 | 0.287 | |
| getProteinsStats | 0.389 | 0.025 | 0.416 | |
| getQuantile4Imp | 0.289 | 0.007 | 0.297 | |
| getTextForAggregation | 0.000 | 0.000 | 0.001 | |
| getTextForAnaDiff | 0.001 | 0.000 | 0.001 | |
| getTextForFiltering | 0.001 | 0.000 | 0.001 | |
| getTextForGOAnalysis | 0.000 | 0.001 | 0.001 | |
| getTextForHypothesisTest | 0.001 | 0.000 | 0.001 | |
| getTextForNewDataset | 0.003 | 0.000 | 0.003 | |
| getTextForNormalization | 0 | 0 | 0 | |
| getTextForpeptideImputation | 0.000 | 0.000 | 0.001 | |
| getTextForproteinImputation | 0.001 | 0.000 | 0.001 | |
| group_GO | 0.000 | 0.000 | 0.001 | |
| hc_logFC_DensityPlot | 1.346 | 0.268 | 1.592 | |
| hc_mvTypePlot2 | 6.676 | 1.308 | 7.837 | |
| heatmap.DAPAR | 0.586 | 0.025 | 0.618 | |
| heatmapD | 0 | 0 | 0 | |
| histPValue_HC | 0.558 | 0.068 | 0.634 | |
| impute.detQuant | 0.830 | 0.491 | 1.317 | |
| impute.pa2 | 0.501 | 0.178 | 0.660 | |
| is.MV | 0.841 | 0.526 | 1.364 | |
| is.OfType | 0.906 | 0.565 | 1.465 | |
| limmaCompleteTest | 0.429 | 0.019 | 0.449 | |
| make.contrast | 0.288 | 0.006 | 0.294 | |
| make.design.1 | 0.307 | 0.005 | 0.314 | |
| make.design.2 | 0 | 0 | 0 | |
| make.design.3 | 0.283 | 0.005 | 0.288 | |
| make.design | 0.302 | 0.003 | 0.306 | |
| mvFilter | 0.426 | 0.018 | 0.447 | |
| mvFilterFromIndices | 0.351 | 0.008 | 0.362 | |
| mvFilterGetIndices | 0.476 | 0.132 | 0.607 | |
| mvHisto | 0.270 | 0.006 | 0.277 | |
| mvHisto_HC | 0.408 | 0.073 | 0.484 | |
| mvImage | 4.398 | 0.257 | 4.634 | |
| mvPerLinesHisto | 0.394 | 0.016 | 0.421 | |
| mvPerLinesHistoPerCondition | 0.337 | 0.006 | 0.347 | |
| mvPerLinesHistoPerCondition_HC | 0.368 | 0.049 | 0.424 | |
| mvPerLinesHisto_HC | 0.390 | 0.058 | 0.455 | |
| my_hc_ExportMenu | 0.176 | 0.130 | 0.314 | |
| my_hc_chart | 0.164 | 0.138 | 0.307 | |
| nonzero | 0.020 | 0.001 | 0.020 | |
| plotJitter | 1.187 | 0.050 | 1.245 | |
| plotPCA_Eigen | 0.321 | 0.004 | 0.328 | |
| plotPCA_Eigen_hc | 0.313 | 0.004 | 0.318 | |
| plotPCA_Ind | 0.308 | 0.003 | 0.314 | |
| plotPCA_Var | 0.274 | 0.004 | 0.278 | |
| proportionConRev_HC | 0.065 | 0.044 | 0.116 | |
| rbindMSnset | 0.405 | 0.019 | 0.427 | |
| reIntroduceMEC | 0.527 | 0.021 | 0.548 | |
| removeLines | 0.315 | 0.006 | 0.327 | |
| saveParameters | 0.318 | 0.005 | 0.322 | |
| setMEC | 0.497 | 0.019 | 0.518 | |
| test.design | 0.337 | 0.005 | 0.346 | |
| translatedRandomBeta | 0.005 | 0.005 | 0.009 | |
| violinPlotD | 1.030 | 0.033 | 1.065 | |
| wrapper.CVDistD | 7.084 | 5.093 | 11.536 | |
| wrapper.CVDistD_HC | 5.489 | 2.977 | 8.104 | |
| wrapper.compareNormalizationD | 0.492 | 0.025 | 0.528 | |
| wrapper.compareNormalizationD_HC | 147.125 | 31.986 | 175.819 | |
| wrapper.corrMatrixD | 0.868 | 0.062 | 0.930 | |
| wrapper.corrMatrixD_HC | 0.493 | 0.074 | 0.575 | |
| wrapper.dapar.impute.mi | 14.177 | 1.281 | 15.375 | |
| wrapper.hc_mvTypePlot2 | 6.998 | 1.360 | 8.213 | |
| wrapper.heatmapD | 0.001 | 0.000 | 0.001 | |
| wrapper.impute.KNN | 0.359 | 0.008 | 0.369 | |
| wrapper.impute.detQuant | 0.314 | 0.007 | 0.326 | |
| wrapper.impute.fixedValue | 0.332 | 0.008 | 0.345 | |
| wrapper.impute.mle | 0.349 | 0.014 | 0.363 | |
| wrapper.impute.pa | 0.566 | 0.187 | 0.731 | |
| wrapper.impute.pa2 | 0.553 | 0.202 | 0.733 | |
| wrapper.impute.slsa | 2.837 | 0.196 | 3.024 | |
| wrapper.mvHisto | 0.297 | 0.004 | 0.305 | |
| wrapper.mvHisto_HC | 0.346 | 0.056 | 0.406 | |
| wrapper.mvImage | 0.828 | 0.043 | 0.874 | |
| wrapper.mvPerLinesHisto | 0.372 | 0.005 | 0.405 | |
| wrapper.mvPerLinesHistoPerCondition | 0.370 | 0.004 | 0.477 | |
| wrapper.mvPerLinesHistoPerCondition_HC | 0.481 | 0.049 | 0.847 | |
| wrapper.mvPerLinesHisto_HC | 0.401 | 0.004 | 0.681 | |
| wrapper.normalizeD | 0.405 | 0.007 | 0.668 | |
| wrapper.pca | 0.513 | 0.022 | 0.867 | |
| wrapper.t_test_Complete | 0.445 | 0.011 | 0.718 | |
| wrapperCalibrationPlot | 0.469 | 0.012 | 0.765 | |
| writeMSnsetToCSV | 0.000 | 0.000 | 0.001 | |
| writeMSnsetToExcel | 0 | 0 | 0 | |