Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
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 509/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.36.1 (landing page) Samuel Wieczorek
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | TIMEOUT | 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: 1.36.1 |
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_1.36.1.tar.gz |
StartedAt: 2024-06-10 12:53:56 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 13:33:57 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 2401.1 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: DAPAR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.36.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/DAPAR.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DAPAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DAPAR’ version ‘1.36.1’ * 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 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 ...
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 ** 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/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 0.409 | 0.013 | 0.652 | |
BuildAdjacencyMatrix | 1.695 | 0.016 | 2.519 | |
BuildColumnToProteinDataset | 0.362 | 0.009 | 0.565 | |
BuildMetaCell | 0.792 | 0.034 | 1.246 | |
CVDistD_HC | 2.189 | 0.165 | 3.821 | |
Children | 0.006 | 0.000 | 0.010 | |
CountPep | 0.313 | 0.007 | 0.516 | |
ExtendPalette | 0.028 | 0.002 | 0.046 | |
GOAnalysisSave | 0 | 0 | 0 | |
GetCC | 4.844 | 0.042 | 8.138 | |
GetColorsForConditions | 0.255 | 0.005 | 0.414 | |
GetDetailedNbPeptides | 0.289 | 0.007 | 0.506 | |
GetDetailedNbPeptidesUsed | 0.001 | 0.000 | 0.000 | |
GetIndices_BasedOnConditions | 0.275 | 0.008 | 0.473 | |
GetIndices_MetacellFiltering | 0.281 | 0.008 | 0.496 | |
GetIndices_WholeLine | 0.272 | 0.007 | 0.463 | |
GetIndices_WholeMatrix | 0.269 | 0.007 | 0.439 | |
GetKeyId | 0.253 | 0.007 | 0.431 | |
GetMatAdj | 0.312 | 0.009 | 0.523 | |
GetMetacell | 0 | 0 | 0 | |
GetMetacellTags | 0.274 | 0.009 | 0.469 | |
GetNbPeptidesUsed | 0.278 | 0.009 | 0.502 | |
GetNbTags | 0 | 0 | 0 | |
GetSoftAvailables | 0.001 | 0.001 | 0.001 | |
GetTypeofData | 0.255 | 0.008 | 0.446 | |
Get_AllComparisons | 0.235 | 0.010 | 0.439 | |
GlobalQuantileAlignment | 0.322 | 0.019 | 0.632 | |
GraphPepProt | 0.283 | 0.007 | 0.494 | |
LH0 | 0 | 0 | 0 | |
LH0.lm | 0 | 0 | 0 | |
LH1 | 0.000 | 0.001 | 0.000 | |
LH1.lm | 0.000 | 0.000 | 0.001 | |
LOESS | 0.845 | 0.019 | 1.623 | |
MeanCentering | 0.270 | 0.011 | 0.475 | |
MetaCellFiltering | 0.494 | 0.020 | 0.843 | |
MetacellFilteringScope | 0.001 | 0.000 | 0.000 | |
Metacell_DIA_NN | 0.689 | 0.018 | 1.154 | |
Metacell_generic | 0.534 | 0.017 | 0.866 | |
Metacell_maxquant | 0.620 | 0.022 | 1.031 | |
Metacell_proline | 0.528 | 0.017 | 0.917 | |
NumericalFiltering | 0.298 | 0.008 | 0.531 | |
NumericalgetIndicesOfLinesToRemove | 0.254 | 0.006 | 0.415 | |
OWAnova | 0.007 | 0.001 | 0.015 | |
QuantileCentering | 0.239 | 0.007 | 0.391 | |
SetCC | 3.200 | 0.034 | 5.254 | |
SetMatAdj | 0.288 | 0.006 | 0.477 | |
Set_POV_MEC_tags | 0.259 | 0.006 | 0.456 | |
StringBasedFiltering | 0.288 | 0.008 | 0.488 | |
StringBasedFiltering2 | 0.287 | 0.007 | 0.511 | |
SumByColumns | 1.197 | 0.017 | 2.029 | |
SymFilteringOperators | 0 | 0 | 0 | |
UpdateMetacellAfterImputation | 0.270 | 0.007 | 0.465 | |
aggregateIter | 0.430 | 0.009 | 0.732 | |
aggregateIterParallel | 0 | 0 | 0 | |
aggregateMean | 0.396 | 0.009 | 0.705 | |
aggregateSum | 0.355 | 0.010 | 0.570 | |
aggregateTopn | 0.320 | 0.007 | 0.492 | |
applyAnovasOnProteins | 0.078 | 0.002 | 0.107 | |
averageIntensities | 0.751 | 0.255 | 8.341 | |
barplotEnrichGO_HC | 14.187 | 5.739 | 239.406 | |
barplotGroupGO_HC | 6.358 | 1.810 | 77.776 | |
boxPlotD_HC | 0.476 | 0.217 | 7.839 | |
buildGraph | 2.454 | 0.117 | 9.114 | |
check.conditions | 0.239 | 0.007 | 0.514 | |
check.design | 0.242 | 0.008 | 0.585 | |
checkClusterability | 8.293 | 8.312 | 359.625 | |
classic1wayAnova | 0 | 0 | 0 | |
compareNormalizationD_HC | 0.179 | 0.130 | 2.053 | |
compute.selection.table | 1.292 | 0.531 | 17.901 | |
compute_t_tests | 2.509 | 0.912 | 33.253 | |
corrMatrixD_HC | 0.565 | 0.232 | 4.969 | |
createMSnset | 2.308 | 0.323 | 12.698 | |
createMSnset2 | 2.290 | 0.296 | 12.235 | |
dapar_hc_ExportMenu | 0.257 | 0.357 | 4.085 | |
dapar_hc_chart | 0.115 | 0.123 | 1.550 | |
deleteLinesFromIndices | 0.377 | 0.072 | 2.922 | |
densityPlotD_HC | 7.859 | 6.394 | 257.018 | |
diffAnaComputeAdjustedPValues | 0.267 | 0.125 | 4.461 | |
diffAnaComputeFDR | 0 | 0 | 0 | |
diffAnaGetSignificant | 0.575 | 0.287 | 10.857 | |
diffAnaSave | 0.517 | 0.249 | 10.320 | |
diffAnaVolcanoplot | 0.277 | 0.125 | 4.836 | |
diffAnaVolcanoplot_rCharts | 0.807 | 0.425 | 14.279 | |
display.CC.visNet | 2.254 | 0.260 | 12.658 | |
enrich_GO | 5.680 | 1.736 | 66.815 | |
finalizeAggregation | 0.000 | 0.000 | 0.001 | |
findMECBlock | 0.351 | 0.044 | 1.978 | |
formatHSDResults | 0 | 0 | 0 | |
formatLimmaResult | 0.249 | 0.112 | 4.524 | |
formatPHResults | 0 | 0 | 0 | |
formatPHTResults | 0.000 | 0.000 | 0.001 | |
fudge2LRT | 0.000 | 0.001 | 0.000 | |
get.pep.prot.cc | 2.378 | 0.072 | 5.453 | |
getDesignLevel | 0.238 | 0.008 | 0.460 | |
getIndicesConditions | 0.239 | 0.009 | 0.499 | |
getIndicesOfLinesToRemove | 0.293 | 0.035 | 1.605 | |
getListNbValuesInLines | 0.227 | 0.007 | 0.426 | |
getNumberOf | 0.303 | 0.044 | 1.974 | |
getNumberOfEmptyLines | 0.269 | 0.021 | 1.000 | |
getPourcentageOfMV | 0.293 | 0.036 | 1.876 | |
getProcessingInfo | 0.242 | 0.010 | 0.478 | |
getProteinsStats | 0.324 | 0.049 | 2.214 | |
getQuantile4Imp | 0.062 | 0.006 | 0.202 | |
getTextForAggregation | 0.001 | 0.000 | 0.001 | |
getTextForAnaDiff | 0.000 | 0.000 | 0.001 | |
getTextForFiltering | 0.000 | 0.000 | 0.001 | |
getTextForGOAnalysis | 0 | 0 | 0 | |
getTextForHypothesisTest | 0 | 0 | 0 | |
getTextForNewDataset | 0.004 | 0.001 | 0.032 | |
getTextForNormalization | 0 | 0 | 0 | |
getTextForpeptideImputation | 0.001 | 0.000 | 0.000 | |
getTextForproteinImputation | 0.001 | 0.000 | 0.001 | |
globalAdjPval | 0.611 | 0.182 | 7.678 | |
group_GO | 5.749 | 1.596 | 62.254 | |
hc_logFC_DensityPlot | 1.545 | 1.155 | 45.618 | |
hc_mvTypePlot2 | 1.570 | 1.089 | 39.069 | |
heatmapD | 0.798 | 0.116 | 3.637 | |
heatmapForMissingValues | 0.227 | 0.063 | 2.657 | |
histPValue_HC | 0.364 | 0.208 | 5.888 | |
impute.pa2 | 0.419 | 0.086 | 3.603 | |
inner.aggregate.iter | 0.440 | 0.077 | 3.397 | |
inner.aggregate.topn | 0.362 | 0.051 | 2.258 | |
inner.mean | 0.343 | 0.040 | 1.659 | |
inner.sum | 0.468 | 0.045 | 1.972 | |
is.subset | 0.000 | 0.000 | 0.001 | |
limmaCompleteTest | 1.614 | 0.186 | 8.000 | |
listSheets | 0.000 | 0.000 | 0.001 | |
make.contrast | 0.283 | 0.010 | 0.581 | |
make.design.1 | 0.288 | 0.009 | 0.532 | |
make.design.2 | 0.285 | 0.010 | 0.494 | |
make.design.3 | 0.292 | 0.012 | 0.589 | |
make.design | 0.289 | 0.009 | 0.506 | |
match.metacell | 0.695 | 0.048 | 2.367 | |
metacell.def | 0.010 | 0.006 | 0.181 | |
metacellHisto_HC | 0.378 | 0.124 | 2.271 | |
metacellPerLinesHistoPerCondition_HC | 0.563 | 0.254 | 5.097 | |
metacellPerLinesHisto_HC | 0.877 | 0.643 | 12.042 | |
metacombine | 0.089 | 0.027 | 1.075 | |
mvImage | 2.683 | 0.496 | 21.102 | |
my_hc_ExportMenu | 0.250 | 0.314 | 4.375 | |
my_hc_chart | 0.241 | 0.281 | 3.952 | |
nonzero | 0.019 | 0.001 | 0.115 | |
normalizeMethods.dapar | 0.000 | 0.001 | 0.000 | |
pepa.test | 0.317 | 0.033 | 2.290 | |
pkgs.require | 0 | 0 | 0 | |
plotJitter | 2.443 | 0.094 | 6.903 | |
plotJitter_rCharts | 2.363 | 0.230 | 8.175 | |
plotPCA_Eigen | 0.446 | 0.131 | 3.808 | |
plotPCA_Eigen_hc | 0.236 | 0.008 | 0.414 | |
plotPCA_Ind | 0.256 | 0.013 | 0.568 | |
plotPCA_Var | 0.241 | 0.008 | 0.411 | |
postHocTest | 0 | 0 | 0 | |
proportionConRev_HC | 0.092 | 0.126 | 1.597 | |
rbindMSnset | 0.514 | 0.153 | 6.220 | |
reIntroduceMEC | 0.403 | 0.089 | 3.736 | |
readExcel | 0 | 0 | 0 | |
removeLines | 0.335 | 0.052 | 1.933 | |
samLRT | 0 | 0 | 0 | |
saveParameters | 0.248 | 0.014 | 0.544 | |
scatterplotEnrichGO_HC | 5.644 | 1.469 | 52.669 | |
search.metacell.tags | 0.019 | 0.010 | 0.403 | |
separateAdjPval | 0.213 | 0.051 | 1.992 | |
splitAdjacencyMat | 0.347 | 0.043 | 1.893 | |
test.design | 0.283 | 0.009 | 0.506 | |
testAnovaModels | 0.139 | 0.042 | 1.570 | |
thresholdpval4fdr | 0 | 0 | 0 | |
translatedRandomBeta | 0.002 | 0.010 | 0.098 | |
univ_AnnotDbPkg | 0.339 | 0.109 | 2.387 | |
violinPlotD | 0.251 | 0.047 | 1.579 | |
visualizeClusters | 2.306 | 0.588 | 24.100 | |
vsn | 0.521 | 0.042 | 2.209 | |
wrapper.CVDistD_HC | 2.515 | 1.269 | 42.179 | |