Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-18 12:03 -0400 (Mon, 18 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4596 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4538 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DAPAR_1.41.0.tar.gz |
StartedAt: 2025-08-17 21:32:42 -0400 (Sun, 17 Aug 2025) |
EndedAt: 2025-08-17 21:41:11 -0400 (Sun, 17 Aug 2025) |
EllapsedTime: 508.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DAPAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings DAPAR_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 35.606 11.594 47.632 wrapper.dapar.impute.mi 13.499 0.242 13.754 barplotEnrichGO_HC 7.172 0.706 7.894 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/DAPAR.Rcheck/00check.log’ for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 32.582 1.843 34.446
DAPAR.Rcheck/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 0.540 | 0.041 | 0.581 | |
BuildAdjacencyMatrix | 0.452 | 0.021 | 0.474 | |
BuildColumnToProteinDataset | 0.568 | 0.011 | 0.578 | |
BuildMetaCell | 0.568 | 0.034 | 0.603 | |
CVDistD_HC | 2.918 | 0.097 | 3.046 | |
Children | 0.004 | 0.000 | 0.004 | |
CountPep | 0.478 | 0.015 | 0.495 | |
ExtendPalette | 0.023 | 0.001 | 0.025 | |
GOAnalysisSave | 0 | 0 | 0 | |
GetCC | 2.582 | 0.059 | 2.641 | |
GetColorsForConditions | 0.444 | 0.006 | 0.450 | |
GetDetailedNbPeptides | 0.469 | 0.023 | 0.492 | |
GetDetailedNbPeptidesUsed | 0 | 0 | 0 | |
GetIndices_BasedOnConditions | 0.450 | 0.012 | 0.461 | |
GetIndices_MetacellFiltering | 0.457 | 0.009 | 0.466 | |
GetIndices_WholeLine | 0.452 | 0.010 | 0.463 | |
GetIndices_WholeMatrix | 0.454 | 0.008 | 0.462 | |
GetKeyId | 0.428 | 0.018 | 0.447 | |
GetMatAdj | 0.476 | 0.015 | 0.492 | |
GetMetacell | 0 | 0 | 0 | |
GetMetacellTags | 0.450 | 0.007 | 0.457 | |
GetNbPeptidesUsed | 0.447 | 0.023 | 0.470 | |
GetNbTags | 0 | 0 | 0 | |
GetSoftAvailables | 0.000 | 0.001 | 0.001 | |
GetTypeofData | 0.433 | 0.011 | 0.444 | |
Get_AllComparisons | 0.273 | 0.017 | 0.289 | |
GlobalQuantileAlignment | 0.459 | 0.014 | 0.475 | |
GraphPepProt | 0.460 | 0.005 | 0.465 | |
LH0 | 0 | 0 | 0 | |
LH0.lm | 0 | 0 | 0 | |
LH1 | 0.001 | 0.000 | 0.000 | |
LH1.lm | 0 | 0 | 0 | |
LOESS | 1.135 | 0.023 | 1.157 | |
MeanCentering | 0.457 | 0.009 | 0.465 | |
MetaCellFiltering | 0.592 | 0.010 | 0.602 | |
MetacellFilteringScope | 0.000 | 0.000 | 0.001 | |
Metacell_DIA_NN | 0.449 | 0.004 | 0.452 | |
Metacell_generic | 0.380 | 0.002 | 0.382 | |
Metacell_maxquant | 0.421 | 0.003 | 0.424 | |
Metacell_proline | 0.387 | 0.002 | 0.389 | |
NumericalFiltering | 0.471 | 0.010 | 0.481 | |
NumericalgetIndicesOfLinesToRemove | 0.441 | 0.007 | 0.447 | |
OWAnova | 0.007 | 0.000 | 0.006 | |
QuantileCentering | 0.453 | 0.021 | 0.474 | |
SetCC | 2.437 | 0.107 | 2.545 | |
SetMatAdj | 0.482 | 0.011 | 0.493 | |
Set_POV_MEC_tags | 0.445 | 0.007 | 0.452 | |
StringBasedFiltering | 0.466 | 0.008 | 0.475 | |
StringBasedFiltering2 | 0.470 | 0.007 | 0.477 | |
SumByColumns | 1.224 | 0.010 | 1.234 | |
SymFilteringOperators | 0 | 0 | 0 | |
UpdateMetacellAfterImputation | 0.451 | 0.010 | 0.462 | |
aggregateIter | 0.595 | 0.005 | 0.600 | |
aggregateIterParallel | 0 | 0 | 0 | |
aggregateMean | 0.527 | 0.005 | 0.533 | |
aggregateSum | 0.545 | 0.013 | 0.558 | |
aggregateTopn | 0.513 | 0.008 | 0.520 | |
applyAnovasOnProteins | 0.135 | 0.002 | 0.136 | |
averageIntensities | 0.472 | 0.041 | 0.515 | |
barplotEnrichGO_HC | 7.172 | 0.706 | 7.894 | |
barplotGroupGO_HC | 4.085 | 0.345 | 4.437 | |
boxPlotD_HC | 0.255 | 0.026 | 0.280 | |
buildGraph | 1.778 | 0.049 | 1.827 | |
check.conditions | 0.421 | 0.000 | 0.422 | |
check.design | 0.427 | 0.004 | 0.431 | |
checkClusterability | 2.240 | 0.831 | 3.110 | |
classic1wayAnova | 0 | 0 | 0 | |
compareNormalizationD_HC | 0.160 | 0.015 | 0.176 | |
compute.selection.table | 0.663 | 0.068 | 0.732 | |
compute_t_tests | 0.939 | 0.080 | 1.023 | |
corrMatrixD_HC | 0.508 | 0.021 | 0.529 | |
createMSnset | 1.502 | 0.080 | 1.583 | |
createMSnset2 | 1.453 | 0.045 | 1.499 | |
dapar_hc_ExportMenu | 0.107 | 0.024 | 0.132 | |
dapar_hc_chart | 0.046 | 0.006 | 0.052 | |
deleteLinesFromIndices | 0.464 | 0.016 | 0.480 | |
densityPlotD_HC | 2.265 | 0.606 | 2.892 | |
diffAnaComputeAdjustedPValues | 0.174 | 0.014 | 0.187 | |
diffAnaComputeFDR | 0 | 0 | 0 | |
diffAnaGetSignificant | 0.257 | 0.023 | 0.281 | |
diffAnaSave | 0.239 | 0.033 | 0.273 | |
diffAnaVolcanoplot | 0.175 | 0.014 | 0.189 | |
diffAnaVolcanoplot_rCharts | 0.335 | 0.040 | 0.376 | |
display.CC.visNet | 1.631 | 0.127 | 1.758 | |
enrich_GO | 3.967 | 0.189 | 4.162 | |
finalizeAggregation | 0 | 0 | 0 | |
findMECBlock | 0.480 | 0.012 | 0.491 | |
formatHSDResults | 0 | 0 | 0 | |
formatLimmaResult | 0.166 | 0.013 | 0.180 | |
formatPHResults | 0 | 0 | 0 | |
formatPHTResults | 0 | 0 | 0 | |
fudge2LRT | 0 | 0 | 0 | |
get.pep.prot.cc | 1.613 | 0.037 | 1.649 | |
getDesignLevel | 0.419 | 0.007 | 0.426 | |
getIndicesConditions | 0.424 | 0.005 | 0.429 | |
getIndicesOfLinesToRemove | 0.439 | 0.008 | 0.447 | |
getListNbValuesInLines | 0.423 | 0.007 | 0.431 | |
getNumberOf | 0.437 | 0.012 | 0.449 | |
getNumberOfEmptyLines | 0.453 | 0.008 | 0.462 | |
getPourcentageOfMV | 0.437 | 0.023 | 0.460 | |
getProcessingInfo | 0.423 | 0.008 | 0.430 | |
getProteinsStats | 0.454 | 0.009 | 0.463 | |
getQuantile4Imp | 0.115 | 0.004 | 0.119 | |
getTextForAggregation | 0.000 | 0.001 | 0.000 | |
getTextForAnaDiff | 0.000 | 0.000 | 0.001 | |
getTextForFiltering | 0 | 0 | 0 | |
getTextForGOAnalysis | 0.000 | 0.000 | 0.001 | |
getTextForHypothesisTest | 0 | 0 | 0 | |
getTextForNewDataset | 0.002 | 0.000 | 0.001 | |
getTextForNormalization | 0.001 | 0.000 | 0.000 | |
getTextForpeptideImputation | 0 | 0 | 0 | |
getTextForproteinImputation | 0.001 | 0.000 | 0.000 | |
globalAdjPval | 0.414 | 0.021 | 0.436 | |
group_GO | 4.158 | 0.217 | 4.381 | |
hc_logFC_DensityPlot | 0.514 | 0.151 | 0.668 | |
hc_mvTypePlot2 | 1.984 | 0.166 | 2.153 | |
heatmapD | 0.680 | 0.022 | 0.703 | |
heatmapForMissingValues | 0.200 | 0.012 | 0.211 | |
histPValue_HC | 0.219 | 0.026 | 0.245 | |
impute.pa2 | 0.470 | 0.015 | 0.487 | |
inner.aggregate.iter | 0.477 | 0.018 | 0.497 | |
inner.aggregate.topn | 0.459 | 0.011 | 0.470 | |
inner.mean | 0.438 | 0.020 | 0.459 | |
inner.sum | 0.452 | 0.015 | 0.467 | |
is.subset | 0.000 | 0.000 | 0.001 | |
limmaCompleteTest | 1.260 | 0.034 | 1.297 | |
listSheets | 0 | 0 | 0 | |
make.contrast | 0.425 | 0.007 | 0.431 | |
make.design.1 | 0.423 | 0.009 | 0.432 | |
make.design.2 | 0.428 | 0.006 | 0.434 | |
make.design.3 | 0.435 | 0.006 | 0.441 | |
make.design | 0.427 | 0.006 | 0.432 | |
match.metacell | 0.441 | 0.008 | 0.449 | |
metacell.def | 0.003 | 0.002 | 0.005 | |
metacellHisto_HC | 0.470 | 0.014 | 0.485 | |
metacellPerLinesHistoPerCondition_HC | 0.573 | 0.036 | 0.609 | |
metacellPerLinesHisto_HC | 0.650 | 0.066 | 0.717 | |
metacombine | 0.143 | 0.004 | 0.147 | |
mvImage | 1.836 | 0.068 | 1.907 | |
my_hc_ExportMenu | 0.114 | 0.025 | 0.139 | |
my_hc_chart | 0.109 | 0.022 | 0.132 | |
nonzero | 0.013 | 0.002 | 0.016 | |
normalizeMethods.dapar | 0 | 0 | 0 | |
pepa.test | 0.446 | 0.009 | 0.455 | |
pkgs.require | 0 | 0 | 0 | |
plotJitter | 1.584 | 0.015 | 1.600 | |
plotJitter_rCharts | 1.593 | 0.020 | 1.613 | |
plotPCA_Eigen | 0.497 | 0.017 | 0.514 | |
plotPCA_Eigen_hc | 0.432 | 0.007 | 0.439 | |
plotPCA_Ind | 0.430 | 0.011 | 0.442 | |
plotPCA_Var | 0.423 | 0.011 | 0.434 | |
postHocTest | 0 | 0 | 0 | |
proportionConRev_HC | 0.042 | 0.007 | 0.050 | |
rbindMSnset | 0.502 | 0.019 | 0.521 | |
reIntroduceMEC | 0.488 | 0.007 | 0.495 | |
readExcel | 0 | 0 | 0 | |
removeLines | 0.451 | 0.023 | 0.475 | |
samLRT | 0 | 0 | 0 | |
saveParameters | 0.427 | 0.008 | 0.435 | |
scatterplotEnrichGO_HC | 4.113 | 0.190 | 4.310 | |
search.metacell.tags | 0.006 | 0.001 | 0.007 | |
separateAdjPval | 0.197 | 0.008 | 0.204 | |
splitAdjacencyMat | 0.487 | 0.010 | 0.497 | |
test.design | 0.455 | 0.007 | 0.461 | |
testAnovaModels | 0.144 | 0.003 | 0.146 | |
thresholdpval4fdr | 0 | 0 | 0 | |
translatedRandomBeta | 0.000 | 0.001 | 0.002 | |
univ_AnnotDbPkg | 0.126 | 0.011 | 0.137 | |
violinPlotD | 0.324 | 0.004 | 0.328 | |
visualizeClusters | 1.064 | 0.060 | 1.126 | |
vsn | 0.717 | 0.010 | 0.727 | |
wrapper.CVDistD_HC | 1.683 | 0.432 | 2.129 | |
wrapper.compareNormalizationD_HC | 35.606 | 11.594 | 47.632 | |
wrapper.corrMatrixD_HC | 0.514 | 0.021 | 0.537 | |
wrapper.dapar.impute.mi | 13.499 | 0.242 | 13.754 | |
wrapper.heatmapD | 0.628 | 0.015 | 0.644 | |
wrapper.impute.KNN | 0.462 | 0.010 | 0.471 | |
wrapper.impute.detQuant | 0.494 | 0.015 | 0.510 | |
wrapper.impute.fixedValue | 0.529 | 0.024 | 0.554 | |
wrapper.impute.mle | 0.465 | 0.018 | 0.483 | |
wrapper.impute.pa | 0.161 | 0.006 | 0.167 | |
wrapper.impute.pa2 | 0.466 | 0.019 | 0.485 | |
wrapper.impute.slsa | 0.581 | 0.020 | 0.601 | |
wrapper.mvImage | 0.169 | 0.009 | 0.178 | |
wrapper.normalizeD | 0.439 | 0.006 | 0.444 | |
wrapper.pca | 0.169 | 0.011 | 0.180 | |
wrapperCalibrationPlot | 0.205 | 0.013 | 0.219 | |
wrapperClassic1wayAnova | 0 | 0 | 0 | |
wrapperRunClustering | 1.900 | 0.150 | 2.054 | |
write.excel | 0.839 | 0.056 | 0.897 | |
writeMSnsetToCSV | 0.466 | 0.016 | 0.481 | |
writeMSnsetToExcel | 1.000 | 0.092 | 1.096 | |