Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:34:07 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DAPAR_1.16.11.tar.gz |
StartedAt: 2019-10-16 03:03:25 -0400 (Wed, 16 Oct 2019) |
EndedAt: 2019-10-16 03:13:39 -0400 (Wed, 16 Oct 2019) |
EllapsedTime: 614.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DAPAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DAPAR_1.16.11.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DAPAR.Rcheck' * using R version 3.6.1 (2019-07-05) * 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 '1.16.11' * 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 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 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 ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed wrapper.compareNormalizationD_HC 25.92 0.25 26.23 wrapper.dapar.impute.mi 16.48 0.06 16.55 CVDistD_HC 2.05 0.16 5.43 BuildColumnToProteinDataset_par 1.41 0.11 14.39 aggregateIterParallel 0.40 0.03 14.71 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed wrapper.compareNormalizationD_HC 22.54 0.21 22.77 wrapper.dapar.impute.mi 14.71 0.00 14.78 aggregateIter 4.74 0.47 5.20 BuildColumnToProteinDataset_par 1.33 0.08 14.01 aggregateIterParallel 0.58 0.03 18.15 * 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-3.9-bioc/meat/DAPAR.Rcheck/00check.log' for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DAPAR_1.16.11.tar.gz && rm -rf DAPAR.buildbin-libdir && mkdir DAPAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAPAR.buildbin-libdir DAPAR_1.16.11.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DAPAR_1.16.11.zip && rm DAPAR_1.16.11.tar.gz DAPAR_1.16.11.zip ### ############################################################################## ############################################################################## % 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 2377k 100 2377k 0 0 23.2M 0 --:--:-- --:--:-- --:--:-- 24.6M install for i386 * installing *source* package 'DAPAR' ... ** using staged installation ** 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 GetNbPeptidesUsed html GraphPepProt html LH0 html LH0.lm html LH1 html LH1.lm html StringBasedFiltering html StringBasedFiltering2 html addOriginOfValue html aggregateIter html aggregateIterParallel html aggregateMean html aggregateSum html aggregateTopn html barplotEnrichGO_HC html barplotGroupGO_HC html boxPlotD html boxPlotD_HC 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 finalizeAggregation html findMECBlock html formatLimmaResult html fudge2LRT html getIndicesConditions html getIndicesOfLinesToRemove html getListNbValuesInLines html getNumberOf html getNumberOfEmptyLines html getPourcentageOfMV html getProcessingInfo html getProteinsStats html getQuantile4Imp html getTextForAggregation html getTextForAnaDiff html getTextForFiltering html getTextForGOAnalysis html getTextForHypothesisTest html getTextForNewDataset html getTextForNormalization html getTextForpeptideImputation html getTextForproteinImputation html group_GO html hc_logFC_DensityPlot html hc_mvTypePlot2 html heatmap.DAPAR html heatmapD html heatmap_HC html histPValue_HC html impute.detQuant html impute.pa2 html inner.aggregate.iter html inner.aggregate.topn html inner.mean html inner.sum 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 mvPerLinesHisto html mvPerLinesHistoPerCondition html mvPerLinesHistoPerCondition_HC html mvPerLinesHisto_HC html my_hc_ExportMenu html my_hc_chart html nonzero html pepa.test html plotPCA_Eigen html plotPCA_Eigen_hc html plotPCA_Ind html plotPCA_Var html proportionConRev_HC html rbindMSnset html reIntroduceMEC html readExcel html removeLines html rep_col html rep_row 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.compareNormalizationD html wrapper.compareNormalizationD_HC html wrapper.corrMatrixD html wrapper.corrMatrixD_HC html wrapper.dapar.impute.mi html wrapper.hc_mvTypePlot2 html wrapper.heatmapD html wrapper.impute.KNN html wrapper.impute.detQuant html wrapper.impute.fixedValue html wrapper.impute.mle html wrapper.impute.pa html wrapper.impute.pa2 html wrapper.impute.slsa html wrapper.mvHisto html wrapper.mvHisto_HC html wrapper.mvImage html wrapper.mvPerLinesHisto html wrapper.mvPerLinesHistoPerCondition html wrapper.mvPerLinesHistoPerCondition_HC html wrapper.mvPerLinesHisto_HC html wrapper.normalizeD html wrapper.pca html wrapper.t_test_Complete html wrapperCalibrationPlot html writeMSnsetToCSV html writeMSnsetToExcel html ** 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 install for x64 * installing *source* package 'DAPAR' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'DAPAR' as DAPAR_1.16.11.zip * DONE (DAPAR) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'DAPAR' successfully unpacked and MD5 sums checked
DAPAR.Rcheck/tests_i386/testthat.Rout R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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) 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 10.60 1.06 14.73 |
DAPAR.Rcheck/tests_x64/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-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) 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 11.81 0.70 12.51 |
DAPAR.Rcheck/examples_i386/DAPAR-Ex.timings
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DAPAR.Rcheck/examples_x64/DAPAR-Ex.timings
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