Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:35:53 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 500/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.34.6 (landing page) Samuel Wieczorek
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.34.6 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DAPAR_1.34.6.tar.gz |
StartedAt: 2024-03-27 21:42:26 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 21:47:21 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 295.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DAPAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings DAPAR_1.34.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/DAPAR.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘DAPAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DAPAR’ version ‘1.34.6’ * 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 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘knitr’ ‘norm’ ‘org.Sc.sgd.db’ ‘parallel’ ‘scales’ ‘tidyverse’ 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 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’ 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 28.546 1.704 30.250 wrapper.dapar.impute.mi 12.700 0.124 12.826 barplotEnrichGO_HC 8.562 0.636 9.199 barplotGroupGO_HC 5.106 0.304 5.411 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/DAPAR.Rcheck/00check.log’ for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 ** 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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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 1.34.6. 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 18 | SKIP 0 | PASS 66 ] [ FAIL 0 | WARN 18 | SKIP 0 | PASS 66 ] > > proc.time() user system elapsed 22.177 0.909 23.083
DAPAR.Rcheck/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 1.643 | 0.060 | 1.704 | |
BuildAdjacencyMatrix | 0.298 | 0.004 | 0.303 | |
BuildColumnToProteinDataset | 0.820 | 0.064 | 0.883 | |
BuildMetaCell | 0.495 | 0.016 | 0.511 | |
CVDistD_HC | 2.201 | 0.076 | 2.286 | |
Children | 0.004 | 0.000 | 0.004 | |
CountPep | 0.352 | 0.004 | 0.356 | |
ExtendPalette | 0.022 | 0.004 | 0.026 | |
GOAnalysisSave | 0 | 0 | 0 | |
GetCC | 1.509 | 0.072 | 1.582 | |
GetColorsForConditions | 0.240 | 0.000 | 0.241 | |
GetDetailedNbPeptides | 0.256 | 0.007 | 0.264 | |
GetDetailedNbPeptidesUsed | 0 | 0 | 0 | |
GetIndices_BasedOnConditions | 0.248 | 0.009 | 0.256 | |
GetIndices_MetacellFiltering | 0.261 | 0.000 | 0.261 | |
GetIndices_WholeLine | 0.251 | 0.003 | 0.254 | |
GetIndices_WholeMatrix | 0.251 | 0.004 | 0.255 | |
GetKeyId | 0.255 | 0.000 | 0.255 | |
GetMatAdj | 0.281 | 0.004 | 0.285 | |
GetMetacell | 0 | 0 | 0 | |
GetMetacellTags | 0.254 | 0.000 | 0.254 | |
GetNbPeptidesUsed | 0.255 | 0.004 | 0.259 | |
GetNbTags | 0 | 0 | 0 | |
GetSoftAvailables | 0 | 0 | 0 | |
GetTypeofData | 0.227 | 0.015 | 0.244 | |
Get_AllComparisons | 0.203 | 0.020 | 0.225 | |
GlobalQuantileAlignment | 0.266 | 0.000 | 0.266 | |
GraphPepProt | 0.258 | 0.000 | 0.259 | |
LH0 | 0 | 0 | 0 | |
LH0.lm | 0 | 0 | 0 | |
LH1 | 0 | 0 | 0 | |
LH1.lm | 0 | 0 | 0 | |
LOESS | 0.985 | 0.008 | 0.992 | |
MeanCentering | 0.245 | 0.000 | 0.244 | |
MetaCellFiltering | 0.411 | 0.024 | 0.434 | |
MetacellFilteringScope | 0 | 0 | 0 | |
Metacell_DIA_NN | 0.428 | 0.012 | 0.440 | |
Metacell_generic | 0.467 | 0.000 | 0.467 | |
Metacell_maxquant | 0.430 | 0.000 | 0.429 | |
Metacell_proline | 0.429 | 0.000 | 0.429 | |
NumericalFiltering | 0.304 | 0.004 | 0.308 | |
NumericalgetIndicesOfLinesToRemove | 0.324 | 0.008 | 0.333 | |
OWAnova | 0.007 | 0.000 | 0.008 | |
QuantileCentering | 0.263 | 0.000 | 0.263 | |
SetCC | 1.380 | 0.052 | 1.432 | |
SetMatAdj | 0.284 | 0.000 | 0.284 | |
Set_POV_MEC_tags | 0.252 | 0.004 | 0.255 | |
StringBasedFiltering | 0.283 | 0.004 | 0.288 | |
StringBasedFiltering2 | 0.282 | 0.000 | 0.282 | |
SumByColumns | 1.091 | 0.028 | 1.120 | |
SymFilteringOperators | 0 | 0 | 0 | |
UpdateMetacellAfterImputation | 0.266 | 0.000 | 0.265 | |
aggregateIter | 0.389 | 0.004 | 0.393 | |
aggregateIterParallel | 0.000 | 0.000 | 0.001 | |
aggregateMean | 0.326 | 0.000 | 0.326 | |
aggregateSum | 0.367 | 0.000 | 0.367 | |
aggregateTopn | 0.315 | 0.016 | 0.331 | |
applyAnovasOnProteins | 0.076 | 0.007 | 0.083 | |
averageIntensities | 0.422 | 0.048 | 0.470 | |
barplotEnrichGO_HC | 8.562 | 0.636 | 9.199 | |
barplotGroupGO_HC | 5.106 | 0.304 | 5.411 | |
boxPlotD_HC | 0.171 | 0.016 | 0.188 | |
buildGraph | 1.017 | 0.064 | 1.081 | |
check.conditions | 0.24 | 0.00 | 0.24 | |
check.design | 0.240 | 0.000 | 0.241 | |
checkClusterability | 1.988 | 0.204 | 2.192 | |
classic1wayAnova | 0 | 0 | 0 | |
compareNormalizationD_HC | 0.103 | 0.012 | 0.116 | |
compute.selection.table | 0.576 | 0.032 | 0.608 | |
compute_t_tests | 0.942 | 0.024 | 0.967 | |
corrMatrixD_HC | 0.309 | 0.012 | 0.320 | |
createMSnset | 1.528 | 0.024 | 1.552 | |
dapar_hc_ExportMenu | 0.094 | 0.024 | 0.119 | |
dapar_hc_chart | 0.041 | 0.008 | 0.048 | |
deleteLinesFromIndices | 0.278 | 0.000 | 0.278 | |
densityPlotD_HC | 1.755 | 0.092 | 1.846 | |
diffAnaComputeAdjustedPValues | 0.123 | 0.000 | 0.122 | |
diffAnaComputeFDR | 0 | 0 | 0 | |
diffAnaGetSignificant | 0.193 | 0.012 | 0.206 | |
diffAnaSave | 0.180 | 0.016 | 0.196 | |
diffAnaVolcanoplot | 0.119 | 0.008 | 0.127 | |
diffAnaVolcanoplot_rCharts | 0.247 | 0.032 | 0.278 | |
display.CC.visNet | 1.248 | 0.116 | 1.364 | |
enrich_GO | 4.229 | 0.180 | 4.410 | |
finalizeAggregation | 0 | 0 | 0 | |
findMECBlock | 0.281 | 0.004 | 0.285 | |
formatHSDResults | 0 | 0 | 0 | |
formatLimmaResult | 0.107 | 0.004 | 0.111 | |
formatPHResults | 0 | 0 | 0 | |
formatPHTResults | 0.001 | 0.000 | 0.000 | |
fudge2LRT | 0 | 0 | 0 | |
get.pep.prot.cc | 1.105 | 0.052 | 1.156 | |
getDesignLevel | 0.241 | 0.000 | 0.241 | |
getIndicesConditions | 0.247 | 0.001 | 0.247 | |
getIndicesOfLinesToRemove | 0.249 | 0.007 | 0.256 | |
getListNbValuesInLines | 0.241 | 0.000 | 0.241 | |
getNumberOf | 0.252 | 0.004 | 0.256 | |
getNumberOfEmptyLines | 0.262 | 0.008 | 0.270 | |
getPourcentageOfMV | 0.256 | 0.004 | 0.260 | |
getProcessingInfo | 0.241 | 0.000 | 0.242 | |
getProteinsStats | 0.261 | 0.004 | 0.264 | |
getQuantile4Imp | 0.057 | 0.004 | 0.061 | |
getTextForAggregation | 0.000 | 0.000 | 0.001 | |
getTextForAnaDiff | 0.001 | 0.000 | 0.000 | |
getTextForFiltering | 0 | 0 | 0 | |
getTextForGOAnalysis | 0.000 | 0.000 | 0.001 | |
getTextForHypothesisTest | 0 | 0 | 0 | |
getTextForNewDataset | 0.002 | 0.000 | 0.002 | |
getTextForNormalization | 0 | 0 | 0 | |
getTextForpeptideImputation | 0 | 0 | 0 | |
getTextForproteinImputation | 0 | 0 | 0 | |
globalAdjPval | 0.340 | 0.020 | 0.359 | |
group_GO | 4.387 | 0.124 | 4.511 | |
hc_logFC_DensityPlot | 0.360 | 0.024 | 0.384 | |
hc_mvTypePlot2 | 0.541 | 0.036 | 0.577 | |
heatmapD | 0.600 | 0.004 | 0.604 | |
heatmapForMissingValues | 0.144 | 0.000 | 0.144 | |
histPValue_HC | 0.162 | 0.004 | 0.165 | |
impute.pa2 | 0.294 | 0.000 | 0.294 | |
inner.aggregate.iter | 0.306 | 0.000 | 0.306 | |
inner.aggregate.topn | 0.316 | 0.008 | 0.324 | |
inner.mean | 0.282 | 0.000 | 0.282 | |
inner.sum | 0.290 | 0.008 | 0.297 | |
is.subset | 0 | 0 | 0 | |
limmaCompleteTest | 1.951 | 0.056 | 2.006 | |
listSheets | 0 | 0 | 0 | |
make.contrast | 0.241 | 0.000 | 0.241 | |
make.design.1 | 0.237 | 0.004 | 0.241 | |
make.design.2 | 0.245 | 0.004 | 0.249 | |
make.design.3 | 0.243 | 0.000 | 0.242 | |
make.design | 0.243 | 0.000 | 0.243 | |
match.metacell | 0.255 | 0.000 | 0.256 | |
metacell.def | 0.003 | 0.000 | 0.004 | |
metacellHisto_HC | 0.284 | 0.004 | 0.289 | |
metacellPerLinesHistoPerCondition_HC | 0.380 | 0.016 | 0.397 | |
metacellPerLinesHisto_HC | 0.467 | 0.028 | 0.496 | |
metacombine | 0.053 | 0.000 | 0.053 | |
mvImage | 1.727 | 0.044 | 1.771 | |
my_hc_ExportMenu | 0.107 | 0.016 | 0.123 | |
my_hc_chart | 0.113 | 0.016 | 0.129 | |
nonzero | 0.019 | 0.000 | 0.019 | |
normalizeMethods.dapar | 0 | 0 | 0 | |
pepa.test | 0.261 | 0.004 | 0.265 | |
pkgs.require | 0 | 0 | 0 | |
plotJitter | 1.074 | 0.020 | 1.094 | |
plotJitter_rCharts | 1.028 | 0.012 | 1.040 | |
plotPCA_Eigen | 0.307 | 0.000 | 0.307 | |
plotPCA_Eigen_hc | 0.242 | 0.000 | 0.242 | |
plotPCA_Ind | 0.249 | 0.000 | 0.249 | |
plotPCA_Var | 0.245 | 0.000 | 0.244 | |
postHocTest | 0 | 0 | 0 | |
proportionConRev_HC | 0.037 | 0.004 | 0.041 | |
rbindMSnset | 0.306 | 0.004 | 0.310 | |
reIntroduceMEC | 0.281 | 0.000 | 0.280 | |
readExcel | 0 | 0 | 0 | |
removeLines | 0.272 | 0.000 | 0.272 | |
samLRT | 0.001 | 0.000 | 0.000 | |
saveParameters | 0.241 | 0.000 | 0.241 | |
scatterplotEnrichGO_HC | 4.373 | 0.120 | 4.494 | |
search.metacell.tags | 0.005 | 0.000 | 0.005 | |
separateAdjPval | 0.134 | 0.004 | 0.138 | |
splitAdjacencyMat | 0.277 | 0.000 | 0.277 | |
test.design | 0.262 | 0.004 | 0.266 | |
testAnovaModels | 0.08 | 0.00 | 0.08 | |
thresholdpval4fdr | 0 | 0 | 0 | |
translatedRandomBeta | 0.000 | 0.002 | 0.003 | |
univ_AnnotDbPkg | 0.118 | 0.004 | 0.123 | |
violinPlotD | 0.213 | 0.000 | 0.213 | |
visualizeClusters | 0.990 | 0.044 | 1.034 | |
vsn | 0.696 | 0.000 | 0.696 | |
wrapper.CVDistD_HC | 1.251 | 0.124 | 1.375 | |
wrapper.compareNormalizationD_HC | 28.546 | 1.704 | 30.250 | |
wrapper.corrMatrixD_HC | 0.314 | 0.012 | 0.326 | |
wrapper.dapar.impute.mi | 12.700 | 0.124 | 12.826 | |
wrapper.heatmapD | 0.478 | 0.004 | 0.482 | |
wrapper.impute.KNN | 0.267 | 0.004 | 0.271 | |
wrapper.impute.detQuant | 0.291 | 0.004 | 0.295 | |
wrapper.impute.fixedValue | 0.293 | 0.004 | 0.297 | |
wrapper.impute.mle | 0.27 | 0.00 | 0.27 | |
wrapper.impute.pa | 0.089 | 0.000 | 0.089 | |
wrapper.impute.pa2 | 0.273 | 0.004 | 0.276 | |
wrapper.impute.slsa | 0.425 | 0.000 | 0.425 | |
wrapper.mvImage | 0.100 | 0.004 | 0.104 | |
wrapper.normalizeD | 0.249 | 0.000 | 0.249 | |
wrapper.pca | 0.101 | 0.000 | 0.101 | |
wrapperCalibrationPlot | 0.135 | 0.004 | 0.139 | |
wrapperClassic1wayAnova | 0 | 0 | 0 | |
wrapperRunClustering | 1.610 | 0.056 | 1.666 | |
write.excel | 0.512 | 0.008 | 0.520 | |
writeMSnsetToCSV | 0.256 | 0.010 | 0.266 | |
writeMSnsetToExcel | 0.647 | 0.020 | 0.668 | |