Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 |
Package 511/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.41.0 (landing page) Samuel Wieczorek
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the DAPAR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: DAPAR |
Version: 1.41.0 |
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_1.41.0.tar.gz |
StartedAt: 2025-08-08 18:59:24 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 19:03:40 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 256.1 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_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DAPAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DAPAR’ version ‘1.41.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Vignette dependency required without any vignettes: ‘knitr’ * 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 DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... 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 Check_Dataset_Validity: no visible global function definition for ‘exprs’ OWAnova: no visible global function definition for ‘aov’ 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’ createMSnset: no visible global function definition for ‘installed.packages’ createMSnset: no visible binding for global variable ‘Prostar.loc’ createMSnset2: no visible global function definition for ‘installed.packages’ createMSnset2: no visible binding for global variable ‘Prostar.loc’ 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’ globalAdjPval: no visible global function definition for ‘stack’ 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<-’ testAnovaModels : <anonymous>: no visible global function definition for ‘TukeyHSD’ 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 Prostar.loc TukeyHSD adjusted_pvalues aov cond condition exprs feature g input installed.packages intensity layout_nicely nodes<- par stack str_c textGOParams x y Consider adding importFrom("graphics", "par") importFrom("stats", "TukeyHSD", "aov") importFrom("utils", "installed.packages", "stack") 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 examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed wrapper.compareNormalizationD_HC 19.302 11.722 51.303 wrapper.dapar.impute.mi 4.982 0.610 6.170 barplotEnrichGO_HC 3.579 0.564 5.803 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.22-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/4.5-arm64/Resources/library’ * installing *source* package ‘DAPAR’ ... ** this is package ‘DAPAR’ version ‘1.41.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 1.41.0. To get started, visit http://www.prostar-proteomics.org/ > > test_check("DAPAR") Iterations: 1 / 1 - Imputation MNAR OK - Imputation MCAR in progress - 3 % - 6 % - 9 % - 12 % - 15 % - 18 % - 21 % - 24 % - 27 % - 30 % - 33 % - 36 % - 39 % - 42 % - 45 % - 48 % - 51 % - 54 % - 57 % - 60 % - 63 % - 66 % - 69 % - 72 % - 75 % - 78 % - 81 % - 84 % - 87 % - 90 % - 93 % - 96 % - 99 % - Iterations: 1 / 1 - Imputation MNAR OK - Imputation MCAR in progress - 3 % - 6 % - 9 % - 12 % - 15 % - 18 % - 21 % - 24 % - 27 % - 30 % - 33 % - 36 % - 39 % - 42 % - 45 % - 48 % - 51 % - 54 % - 57 % - 60 % - 63 % - 66 % - 69 % - 72 % - 75 % - 78 % - 81 % - 84 % - 87 % - 90 % - 93 % - 96 % - 99 % - Imputation in condition 1 ... In progress: 10 % - 20 % - 30 % - 40 % - 50 % - 60 % - 70 % - 80 % - 90 % - 100 % - Imputation in condition 2 ... In progress: 10 % - 20 % - 30 % - 40 % - 50 % - 60 % - 70 % - 80 % - 90 % - 100 % - [ FAIL 0 | WARN 17 | SKIP 0 | PASS 66 ] [ FAIL 0 | WARN 17 | SKIP 0 | PASS 66 ] > > proc.time() user system elapsed 12.541 0.713 13.334
DAPAR.Rcheck/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 0.228 | 0.008 | 0.243 | |
BuildAdjacencyMatrix | 0.195 | 0.003 | 0.199 | |
BuildColumnToProteinDataset | 0.226 | 0.003 | 0.230 | |
BuildMetaCell | 0.283 | 0.011 | 0.296 | |
CVDistD_HC | 1.173 | 0.034 | 1.240 | |
Children | 0.002 | 0.000 | 0.001 | |
CountPep | 0.198 | 0.003 | 0.210 | |
ExtendPalette | 0.008 | 0.000 | 0.008 | |
GOAnalysisSave | 0 | 0 | 0 | |
GetCC | 1.073 | 0.008 | 1.087 | |
GetColorsForConditions | 0.182 | 0.002 | 0.192 | |
GetDetailedNbPeptides | 0.187 | 0.001 | 0.196 | |
GetDetailedNbPeptidesUsed | 0 | 0 | 0 | |
GetIndices_BasedOnConditions | 0.187 | 0.002 | 0.189 | |
GetIndices_MetacellFiltering | 0.197 | 0.002 | 0.200 | |
GetIndices_WholeLine | 0.200 | 0.002 | 0.201 | |
GetIndices_WholeMatrix | 0.197 | 0.002 | 0.201 | |
GetKeyId | 0.185 | 0.002 | 0.187 | |
GetMatAdj | 0.213 | 0.003 | 0.216 | |
GetMetacell | 0 | 0 | 0 | |
GetMetacellTags | 0.203 | 0.003 | 0.208 | |
GetNbPeptidesUsed | 0.206 | 0.002 | 0.210 | |
GetNbTags | 0 | 0 | 0 | |
GetSoftAvailables | 0 | 0 | 0 | |
GetTypeofData | 0.181 | 0.002 | 0.190 | |
Get_AllComparisons | 0.111 | 0.006 | 0.121 | |
GlobalQuantileAlignment | 0.200 | 0.003 | 0.202 | |
GraphPepProt | 0.205 | 0.003 | 0.208 | |
LH0 | 0 | 0 | 0 | |
LH0.lm | 0 | 0 | 0 | |
LH1 | 0 | 0 | 0 | |
LH1.lm | 0 | 0 | 0 | |
LOESS | 0.492 | 0.009 | 0.505 | |
MeanCentering | 0.190 | 0.004 | 0.199 | |
MetaCellFiltering | 0.228 | 0.003 | 0.230 | |
MetacellFilteringScope | 0 | 0 | 0 | |
Metacell_DIA_NN | 0.211 | 0.005 | 0.224 | |
Metacell_generic | 0.166 | 0.005 | 0.174 | |
Metacell_maxquant | 0.178 | 0.006 | 0.186 | |
Metacell_proline | 0.165 | 0.005 | 0.171 | |
NumericalFiltering | 0.192 | 0.002 | 0.194 | |
NumericalgetIndicesOfLinesToRemove | 0.190 | 0.002 | 0.191 | |
OWAnova | 0.002 | 0.000 | 0.002 | |
QuantileCentering | 0.197 | 0.005 | 0.202 | |
SetCC | 1.004 | 0.005 | 1.020 | |
SetMatAdj | 0.192 | 0.002 | 0.197 | |
Set_POV_MEC_tags | 0.203 | 0.003 | 0.207 | |
StringBasedFiltering | 0.193 | 0.002 | 0.194 | |
StringBasedFiltering2 | 0.190 | 0.002 | 0.192 | |
SumByColumns | 0.485 | 0.006 | 0.498 | |
SymFilteringOperators | 0 | 0 | 0 | |
UpdateMetacellAfterImputation | 0.193 | 0.002 | 0.196 | |
aggregateIter | 0.236 | 0.003 | 0.238 | |
aggregateIterParallel | 0 | 0 | 0 | |
aggregateMean | 0.216 | 0.003 | 0.219 | |
aggregateSum | 0.229 | 0.002 | 0.231 | |
aggregateTopn | 0.215 | 0.003 | 0.218 | |
applyAnovasOnProteins | 0.064 | 0.001 | 0.064 | |
averageIntensities | 0.228 | 0.037 | 0.352 | |
barplotEnrichGO_HC | 3.579 | 0.564 | 5.803 | |
barplotGroupGO_HC | 2.108 | 0.257 | 2.816 | |
boxPlotD_HC | 0.100 | 0.024 | 0.126 | |
buildGraph | 0.774 | 0.031 | 0.812 | |
check.conditions | 0.175 | 0.002 | 0.178 | |
check.design | 0.176 | 0.002 | 0.178 | |
checkClusterability | 1.533 | 1.222 | 3.020 | |
classic1wayAnova | 0.000 | 0.001 | 0.000 | |
compareNormalizationD_HC | 0.071 | 0.019 | 0.149 | |
compute.selection.table | 0.451 | 0.068 | 0.528 | |
compute_t_tests | 0.697 | 0.117 | 0.849 | |
corrMatrixD_HC | 0.268 | 0.033 | 0.308 | |
createMSnset | 0.672 | 0.043 | 0.842 | |
createMSnset2 | 0.647 | 0.043 | 0.853 | |
dapar_hc_ExportMenu | 0.042 | 0.048 | 0.304 | |
dapar_hc_chart | 0.018 | 0.016 | 0.062 | |
deleteLinesFromIndices | 0.224 | 0.007 | 0.235 | |
densityPlotD_HC | 1.716 | 0.713 | 2.555 | |
diffAnaComputeAdjustedPValues | 0.115 | 0.016 | 0.135 | |
diffAnaComputeFDR | 0 | 0 | 0 | |
diffAnaGetSignificant | 0.121 | 0.031 | 0.468 | |
diffAnaSave | 0.151 | 0.023 | 0.182 | |
diffAnaVolcanoplot | 0.113 | 0.011 | 0.130 | |
diffAnaVolcanoplot_rCharts | 0.245 | 0.058 | 0.326 | |
display.CC.visNet | 0.882 | 0.033 | 1.094 | |
enrich_GO | 2.639 | 0.263 | 3.186 | |
finalizeAggregation | 0 | 0 | 0 | |
findMECBlock | 0.221 | 0.006 | 0.270 | |
formatHSDResults | 0 | 0 | 0 | |
formatLimmaResult | 0.110 | 0.013 | 0.128 | |
formatPHResults | 0 | 0 | 0 | |
formatPHTResults | 0 | 0 | 0 | |
fudge2LRT | 0.001 | 0.000 | 0.000 | |
get.pep.prot.cc | 0.807 | 0.022 | 0.833 | |
getDesignLevel | 0.179 | 0.002 | 0.191 | |
getIndicesConditions | 0.202 | 0.002 | 0.214 | |
getIndicesOfLinesToRemove | 0.226 | 0.005 | 0.241 | |
getListNbValuesInLines | 0.182 | 0.003 | 0.187 | |
getNumberOf | 0.200 | 0.006 | 0.208 | |
getNumberOfEmptyLines | 0.206 | 0.004 | 0.212 | |
getPourcentageOfMV | 0.200 | 0.006 | 0.210 | |
getProcessingInfo | 0.183 | 0.003 | 0.191 | |
getProteinsStats | 0.211 | 0.007 | 0.223 | |
getQuantile4Imp | 0.058 | 0.002 | 0.059 | |
getTextForAggregation | 0 | 0 | 0 | |
getTextForAnaDiff | 0 | 0 | 0 | |
getTextForFiltering | 0.000 | 0.000 | 0.001 | |
getTextForGOAnalysis | 0.000 | 0.001 | 0.000 | |
getTextForHypothesisTest | 0 | 0 | 0 | |
getTextForNewDataset | 0.001 | 0.000 | 0.001 | |
getTextForNormalization | 0.000 | 0.000 | 0.001 | |
getTextForpeptideImputation | 0 | 0 | 0 | |
getTextForproteinImputation | 0 | 0 | 0 | |
globalAdjPval | 0.273 | 0.024 | 0.313 | |
group_GO | 2.325 | 0.222 | 3.061 | |
hc_logFC_DensityPlot | 0.190 | 0.090 | 0.654 | |
hc_mvTypePlot2 | 0.911 | 0.134 | 1.507 | |
heatmapD | 0.307 | 0.027 | 0.338 | |
heatmapForMissingValues | 0.111 | 0.012 | 0.126 | |
histPValue_HC | 0.144 | 0.037 | 0.186 | |
impute.pa2 | 0.233 | 0.010 | 0.252 | |
inner.aggregate.iter | 0.232 | 0.009 | 0.244 | |
inner.aggregate.topn | 0.226 | 0.006 | 0.243 | |
inner.mean | 0.219 | 0.006 | 0.229 | |
inner.sum | 0.193 | 0.004 | 0.202 | |
is.subset | 0 | 0 | 0 | |
limmaCompleteTest | 0.806 | 0.033 | 0.849 | |
listSheets | 0 | 0 | 0 | |
make.contrast | 0.196 | 0.004 | 0.200 | |
make.design.1 | 0.199 | 0.003 | 0.202 | |
make.design.2 | 0.219 | 0.003 | 0.225 | |
make.design.3 | 0.221 | 0.003 | 0.230 | |
make.design | 0.242 | 0.004 | 0.250 | |
match.metacell | 0.218 | 0.007 | 0.233 | |
metacell.def | 0.003 | 0.002 | 0.004 | |
metacellHisto_HC | 0.237 | 0.034 | 0.280 | |
metacellPerLinesHistoPerCondition_HC | 0.306 | 0.075 | 0.409 | |
metacellPerLinesHisto_HC | 0.385 | 0.169 | 0.746 | |
metacombine | 0.128 | 0.006 | 0.139 | |
mvImage | 1.432 | 0.090 | 1.568 | |
my_hc_ExportMenu | 0.091 | 0.079 | 0.169 | |
my_hc_chart | 0.091 | 0.081 | 0.172 | |
nonzero | 0.018 | 0.001 | 0.020 | |
normalizeMethods.dapar | 0 | 0 | 0 | |
pepa.test | 0.254 | 0.006 | 0.261 | |
pkgs.require | 0 | 0 | 0 | |
plotJitter | 0.856 | 0.033 | 0.953 | |
plotJitter_rCharts | 0.762 | 0.032 | 1.059 | |
plotPCA_Eigen | 0.248 | 0.022 | 0.280 | |
plotPCA_Eigen_hc | 0.232 | 0.002 | 0.238 | |
plotPCA_Ind | 0.233 | 0.006 | 0.251 | |
plotPCA_Var | 0.230 | 0.004 | 0.242 | |
postHocTest | 0.000 | 0.001 | 0.000 | |
proportionConRev_HC | 0.031 | 0.028 | 0.060 | |
rbindMSnset | 0.279 | 0.021 | 0.308 | |
reIntroduceMEC | 0.261 | 0.016 | 0.287 | |
readExcel | 0 | 0 | 0 | |
removeLines | 0.227 | 0.012 | 0.252 | |
samLRT | 0 | 0 | 0 | |
saveParameters | 0.216 | 0.004 | 0.223 | |
scatterplotEnrichGO_HC | 2.615 | 0.341 | 3.539 | |
search.metacell.tags | 0.003 | 0.002 | 0.006 | |
separateAdjPval | 0.096 | 0.012 | 0.169 | |
splitAdjacencyMat | 0.233 | 0.014 | 0.255 | |
test.design | 0.213 | 0.005 | 0.222 | |
testAnovaModels | 0.086 | 0.011 | 0.106 | |
thresholdpval4fdr | 0 | 0 | 0 | |
translatedRandomBeta | 0.001 | 0.004 | 0.008 | |
univ_AnnotDbPkg | 0.116 | 0.041 | 0.170 | |
violinPlotD | 0.151 | 0.013 | 0.179 | |
visualizeClusters | 0.447 | 0.121 | 1.515 | |
vsn | 0.344 | 0.029 | 0.414 | |
wrapper.CVDistD_HC | 1.28 | 0.83 | 2.32 | |
wrapper.compareNormalizationD_HC | 19.302 | 11.722 | 51.303 | |
wrapper.corrMatrixD_HC | 0.212 | 0.023 | 0.235 | |
wrapper.dapar.impute.mi | 4.982 | 0.610 | 6.170 | |
wrapper.heatmapD | 0.251 | 0.013 | 0.280 | |
wrapper.impute.KNN | 0.204 | 0.012 | 0.261 | |
wrapper.impute.detQuant | 0.211 | 0.016 | 0.239 | |
wrapper.impute.fixedValue | 0.230 | 0.012 | 0.242 | |
wrapper.impute.mle | 0.212 | 0.010 | 0.225 | |
wrapper.impute.pa | 0.084 | 0.008 | 0.091 | |
wrapper.impute.pa2 | 0.218 | 0.009 | 0.226 | |
wrapper.impute.slsa | 0.309 | 0.020 | 0.336 | |
wrapper.mvImage | 0.090 | 0.015 | 0.111 | |
wrapper.normalizeD | 0.193 | 0.004 | 0.198 | |
wrapper.pca | 0.093 | 0.010 | 0.103 | |
wrapperCalibrationPlot | 0.117 | 0.014 | 0.132 | |
wrapperClassic1wayAnova | 0.000 | 0.001 | 0.000 | |
wrapperRunClustering | 1.245 | 0.203 | 1.517 | |
write.excel | 0.415 | 0.072 | 0.505 | |
writeMSnsetToCSV | 0.198 | 0.013 | 0.217 | |
writeMSnsetToExcel | 0.533 | 0.102 | 0.638 | |