Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:22:48 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 469/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.28.5 (landing page) Samuel Wieczorek
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: DAPAR |
Version: 1.28.5 |
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_1.28.5.tar.gz |
StartedAt: 2022-10-19 01:17:06 -0400 (Wed, 19 Oct 2022) |
EndedAt: 2022-10-19 01:40:51 -0400 (Wed, 19 Oct 2022) |
EllapsedTime: 1424.6 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_1.28.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/DAPAR.Rcheck’ * using R version 4.2.1 (2022-06-23) * 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 ‘1.28.5’ * 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 ... 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 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’ 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’ heatmapForMissingValues: no visible binding for global variable ‘par’ 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 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’ wrapperRunClustering: no visible global function definition for ‘str_c’ Undefined global functions or variables: A B Condition FDR_threshold Intensity P.Value Pr(>F)1 adjusted_pvalues cond condition feature g input layout_nicely nodes<- par str_c textGOParams tsop x y Consider adding importFrom("graphics", "par") 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 wrapper.compareNormalizationD_HC 560.787 270.442 823.381 metacombine 27.710 7.206 34.454 wrapper.dapar.impute.mi 27.137 1.651 28.712 barplotEnrichGO_HC 16.677 3.018 19.629 barplotGroupGO_HC 10.182 0.961 11.126 enrich_GO 9.239 0.928 10.156 group_GO 9.243 0.899 10.115 scatterplotEnrichGO_HC 9.135 0.805 9.918 densityPlotD_HC 5.876 2.467 8.065 formatPHResults 6.617 1.132 7.690 wrapper.CVDistD_HC 4.862 2.801 7.519 postHocTest 6.307 1.096 7.422 CVDistD_HC 5.885 0.137 6.038 wrapperRunClustering 4.567 0.894 6.510 mvImage 5.118 0.308 5.418 AggregateMetacell 5.155 0.162 5.327 * 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 ‘/Users/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid" 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) This is the 'DAPAR' version 1.28.5. To get started, visit http://www.prostar-proteomics.org/ > > test_check("DAPAR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ] > > proc.time() user system elapsed 14.560 0.539 15.099
DAPAR.Rcheck/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 5.155 | 0.162 | 5.327 | |
BuildAdjacencyMatrix | 0.857 | 0.007 | 0.865 | |
BuildColumnToProteinDataset | 2.222 | 0.014 | 2.239 | |
BuildColumnToProteinDataset_par | 2.324 | 0.160 | 2.377 | |
BuildMetaCell | 1.816 | 0.212 | 2.031 | |
CVDistD_HC | 5.885 | 0.137 | 6.038 | |
CountPep | 0.847 | 0.007 | 0.855 | |
ExtendPalette | 0.050 | 0.002 | 0.052 | |
GOAnalysisSave | 0 | 0 | 0 | |
GetCC | 2.333 | 0.018 | 2.355 | |
GetColorsForConditions | 0.750 | 0.004 | 0.755 | |
GetDetailedNbPeptides | 0.791 | 0.005 | 0.797 | |
GetDetailedNbPeptidesUsed | 0.001 | 0.000 | 0.001 | |
GetIndices_BasedOnConditions | 0.798 | 0.006 | 0.806 | |
GetIndices_MetacellFiltering | 0.787 | 0.006 | 0.794 | |
GetIndices_WholeLine | 0.808 | 0.006 | 0.815 | |
GetIndices_WholeMatrix | 0.782 | 0.006 | 0.789 | |
GetKeyId | 0.785 | 0.007 | 0.792 | |
GetMatAdj | 0.801 | 0.005 | 0.808 | |
GetMetacell | 0 | 0 | 0 | |
GetNbPeptidesUsed | 0.794 | 0.005 | 0.800 | |
GetTypeofData | 0.741 | 0.005 | 0.748 | |
Get_AllComparisons | 0.514 | 0.007 | 0.523 | |
GlobalQuantileAlignment | 0.847 | 0.008 | 0.886 | |
GraphPepProt | 0.829 | 0.007 | 0.855 | |
LH0 | 0 | 0 | 0 | |
LH0.lm | 0.000 | 0.001 | 0.001 | |
LH1 | 0 | 0 | 0 | |
LH1.lm | 0 | 0 | 0 | |
LOESS | 1.936 | 0.022 | 1.964 | |
MeanCentering | 0.737 | 0.007 | 0.744 | |
MetaCellFiltering | 0.832 | 0.010 | 0.843 | |
MetacellFilteringScope | 0 | 0 | 0 | |
Metacell_generic | 0.797 | 0.018 | 0.815 | |
Metacell_maxquant | 0.757 | 0.013 | 0.770 | |
Metacell_proline | 0.741 | 0.015 | 0.757 | |
NumericalFiltering | 1.380 | 0.009 | 1.391 | |
NumericalgetIndicesOfLinesToRemove | 0.720 | 0.004 | 0.726 | |
QuantileCentering | 0.739 | 0.004 | 0.744 | |
SetCC | 1.975 | 0.010 | 1.988 | |
SetMatAdj | 0.807 | 0.005 | 0.813 | |
Set_POV_MEC_tags | 0.812 | 0.005 | 0.818 | |
StringBasedFiltering | 0.827 | 0.006 | 0.833 | |
StringBasedFiltering2 | 0.839 | 0.005 | 0.844 | |
SumByColumns | 3.352 | 0.022 | 3.382 | |
SymFilteringOperators | 0 | 0 | 0 | |
UpdateMetacell | 0.000 | 0.000 | 0.001 | |
aggregateIter | 2.263 | 0.008 | 2.273 | |
aggregateIterParallel | 2.459 | 0.114 | 2.544 | |
aggregateMean | 2.362 | 0.119 | 2.483 | |
aggregateSum | 3.617 | 0.016 | 3.637 | |
aggregateTopn | 2.132 | 0.013 | 2.146 | |
averageIntensities | 0.958 | 0.141 | 1.164 | |
barplotEnrichGO_HC | 16.677 | 3.018 | 19.629 | |
barplotGroupGO_HC | 10.182 | 0.961 | 11.126 | |
boxPlotD_HC | 0.472 | 0.102 | 0.566 | |
buildGraph | 1.862 | 0.047 | 1.907 | |
check.conditions | 0.744 | 0.006 | 0.749 | |
check.design | 0.738 | 0.006 | 0.745 | |
checkClusterability | 0.392 | 0.046 | 0.433 | |
classic1wayAnova | 2.694 | 0.427 | 3.109 | |
compareNormalizationD_HC | 0.298 | 0.061 | 0.356 | |
compute_t_tests | 2.030 | 0.416 | 2.442 | |
corrMatrixD_HC | 0.930 | 0.079 | 1.008 | |
createMSnset | 3.126 | 0.233 | 3.345 | |
dapar_hc_ExportMenu | 0.246 | 0.135 | 0.385 | |
dapar_hc_chart | 0.098 | 0.046 | 0.143 | |
deleteLinesFromIndices | 0.844 | 0.028 | 0.870 | |
densityPlotD_HC | 5.876 | 2.467 | 8.065 | |
diffAnaComputeFDR | 0.771 | 0.145 | 0.905 | |
diffAnaGetSignificant | 0.551 | 0.104 | 0.645 | |
diffAnaSave | 0.509 | 0.096 | 0.594 | |
diffAnaVolcanoplot | 0.332 | 0.041 | 0.370 | |
diffAnaVolcanoplot_rCharts | 0.760 | 0.176 | 0.922 | |
display.CC.visNet | 2.114 | 0.099 | 2.226 | |
enrich_GO | 9.239 | 0.928 | 10.156 | |
finalizeAggregation | 0 | 0 | 0 | |
findMECBlock | 0.826 | 0.021 | 0.846 | |
formatLimmaResult | 1.164 | 0.049 | 1.211 | |
formatPHResults | 6.617 | 1.132 | 7.690 | |
fudge2LRT | 0 | 0 | 0 | |
get.pep.prot.cc | 1.657 | 0.023 | 1.681 | |
getIndicesConditions | 0.753 | 0.006 | 0.760 | |
getIndicesOfLinesToRemove | 0.776 | 0.017 | 0.791 | |
getListNbValuesInLines | 0.723 | 0.005 | 0.728 | |
getNumberOf | 0.757 | 0.016 | 0.772 | |
getNumberOfEmptyLines | 0.813 | 0.010 | 0.823 | |
getPourcentageOfMV | 0.757 | 0.016 | 0.773 | |
getProcessingInfo | 0.714 | 0.005 | 0.720 | |
getProteinsStats | 0.823 | 0.021 | 0.844 | |
getQuantile4Imp | 0.247 | 0.010 | 0.257 | |
getTextForAggregation | 0.000 | 0.000 | 0.001 | |
getTextForAnaDiff | 0.000 | 0.001 | 0.001 | |
getTextForFiltering | 0.001 | 0.000 | 0.000 | |
getTextForGOAnalysis | 0.001 | 0.001 | 0.000 | |
getTextForHypothesisTest | 0.000 | 0.000 | 0.001 | |
getTextForNewDataset | 0.003 | 0.001 | 0.004 | |
getTextForNormalization | 0.001 | 0.000 | 0.001 | |
getTextForpeptideImputation | 0 | 0 | 0 | |
getTextForproteinImputation | 0 | 0 | 0 | |
group_GO | 9.243 | 0.899 | 10.115 | |
hc_logFC_DensityPlot | 1.261 | 0.508 | 1.714 | |
hc_mvTypePlot2 | 2.597 | 0.488 | 3.036 | |
heatmapD | 1.185 | 0.061 | 1.246 | |
heatmapForMissingValues | 0.351 | 0.035 | 0.386 | |
histPValue_HC | 0.446 | 0.099 | 0.548 | |
impute.pa2 | 0.874 | 0.052 | 0.935 | |
inner.aggregate.iter | 0.868 | 0.040 | 0.908 | |
inner.aggregate.topn | 0.793 | 0.018 | 0.810 | |
inner.mean | 0.833 | 0.022 | 0.856 | |
inner.sum | 0.775 | 0.018 | 0.793 | |
limmaCompleteTest | 3.282 | 0.128 | 3.399 | |
listSheets | 0.000 | 0.001 | 0.000 | |
make.contrast | 0.758 | 0.006 | 0.765 | |
make.design.1 | 0.761 | 0.006 | 0.767 | |
make.design.2 | 0.756 | 0.006 | 0.762 | |
make.design.3 | 0.747 | 0.005 | 0.753 | |
make.design | 0.748 | 0.006 | 0.755 | |
match.metacell | 0.853 | 0.022 | 0.874 | |
metacell.def | 0.009 | 0.003 | 0.011 | |
metacellHisto_HC | 0.861 | 0.056 | 0.915 | |
metacellPerLinesHistoPerCondition_HC | 1.073 | 0.133 | 1.253 | |
metacellPerLinesHisto_HC | 0.867 | 0.071 | 0.950 | |
metacombine | 27.710 | 7.206 | 34.454 | |
mvImage | 5.118 | 0.308 | 5.418 | |
my_hc_ExportMenu | 0.238 | 0.139 | 0.374 | |
my_hc_chart | 0.247 | 0.144 | 0.388 | |
nonzero | 0.027 | 0.001 | 0.028 | |
normalizeMethods.dapar | 0.000 | 0.000 | 0.001 | |
pepa.test | 0.776 | 0.017 | 0.793 | |
plotJitter | 1.717 | 0.041 | 1.759 | |
plotJitter_rCharts | 1.706 | 0.081 | 1.785 | |
plotPCA_Eigen | 0.881 | 0.043 | 0.922 | |
plotPCA_Eigen_hc | 0.754 | 0.005 | 0.760 | |
plotPCA_Ind | 0.774 | 0.008 | 0.796 | |
plotPCA_Var | 0.750 | 0.006 | 0.757 | |
postHocTest | 6.307 | 1.096 | 7.422 | |
proportionConRev_HC | 0.075 | 0.047 | 0.123 | |
rbindMSnset | 0.915 | 0.063 | 0.975 | |
reIntroduceMEC | 0.934 | 0.063 | 0.995 | |
readExcel | 0 | 0 | 0 | |
removeLines | 0.838 | 0.031 | 0.866 | |
samLRT | 0 | 0 | 0 | |
saveParameters | 0.761 | 0.007 | 0.769 | |
scatterplotEnrichGO_HC | 9.135 | 0.805 | 9.918 | |
search.metacell.tags | 0.018 | 0.004 | 0.023 | |
splitAdjacencyMat | 0.829 | 0.017 | 0.847 | |
test.design | 0.905 | 0.009 | 0.915 | |
translatedRandomBeta | 0.004 | 0.005 | 0.009 | |
univ_AnnotDbPkg | 0.268 | 0.057 | 0.324 | |
violinPlotD | 0.491 | 0.023 | 0.515 | |
visualizeClusters | 2.357 | 0.436 | 2.748 | |
vsn | 2.054 | 0.022 | 2.089 | |
wrapper.CVDistD_HC | 4.862 | 2.801 | 7.519 | |
wrapper.compareNormalizationD_HC | 560.787 | 270.442 | 823.381 | |
wrapper.corrMatrixD_HC | 0.900 | 0.075 | 0.970 | |
wrapper.dapar.impute.mi | 27.137 | 1.651 | 28.712 | |
wrapper.heatmapD | 1.048 | 0.040 | 1.089 | |
wrapper.impute.KNN | 0.793 | 0.030 | 0.822 | |
wrapper.impute.detQuant | 1.138 | 0.121 | 1.248 | |
wrapper.impute.fixedValue | 0.923 | 0.062 | 0.980 | |
wrapper.impute.mle | 0.803 | 0.032 | 0.833 | |
wrapper.impute.pa | 0.291 | 0.038 | 0.328 | |
wrapper.impute.pa2 | 0.842 | 0.055 | 0.897 | |
wrapper.impute.slsa | 1.093 | 0.063 | 1.152 | |
wrapper.mvImage | 0.338 | 0.045 | 0.379 | |
wrapper.normalizeD | 0.777 | 0.008 | 0.789 | |
wrapper.pca | 0.331 | 0.042 | 0.378 | |
wrapperCalibrationPlot | 0.392 | 0.048 | 0.511 | |
wrapperClassic1wayAnova | 3.722 | 0.474 | 4.978 | |
wrapperRunClustering | 4.567 | 0.894 | 6.510 | |
write.excel | 1.553 | 0.212 | 2.090 | |
writeMSnsetToCSV | 0.834 | 0.030 | 1.007 | |
writeMSnsetToExcel | 1.941 | 0.357 | 2.395 | |