Back to Multiple platform build/check report for BioC 3.16 |
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This page was generated on 2022-06-22 11:07:23 -0400 (Wed, 22 Jun 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" | 4331 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" | 4136 |
lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4147 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 463/2118 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.29.0 (landing page) Samuel Wieczorek
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: DAPAR |
Version: 1.29.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.29.0.tar.gz |
StartedAt: 2022-06-21 19:47:32 -0400 (Tue, 21 Jun 2022) |
EndedAt: 2022-06-21 19:52:27 -0400 (Tue, 21 Jun 2022) |
EllapsedTime: 295.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DAPAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DAPAR_1.29.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/DAPAR.Rcheck’ * using R version 4.2.0 Patched (2022-05-29 r82424) * using platform: x86_64-apple-darwin17.0 (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 ‘1.29.0’ * 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 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 ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘igraph’ A package should be listed in only one of these fields. * 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 'library' or 'require' calls in package code: ‘doParallel’ ‘foreach’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespaces in Imports field not imported from: ‘Cairo’ ‘DAPARdata’ ‘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' BuildColumnToProteinDataset_par: no visible global function definition for ‘%dopar%’ BuildColumnToProteinDataset_par: no visible global function definition for ‘foreach’ GetIndices_MetacellFiltering: no visible global function definition for ‘tsop’ aggregateIterParallel: no visible global function definition for ‘%dopar%’ aggregateIterParallel: no visible global function definition for ‘foreach’ 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’ createMSnset: no visible global function definition for ‘package.version’ 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’ finalizeAggregation: no visible global function definition for ‘package.version’ 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’ 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<-’ pepa.test: no visible binding for global variable ‘de’ 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’ wrapperRunClustering: no visible global function definition for ‘ExpressionSet’ Undefined global functions or variables: %dopar% A B Condition ExpressionSet FDR_threshold P.Value Pr(>F)1 adjusted_pvalues bitr cond condition de desc enrichGO feature foreach g input intensity last layout_nicely nodes<- package.version post_hoc str_c textGOParams tsop x y Consider adding importFrom("utils", "de") to your NAMESPACE file. * 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AggregateMetacell 6.764 0.101 6.892 get.pep.prot.cc 4.788 0.966 5.771 checkClusterability 3.388 2.111 5.487 compareNormalizationD_HC 3.709 1.646 5.397 densityPlotD_HC 3.665 1.574 5.239 * 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-3.16-bioc/meat/DAPAR.Rcheck/00check.log’ for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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) > > test_check("DAPAR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 9.195 0.473 9.695
DAPAR.Rcheck/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 6.764 | 0.101 | 6.892 | |
BuildAdjacencyMatrix | 0.270 | 0.003 | 0.274 | |
BuildColumnToProteinDataset | 0.951 | 0.016 | 0.972 | |
BuildColumnToProteinDataset_par | 0.000 | 0.001 | 0.000 | |
BuildMetaCell | 0.621 | 0.035 | 0.661 | |
CVDistD_HC | 2.111 | 0.136 | 2.268 | |
CountPep | 0.367 | 0.010 | 0.381 | |
ExtendPalette | 0.027 | 0.001 | 0.029 | |
GetCC | 2.261 | 0.063 | 2.335 | |
GetColorsForConditions | 0.239 | 0.003 | 0.242 | |
GetDetailedNbPeptides | 0.388 | 0.012 | 0.401 | |
GetIndices_MetacellFiltering | 0.284 | 0.004 | 0.289 | |
GetIndices_WholeLine | 0.285 | 0.004 | 0.289 | |
GetIndices_WholeMatrix | 0.269 | 0.005 | 0.274 | |
GetMatAdj | 0.355 | 0.018 | 0.375 | |
Get_AllComparisons | 0.192 | 0.005 | 0.198 | |
GlobalQuantileAlignment | 0.290 | 0.004 | 0.295 | |
GraphPepProt | 0.291 | 0.005 | 0.298 | |
LOESS | 0.910 | 0.018 | 0.931 | |
MeanCentering | 0.274 | 0.009 | 0.284 | |
MetaCellFiltering | 0.286 | 0.003 | 0.290 | |
Metacell_generic | 0.540 | 0.013 | 0.556 | |
Metacell_maxquant | 0.555 | 0.021 | 0.582 | |
Metacell_proline | 0.000 | 0.001 | 0.001 | |
NumericalFiltering | 0.262 | 0.005 | 0.267 | |
NumericalgetIndicesOfLinesToRemove | 0.303 | 0.003 | 0.308 | |
QuantileCentering | 0.293 | 0.003 | 0.297 | |
SetCC | 1.638 | 0.045 | 1.688 | |
SetMatAdj | 0.352 | 0.008 | 0.360 | |
Set_POV_MEC_tags | 0.319 | 0.004 | 0.326 | |
StringBasedFiltering | 0.316 | 0.004 | 0.322 | |
StringBasedFiltering2 | 0.289 | 0.004 | 0.295 | |
SumByColumns | 1.088 | 0.020 | 1.111 | |
aggregateIter | 0.864 | 0.005 | 0.870 | |
aggregateIterParallel | 0 | 0 | 0 | |
aggregateMean | 0.916 | 0.007 | 0.926 | |
aggregateSum | 1.582 | 0.027 | 1.616 | |
aggregateTopn | 0 | 0 | 0 | |
averageIntensities | 0.470 | 0.099 | 0.585 | |
boxPlotD_HC | 0.438 | 0.200 | 0.643 | |
buildGraph | 1.214 | 0.084 | 1.303 | |
check.conditions | 0.282 | 0.006 | 0.292 | |
check.design | 0.262 | 0.005 | 0.267 | |
checkClusterability | 3.388 | 2.111 | 5.487 | |
classic1wayAnova | 1.233 | 0.243 | 1.486 | |
compareNormalizationD_HC | 3.709 | 1.646 | 5.397 | |
compute_t_tests | 1.057 | 0.275 | 1.341 | |
corrMatrixD_HC | 0.402 | 0.077 | 0.481 | |
createMSnset | 2.067 | 0.161 | 2.240 | |
dapar_hc_ExportMenu | 0.157 | 0.150 | 0.310 | |
dapar_hc_chart | 0.062 | 0.052 | 0.116 | |
deleteLinesFromIndices | 0.473 | 0.037 | 0.513 | |
densityPlotD_HC | 3.665 | 1.574 | 5.239 | |
diffAnaComputeFDR | 0.457 | 0.117 | 0.579 | |
diffAnaGetSignificant | 0.283 | 0.064 | 0.349 | |
diffAnaSave | 0.304 | 0.060 | 0.367 | |
diffAnaVolcanoplot | 0.159 | 0.030 | 0.190 | |
diffAnaVolcanoplot_rCharts | 0.000 | 0.001 | 0.001 | |
display.CC.visNet | 1.782 | 0.134 | 1.923 | |
enrich_GO | 0 | 0 | 0 | |
findMECBlock | 0.281 | 0.013 | 0.296 | |
formatLimmaResult | 0.146 | 0.028 | 0.175 | |
formatPHResults | 3.427 | 0.735 | 4.194 | |
get.pep.prot.cc | 4.788 | 0.966 | 5.771 | |
getIndicesConditions | 0.261 | 0.004 | 0.266 | |
getIndicesOfLinesToRemove | 0.257 | 0.010 | 0.268 | |
getListNbValuesInLines | 0.232 | 0.003 | 0.235 | |
getNumberOf | 0.284 | 0.029 | 0.318 | |
getNumberOfEmptyLines | 0.292 | 0.009 | 0.305 | |
getPourcentageOfMV | 0.258 | 0.011 | 0.269 | |
getProcessingInfo | 0.251 | 0.004 | 0.256 | |
getProteinsStats | 0.306 | 0.012 | 0.320 | |
getQuantile4Imp | 0.260 | 0.004 | 0.267 | |
getTextForAggregation | 0.001 | 0.000 | 0.001 | |
getTextForAnaDiff | 0.001 | 0.000 | 0.000 | |
getTextForGOAnalysis | 0.001 | 0.001 | 0.001 | |
getTextForHypothesisTest | 0 | 0 | 0 | |
getTextForNewDataset | 0.002 | 0.000 | 0.003 | |
getTextForNormalization | 0.001 | 0.000 | 0.000 | |
getTextForpeptideImputation | 0.001 | 0.001 | 0.001 | |
getTextForproteinImputation | 0 | 0 | 0 | |
group_GO | 0.000 | 0.001 | 0.000 | |
hc_logFC_DensityPlot | 1.332 | 0.651 | 1.991 | |
hc_mvTypePlot2 | 1.594 | 0.684 | 2.297 | |
heatmapD | 0 | 0 | 0 | |
heatmapForMissingValues | 0.174 | 0.027 | 0.201 | |
histPValue_HC | 0.204 | 0.076 | 0.282 | |
impute.pa2 | 0.329 | 0.034 | 0.366 | |
limmaCompleteTest | 1.242 | 0.086 | 1.339 | |
make.contrast | 0.253 | 0.004 | 0.259 | |
make.design.1 | 0.256 | 0.004 | 0.259 | |
make.design.2 | 0.000 | 0.000 | 0.001 | |
make.design.3 | 0.283 | 0.004 | 0.288 | |
make.design | 0.278 | 0.004 | 0.284 | |
match.metacell | 0.311 | 0.015 | 0.329 | |
metacellHisto_HC | 0.347 | 0.060 | 0.411 | |
metacellPerLinesHistoPerCondition_HC | 0.492 | 0.119 | 0.623 | |
metacellPerLinesHisto_HC | 0.340 | 0.064 | 0.406 | |
metacombine | 0.000 | 0.001 | 0.001 | |
mvImage | 2.104 | 0.199 | 2.307 | |
my_hc_ExportMenu | 0.146 | 0.149 | 0.311 | |
my_hc_chart | 0.150 | 0.151 | 0.306 | |
nonzero | 0.020 | 0.001 | 0.021 | |
plotJitter | 1.188 | 0.110 | 1.303 | |
plotPCA_Eigen | 0.264 | 0.003 | 0.268 | |
plotPCA_Eigen_hc | 0.214 | 0.003 | 0.216 | |
plotPCA_Ind | 0.281 | 0.005 | 0.287 | |
plotPCA_Var | 0.276 | 0.004 | 0.282 | |
postHocTest | 3.479 | 0.751 | 4.247 | |
proportionConRev_HC | 0.061 | 0.070 | 0.133 | |
rbindMSnset | 0.355 | 0.034 | 0.391 | |
reIntroduceMEC | 0.423 | 0.039 | 0.464 | |
removeLines | 0.334 | 0.024 | 0.358 | |
saveParameters | 0.296 | 0.006 | 0.305 | |
search.metacell.tags | 0.008 | 0.002 | 0.010 | |
test.design | 0.291 | 0.004 | 0.297 | |
translatedRandomBeta | 0.003 | 0.007 | 0.009 | |
violinPlotD | 0.275 | 0.027 | 0.306 | |
visualizeClusters | 1.242 | 0.301 | 1.550 | |
vsn | 0.554 | 0.016 | 0.573 | |
wrapper.CVDistD_HC | 2.641 | 1.789 | 4.402 | |
wrapper.compareNormalizationD_HC | 0.269 | 0.004 | 0.274 | |
wrapper.corrMatrixD_HC | 0.390 | 0.071 | 0.463 | |
wrapper.dapar.impute.mi | 0 | 0 | 0 | |
wrapper.heatmapD | 0 | 0 | 0 | |
wrapper.impute.KNN | 0.335 | 0.020 | 0.357 | |
wrapper.impute.detQuant | 0.518 | 0.074 | 0.594 | |
wrapper.impute.fixedValue | 0.383 | 0.038 | 0.421 | |
wrapper.impute.mle | 0.342 | 0.021 | 0.365 | |
wrapper.impute.pa | 0.358 | 0.022 | 0.380 | |
wrapper.impute.pa2 | 0.329 | 0.027 | 0.356 | |
wrapper.impute.slsa | 0.435 | 0.037 | 0.470 | |
wrapper.mvImage | 0.141 | 0.028 | 0.170 | |
wrapper.normalizeD | 0.283 | 0.004 | 0.287 | |
wrapper.pca | 0.135 | 0.023 | 0.158 | |
wrapperCalibrationPlot | 0.155 | 0.026 | 0.182 | |
wrapperClassic1wayAnova | 1.792 | 0.334 | 2.122 | |
wrapperRunClustering | 2.406 | 0.586 | 2.998 | |
write.excel | 0.684 | 0.146 | 0.837 | |
writeMSnsetToCSV | 0 | 0 | 0 | |
writeMSnsetToExcel | 0.000 | 0.000 | 0.001 | |