Samuel Wieczorek
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/DAPAR |
| Branch: RELEASE_3_9 |
| Last Commit: 391e26f |
| Last Changed Date: 2019-10-07 23:25:56 -0400 (Mon, 07 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:07:31 -0400 (Wed, 16 Oct 2019).
| Package 388/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| DAPAR 1.16.11 Samuel Wieczorek
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: DAPAR |
| Version: 1.16.11 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DAPAR_1.16.11.tar.gz |
| StartedAt: 2019-10-16 00:57:29 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:04:32 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 422.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DAPAR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings DAPAR_1.16.11.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.11’
* 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
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’
boxPlotD: no visible binding for global variable ‘conds’
densityPlotD: no visible binding for global variable ‘conds’
diffAnaVolcanoplot_rCharts: no visible binding for global variable
‘swap’
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’
heatmap_HC: no visible binding for global variable ‘Exp1_R25_pept’
heatmap_HC: no visible binding for global variable ‘condition’
heatmap_HC: no visible binding for global variable ‘id’
heatmap_HC: no visible binding for global variable ‘value’
Undefined global functions or variables:
Exp1_R25_pept cond condition conds g id input swap textGOParams value
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 39.506 9.151 52.212
wrapper.dapar.impute.mi 15.239 0.363 16.265
CVDistD 4.947 1.982 7.457
wrapper.CVDistD 4.891 1.978 7.487
* 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-3.9-bioc/meat/DAPAR.Rcheck/00check.log’
for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
Loading required package: foreach
Loading required package: parallel
Loading required package: doParallel
Loading required package: iterators
>
> test_check("DAPAR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 3 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
9.551 0.423 9.942
DAPAR.Rcheck/DAPAR-Ex.timings
| name | user | system | elapsed | |
| BuildAdjacencyMatrix | 1.279 | 0.072 | 1.461 | |
| BuildColumnToProteinDataset | 1.179 | 0.068 | 1.262 | |
| BuildColumnToProteinDataset_par | 2.358 | 0.938 | 1.926 | |
| CVDistD | 4.947 | 1.982 | 7.457 | |
| CVDistD_HC | 3.041 | 1.170 | 4.747 | |
| CountPep | 0.572 | 0.079 | 0.667 | |
| GraphPepProt | 0.486 | 0.032 | 0.518 | |
| StringBasedFiltering | 0.726 | 0.015 | 0.770 | |
| StringBasedFiltering2 | 0.479 | 0.004 | 0.492 | |
| addOriginOfValue | 0.423 | 0.000 | 0.431 | |
| aggregateIter | 2.882 | 0.118 | 3.064 | |
| aggregateIterParallel | 3.067 | 1.047 | 2.541 | |
| aggregateMean | 0.486 | 0.035 | 0.526 | |
| aggregateSum | 0.530 | 0.000 | 0.554 | |
| aggregateTopn | 2.731 | 0.147 | 2.917 | |
| boxPlotD | 0.431 | 0.002 | 0.451 | |
| boxPlotD_HC | 2.057 | 0.251 | 2.471 | |
| check.conditions | 0.371 | 0.004 | 0.374 | |
| check.design | 0.402 | 0.000 | 0.403 | |
| compareNormalizationD | 0.632 | 0.020 | 0.652 | |
| compareNormalizationD_HC | 3.094 | 0.684 | 3.977 | |
| compute.t.tests | 1.459 | 0.141 | 1.738 | |
| corrMatrixD | 0.808 | 0.024 | 0.833 | |
| corrMatrixD_HC | 0.518 | 0.019 | 0.549 | |
| createMSnset | 0.903 | 0.048 | 1.006 | |
| deleteLinesFromIndices | 0.455 | 0.011 | 0.470 | |
| densityPlotD | 0.508 | 0.003 | 0.547 | |
| densityPlotD_HC | 1.671 | 0.359 | 2.229 | |
| diffAnaComputeFDR | 0.469 | 0.000 | 0.474 | |
| diffAnaGetSignificant | 0.747 | 0.019 | 0.803 | |
| diffAnaSave | 0.706 | 0.023 | 0.748 | |
| diffAnaVolcanoplot | 0.445 | 0.003 | 0.452 | |
| diffAnaVolcanoplot_rCharts | 0 | 0 | 0 | |
| enrich_GO | 0.000 | 0.000 | 0.001 | |
| finalizeAggregation | 0.528 | 0.000 | 0.531 | |
| findMECBlock | 0.751 | 0.048 | 0.798 | |
| formatLimmaResult | 0.356 | 0.000 | 0.354 | |
| getIndicesConditions | 0.216 | 0.000 | 0.216 | |
| getIndicesOfLinesToRemove | 0.256 | 0.000 | 0.256 | |
| getListNbValuesInLines | 0.483 | 0.000 | 0.482 | |
| getNumberOf | 0.356 | 0.008 | 0.369 | |
| getNumberOfEmptyLines | 0.429 | 0.004 | 0.432 | |
| getPourcentageOfMV | 0.388 | 0.004 | 0.391 | |
| getProcessingInfo | 0.392 | 0.004 | 0.396 | |
| getProteinsStats | 0.491 | 0.016 | 0.510 | |
| getQuantile4Imp | 0.425 | 0.000 | 0.425 | |
| getTextForAggregation | 0.001 | 0.000 | 0.000 | |
| getTextForAnaDiff | 0.001 | 0.000 | 0.001 | |
| getTextForFiltering | 0.000 | 0.000 | 0.001 | |
| getTextForGOAnalysis | 0.001 | 0.000 | 0.000 | |
| getTextForHypothesisTest | 0.000 | 0.000 | 0.001 | |
| getTextForNewDataset | 0.003 | 0.000 | 0.003 | |
| getTextForNormalization | 0.000 | 0.000 | 0.001 | |
| getTextForpeptideImputation | 0.001 | 0.000 | 0.001 | |
| getTextForproteinImputation | 0.001 | 0.000 | 0.000 | |
| group_GO | 0 | 0 | 0 | |
| hc_logFC_DensityPlot | 0.763 | 0.117 | 0.858 | |
| hc_mvTypePlot2 | 2.685 | 0.391 | 3.202 | |
| heatmap.DAPAR | 0.789 | 0.008 | 0.804 | |
| heatmapD | 0.001 | 0.000 | 0.000 | |
| heatmap_HC | 0.943 | 0.115 | 1.082 | |
| histPValue_HC | 0.735 | 0.020 | 0.756 | |
| impute.detQuant | 0.771 | 0.208 | 1.011 | |
| impute.pa2 | 0.554 | 0.080 | 0.657 | |
| is.MV | 0.660 | 0.277 | 0.970 | |
| is.OfType | 0.708 | 0.246 | 1.038 | |
| limmaCompleteTest | 0.519 | 0.011 | 0.531 | |
| make.contrast | 0.386 | 0.000 | 0.386 | |
| make.design.1 | 0.387 | 0.004 | 0.391 | |
| make.design.2 | 0 | 0 | 0 | |
| make.design.3 | 0 | 0 | 0 | |
| make.design | 0.41 | 0.00 | 0.41 | |
| mvFilter | 0.470 | 0.011 | 0.482 | |
| mvFilterFromIndices | 0.409 | 0.009 | 0.427 | |
| mvFilterGetIndices | 0.555 | 0.051 | 0.608 | |
| mvHisto | 0.402 | 0.004 | 0.406 | |
| mvHisto_HC | 0.456 | 0.017 | 0.478 | |
| mvImage | 3.484 | 0.137 | 3.838 | |
| mvPerLinesHisto | 0.510 | 0.000 | 0.511 | |
| mvPerLinesHistoPerCondition | 0.434 | 0.000 | 0.433 | |
| mvPerLinesHistoPerCondition_HC | 0.463 | 0.015 | 0.498 | |
| mvPerLinesHisto_HC | 0.466 | 0.016 | 0.486 | |
| my_hc_ExportMenu | 0.121 | 0.060 | 0.198 | |
| my_hc_chart | 0.137 | 0.036 | 0.173 | |
| nonzero | 0.022 | 0.000 | 0.022 | |
| plotPCA_Eigen | 0.428 | 0.000 | 0.432 | |
| plotPCA_Eigen_hc | 0.373 | 0.003 | 0.377 | |
| plotPCA_Ind | 0.361 | 0.000 | 0.360 | |
| plotPCA_Var | 0.344 | 0.000 | 0.346 | |
| proportionConRev_HC | 0.050 | 0.016 | 0.066 | |
| rbindMSnset | 0.391 | 0.007 | 0.431 | |
| reIntroduceMEC | 0.603 | 0.004 | 0.624 | |
| removeLines | 0.436 | 0.008 | 0.446 | |
| rep_col | 0 | 0 | 0 | |
| rep_row | 0 | 0 | 0 | |
| saveParameters | 0.391 | 0.000 | 0.393 | |
| setMEC | 1.131 | 0.003 | 1.136 | |
| test.design | 0.399 | 0.008 | 0.406 | |
| translatedRandomBeta | 0.000 | 0.006 | 0.006 | |
| violinPlotD | 1.233 | 0.013 | 1.243 | |
| wrapper.CVDistD | 4.891 | 1.978 | 7.487 | |
| wrapper.CVDistD_HC | 2.920 | 1.089 | 4.535 | |
| wrapper.compareNormalizationD | 0.617 | 0.003 | 0.626 | |
| wrapper.compareNormalizationD_HC | 39.506 | 9.151 | 52.212 | |
| wrapper.corrMatrixD | 0.822 | 0.017 | 0.852 | |
| wrapper.corrMatrixD_HC | 0.477 | 0.015 | 0.499 | |
| wrapper.dapar.impute.mi | 15.239 | 0.363 | 16.265 | |
| wrapper.hc_mvTypePlot2 | 2.508 | 0.434 | 2.904 | |
| wrapper.heatmapD | 0 | 0 | 0 | |
| wrapper.impute.KNN | 0.254 | 0.003 | 0.257 | |
| wrapper.impute.detQuant | 0.255 | 0.000 | 0.255 | |
| wrapper.impute.fixedValue | 0.248 | 0.000 | 0.247 | |
| wrapper.impute.mle | 0.256 | 0.020 | 0.275 | |
| wrapper.impute.pa | 0.389 | 0.042 | 0.415 | |
| wrapper.impute.pa2 | 0.309 | 0.076 | 0.367 | |
| wrapper.impute.slsa | 2.334 | 0.095 | 2.423 | |
| wrapper.mvHisto | 0.4 | 0.0 | 0.4 | |
| wrapper.mvHisto_HC | 0.446 | 0.015 | 0.461 | |
| wrapper.mvImage | 0.808 | 0.012 | 0.819 | |
| wrapper.mvPerLinesHisto | 0.433 | 0.000 | 0.433 | |
| wrapper.mvPerLinesHistoPerCondition | 0.248 | 0.004 | 0.251 | |
| wrapper.mvPerLinesHistoPerCondition_HC | 0.307 | 0.019 | 0.325 | |
| wrapper.mvPerLinesHisto_HC | 0.250 | 0.004 | 0.255 | |
| wrapper.normalizeD | 0.238 | 0.003 | 0.240 | |
| wrapper.pca | 0.216 | 0.000 | 0.215 | |
| wrapper.t_test_Complete | 0.305 | 0.000 | 0.304 | |
| wrapperCalibrationPlot | 0.275 | 0.007 | 0.280 | |
| writeMSnsetToCSV | 0 | 0 | 0 | |
| writeMSnsetToExcel | 0 | 0 | 0 | |