Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:02 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the DAPAR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DAPAR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 442/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.24.8 (landing page) Samuel Wieczorek
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: DAPAR |
Version: 1.24.8 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DAPAR_1.24.8.tar.gz |
StartedAt: 2021-10-14 21:54:08 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:02:15 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 486.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DAPAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DAPAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings DAPAR_1.24.8.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DAPAR.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.24.8' * package encoding: UTF-8 * 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 ... NOTE Namespaces in Imports field not imported from: 'Cairo' 'DAPARdata' 'clusterProfiler' 'igraph' 'knitr' 'lattice' 'norm' 'pcaMethods' 'png' 'scales' 'siggenes' 'tidyverse' 'tmvtnorm' All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE heatmapForMissingValues: 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' heatmapForMissingValues: warning in axis(1, 1:nc, label = rep("", nc), las = 2, tick = 0): partial argument match of 'label' to 'labels' heatmapForMissingValues: 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' heatmapForMissingValues: warning in axis(4, iy, label = rep("", nr), las = 2, line = -0.5, tick = 0): partial argument match of 'label' to 'labels' GetIndices_MetacellFiltering: no visible global function definition for 'tsop' aggregateIterParallel: no visible binding for global variable 'cond' averageIntensities: no visible binding for global variable 'condition' averageIntensities: no visible binding for global variable 'feature' averageIntensities: no visible binding for global variable 'intensity' barplotEnrichGO_HC : <anonymous>: no visible global function definition for 'last' 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' enrich_GO: no visible global function definition for 'bitr' enrich_GO: no visible global function definition for 'enrichGO' getTextForGOAnalysis: no visible binding for global variable 'textGOParams' getTextForGOAnalysis: no visible binding for global variable 'input' group_GO: no visible global function definition for 'bitr' group_GO: no visible global function definition for 'groupGO' limmaCompleteTest: no visible binding for global variable 'A' limmaCompleteTest: no visible binding for global variable 'B' limmaCompleteTest: no visible binding for global variable 'P.Value' pepa.test: no visible global function definition for 'nodes<-' visualizeClusters: no visible global function definition for 'desc' visualizeClusters: no visible binding for global variable 'adjusted_pvalues' visualizeClusters: no visible binding for global variable 'Condition' visualizeClusters: no visible binding for global variable 'intensity' visualizeClusters: no visible binding for global variable 'FDR_threshold' visualizeClusters: no visible binding for global variable 'feature' wrapperClassic1wayAnova: no visible binding for global variable 'Pr(>F)1' wrapperClassic1wayAnova: no visible binding for global variable 'post_hoc' wrapperRunClustering: no visible global function definition for 'str_c' Undefined global functions or variables: A B Condition FDR_threshold P.Value Pr(>F)1 adjusted_pvalues bitr cond condition desc enrichGO feature g groupGO input intensity last layout_nicely nodes<- post_hoc str_c textGOParams tsop 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 (user + system) or elapsed time > 5s user system elapsed AggregateMetacell 7.72 0.12 8.78 get.pep.prot.cc 3.95 1.14 5.10 CVDistD_HC 3.18 0.25 5.72 diffAnaComputeFDR 0.67 0.06 8.01 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AggregateMetacell 8.14 0.09 8.25 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/DAPAR.Rcheck/00check.log' for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/DAPAR_1.24.8.tar.gz && rm -rf DAPAR.buildbin-libdir && mkdir DAPAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DAPAR.buildbin-libdir DAPAR_1.24.8.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL DAPAR_1.24.8.zip && rm DAPAR_1.24.8.tar.gz DAPAR_1.24.8.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 12 4692k 12 607k 0 0 1133k 0 0:00:04 --:--:-- 0:00:04 1133k 58 4692k 58 2750k 0 0 1744k 0 0:00:02 0:00:01 0:00:01 1744k 100 4692k 100 4692k 0 0 2083k 0 0:00:02 0:00:02 --:--:-- 2084k 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 AggregateMetacell html BuildAdjacencyMatrix html BuildColumnToProteinDataset html BuildColumnToProteinDataset_par html BuildMetaCell html CVDistD_HC html CountPep html ExtendPalette html GOAnalysisSave html finding level-2 HTML links ... done GetCC html GetColorsForConditions html GetDetailedNbPeptides html GetDetailedNbPeptidesUsed html GetIndices_BasedOnConditions html GetIndices_MetacellFiltering html GetIndices_WholeLine html GetIndices_WholeMatrix html GetKeyId html GetMatAdj html GetMetacell html GetNbPeptidesUsed html GetTypeofData html Get_AllComparisons html GlobalQuantileAlignment html GraphPepProt html LH0 html LH0.lm html LH1 html LH1.lm html LOESS html MeanCentering html MetaCellFiltering html MetacellFilteringScope html Metacell_generic html Metacell_maxquant html Metacell_proline html NumericalFiltering html NumericalgetIndicesOfLinesToRemove html QuantileCentering html SetCC html SetMatAdj html Set_POV_MEC_tags html StringBasedFiltering html StringBasedFiltering2 html SumByColumns html SymFilteringOperators html UpdateMetacell html aggregateIter html aggregateIterParallel html aggregateMean html aggregateSum html aggregateTopn html averageIntensities html barplotEnrichGO_HC html barplotGroupGO_HC html boxPlotD_HC html buildGraph html check.conditions html check.design html checkClusterability html classic1wayAnova html compareNormalizationD_HC html compute_t_tests html corrMatrixD_HC html createMSnset html dapar_hc_ExportMenu html dapar_hc_chart html deleteLinesFromIndices html densityPlotD_HC html diffAnaComputeFDR html diffAnaGetSignificant html diffAnaSave html diffAnaVolcanoplot html diffAnaVolcanoplot_rCharts html display.CC.visNet html enrich_GO html finalizeAggregation html findMECBlock html formatLimmaResult html formatPHResults html fudge2LRT html get.pep.prot.cc 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 heatmapD html heatmapForMissingValues html histPValue_HC html impute.pa2 html inner.aggregate.iter html inner.aggregate.topn html inner.mean html inner.sum html limmaCompleteTest html listSheets html make.contrast html make.design.1 html make.design.2 html make.design.3 html make.design html match.metacell html metacell.def html metacellHisto_HC html metacellPerLinesHistoPerCondition_HC html metacellPerLinesHisto_HC html metacombine html mvImage html my_hc_ExportMenu html my_hc_chart html nonzero html normalizeMethods.dapar html pepa.test html plotJitter html plotJitter_rCharts html plotPCA_Eigen html plotPCA_Eigen_hc html plotPCA_Ind html plotPCA_Var html postHocTest html proportionConRev_HC html rbindMSnset html reIntroduceMEC html readExcel html removeLines html samLRT html saveParameters html scatterplotEnrichGO_HC html search.metacell.tags html splitAdjacencyMat html test.design html translatedRandomBeta html univ_AnnotDbPkg html violinPlotD html visualizeClusters html vsn html wrapper.CVDistD_HC html wrapper.compareNormalizationD_HC html wrapper.corrMatrixD_HC html wrapper.dapar.impute.mi 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.mvImage html wrapper.normalizeD html wrapper.pca html wrapperCalibrationPlot html wrapperClassic1wayAnova html wrapperRunClustering html write.excel 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_1.24.8.zip * DONE (DAPAR) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'DAPAR' successfully unpacked and MD5 sums checked
DAPAR.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'DynDoc' The following object is masked from 'package:BiocGenerics': path > > test_check("DAPAR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 11.37 1.15 12.78 |
DAPAR.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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: Biobase Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'DynDoc' The following object is masked from 'package:BiocGenerics': path > > test_check("DAPAR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 10.25 0.51 10.75 |
DAPAR.Rcheck/examples_i386/DAPAR-Ex.timings
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DAPAR.Rcheck/examples_x64/DAPAR-Ex.timings
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