Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 504/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.38.0 (landing page) Samuel Wieczorek
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 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: 1.38.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DAPAR_1.38.0.tar.gz |
StartedAt: 2024-12-19 22:24:41 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 22:35:59 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 677.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: DAPAR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DAPAR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DAPAR_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘DAPAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DAPAR’ version ‘1.38.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' NOTE 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 33.226 10.935 44.534 wrapper.dapar.impute.mi 13.479 0.346 13.837 barplotEnrichGO_HC 6.809 0.936 7.761 * 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-3.20-bioc/meat/DAPAR.Rcheck/00check.log’ for details.
DAPAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DAPAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 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 1.38.0. 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 28.996 1.291 30.373
DAPAR.Rcheck/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 0.536 | 0.013 | 0.548 | |
BuildAdjacencyMatrix | 0.461 | 0.007 | 0.468 | |
BuildColumnToProteinDataset | 0.504 | 0.014 | 0.519 | |
BuildMetaCell | 0.502 | 0.038 | 0.541 | |
CVDistD_HC | 2.123 | 0.189 | 2.331 | |
Children | 0.004 | 0.001 | 0.005 | |
CountPep | 1.297 | 0.327 | 1.624 | |
ExtendPalette | 0.023 | 0.001 | 0.023 | |
GOAnalysisSave | 0 | 0 | 0 | |
GetCC | 1.999 | 0.076 | 2.074 | |
GetColorsForConditions | 0.410 | 0.024 | 0.435 | |
GetDetailedNbPeptides | 0.439 | 0.005 | 0.445 | |
GetDetailedNbPeptidesUsed | 0 | 0 | 0 | |
GetIndices_BasedOnConditions | 0.431 | 0.010 | 0.441 | |
GetIndices_MetacellFiltering | 0.445 | 0.015 | 0.460 | |
GetIndices_WholeLine | 0.439 | 0.010 | 0.449 | |
GetIndices_WholeMatrix | 0.435 | 0.015 | 0.451 | |
GetKeyId | 0.420 | 0.012 | 0.432 | |
GetMatAdj | 0.463 | 0.014 | 0.477 | |
GetMetacell | 0.000 | 0.000 | 0.001 | |
GetMetacellTags | 0.430 | 0.018 | 0.447 | |
GetNbPeptidesUsed | 0.435 | 0.025 | 0.459 | |
GetNbTags | 0 | 0 | 0 | |
GetSoftAvailables | 0.000 | 0.000 | 0.001 | |
GetTypeofData | 0.418 | 0.015 | 0.433 | |
Get_AllComparisons | 0.254 | 0.024 | 0.278 | |
GlobalQuantileAlignment | 0.442 | 0.012 | 0.456 | |
GraphPepProt | 0.440 | 0.009 | 0.449 | |
LH0 | 0 | 0 | 0 | |
LH0.lm | 0 | 0 | 0 | |
LH1 | 0 | 0 | 0 | |
LH1.lm | 0 | 0 | 0 | |
LOESS | 1.125 | 0.014 | 1.139 | |
MeanCentering | 0.442 | 0.025 | 0.467 | |
MetaCellFiltering | 0.560 | 0.006 | 0.566 | |
MetacellFilteringScope | 0 | 0 | 0 | |
Metacell_DIA_NN | 0.424 | 0.005 | 0.429 | |
Metacell_generic | 0.358 | 0.002 | 0.360 | |
Metacell_maxquant | 0.382 | 0.001 | 0.384 | |
Metacell_proline | 0.358 | 0.002 | 0.360 | |
NumericalFiltering | 0.454 | 0.008 | 0.462 | |
NumericalgetIndicesOfLinesToRemove | 0.424 | 0.009 | 0.433 | |
OWAnova | 0.005 | 0.001 | 0.006 | |
QuantileCentering | 0.416 | 0.009 | 0.425 | |
SetCC | 1.964 | 0.108 | 2.072 | |
SetMatAdj | 0.448 | 0.013 | 0.461 | |
Set_POV_MEC_tags | 0.435 | 0.002 | 0.437 | |
StringBasedFiltering | 0.453 | 0.008 | 0.461 | |
StringBasedFiltering2 | 0.447 | 0.008 | 0.455 | |
SumByColumns | 1.172 | 0.021 | 1.193 | |
SymFilteringOperators | 0 | 0 | 0 | |
UpdateMetacellAfterImputation | 0.447 | 0.006 | 0.453 | |
aggregateIter | 0.569 | 0.010 | 0.579 | |
aggregateIterParallel | 0 | 0 | 0 | |
aggregateMean | 0.490 | 0.008 | 0.498 | |
aggregateSum | 0.512 | 0.004 | 0.517 | |
aggregateTopn | 0.474 | 0.014 | 0.488 | |
applyAnovasOnProteins | 0.128 | 0.001 | 0.130 | |
averageIntensities | 0.435 | 0.042 | 0.478 | |
barplotEnrichGO_HC | 6.809 | 0.936 | 7.761 | |
barplotGroupGO_HC | 4.030 | 0.339 | 4.377 | |
boxPlotD_HC | 0.271 | 0.030 | 0.302 | |
buildGraph | 1.455 | 0.143 | 1.599 | |
check.conditions | 0.406 | 0.007 | 0.412 | |
check.design | 0.404 | 0.020 | 0.423 | |
checkClusterability | 2.575 | 0.912 | 3.516 | |
classic1wayAnova | 0 | 0 | 0 | |
compareNormalizationD_HC | 0.154 | 0.011 | 0.166 | |
compute.selection.table | 0.598 | 0.056 | 0.655 | |
compute_t_tests | 0.947 | 0.110 | 1.059 | |
corrMatrixD_HC | 0.523 | 0.037 | 0.559 | |
createMSnset | 1.376 | 0.086 | 1.463 | |
createMSnset2 | 1.332 | 0.048 | 1.380 | |
dapar_hc_ExportMenu | 0.102 | 0.029 | 0.131 | |
dapar_hc_chart | 0.041 | 0.012 | 0.054 | |
deleteLinesFromIndices | 0.444 | 0.016 | 0.460 | |
densityPlotD_HC | 2.259 | 0.682 | 2.955 | |
diffAnaComputeAdjustedPValues | 0.168 | 0.016 | 0.185 | |
diffAnaComputeFDR | 0.001 | 0.000 | 0.000 | |
diffAnaGetSignificant | 0.241 | 0.030 | 0.272 | |
diffAnaSave | 0.233 | 0.018 | 0.251 | |
diffAnaVolcanoplot | 0.17 | 0.01 | 0.18 | |
diffAnaVolcanoplot_rCharts | 0.324 | 0.051 | 0.376 | |
display.CC.visNet | 1.572 | 0.143 | 1.715 | |
enrich_GO | 3.859 | 0.188 | 4.054 | |
finalizeAggregation | 0.001 | 0.000 | 0.001 | |
findMECBlock | 0.452 | 0.010 | 0.461 | |
formatHSDResults | 0 | 0 | 0 | |
formatLimmaResult | 0.160 | 0.009 | 0.169 | |
formatPHResults | 0 | 0 | 0 | |
formatPHTResults | 0 | 0 | 0 | |
fudge2LRT | 0 | 0 | 0 | |
get.pep.prot.cc | 1.484 | 0.117 | 1.602 | |
getDesignLevel | 0.413 | 0.008 | 0.422 | |
getIndicesConditions | 0.407 | 0.010 | 0.416 | |
getIndicesOfLinesToRemove | 0.419 | 0.012 | 0.431 | |
getListNbValuesInLines | 0.405 | 0.010 | 0.415 | |
getNumberOf | 0.419 | 0.012 | 0.431 | |
getNumberOfEmptyLines | 0.431 | 0.009 | 0.440 | |
getPourcentageOfMV | 0.425 | 0.012 | 0.436 | |
getProcessingInfo | 0.405 | 0.009 | 0.413 | |
getProteinsStats | 0.434 | 0.009 | 0.443 | |
getQuantile4Imp | 0.111 | 0.002 | 0.114 | |
getTextForAggregation | 0 | 0 | 0 | |
getTextForAnaDiff | 0.001 | 0.000 | 0.000 | |
getTextForFiltering | 0 | 0 | 0 | |
getTextForGOAnalysis | 0.000 | 0.000 | 0.001 | |
getTextForHypothesisTest | 0 | 0 | 0 | |
getTextForNewDataset | 0.001 | 0.000 | 0.002 | |
getTextForNormalization | 0.000 | 0.000 | 0.001 | |
getTextForpeptideImputation | 0 | 0 | 0 | |
getTextForproteinImputation | 0.000 | 0.000 | 0.001 | |
globalAdjPval | 0.385 | 0.016 | 0.402 | |
group_GO | 3.841 | 0.132 | 3.978 | |
hc_logFC_DensityPlot | 0.465 | 0.096 | 0.565 | |
hc_mvTypePlot2 | 0.799 | 0.100 | 0.902 | |
heatmapD | 0.672 | 0.024 | 0.696 | |
heatmapForMissingValues | 0.189 | 0.007 | 0.197 | |
histPValue_HC | 0.214 | 0.012 | 0.227 | |
impute.pa2 | 0.463 | 0.013 | 0.476 | |
inner.aggregate.iter | 0.472 | 0.016 | 0.487 | |
inner.aggregate.topn | 0.451 | 0.012 | 0.463 | |
inner.mean | 0.487 | 0.008 | 0.495 | |
inner.sum | 0.455 | 0.004 | 0.458 | |
is.subset | 0 | 0 | 0 | |
limmaCompleteTest | 1.259 | 0.018 | 1.277 | |
listSheets | 0 | 0 | 0 | |
make.contrast | 0.434 | 0.010 | 0.444 | |
make.design.1 | 0.432 | 0.009 | 0.441 | |
make.design.2 | 0.430 | 0.016 | 0.446 | |
make.design.3 | 0.531 | 0.019 | 0.550 | |
make.design | 0.432 | 0.005 | 0.438 | |
match.metacell | 0.447 | 0.011 | 0.458 | |
metacell.def | 0.004 | 0.000 | 0.004 | |
metacellHisto_HC | 0.473 | 0.012 | 0.485 | |
metacellPerLinesHistoPerCondition_HC | 0.559 | 0.021 | 0.580 | |
metacellPerLinesHisto_HC | 0.656 | 0.042 | 0.698 | |
metacombine | 0.049 | 0.002 | 0.052 | |
mvImage | 1.853 | 0.058 | 1.914 | |
my_hc_ExportMenu | 0.105 | 0.023 | 0.128 | |
my_hc_chart | 0.099 | 0.025 | 0.124 | |
nonzero | 0.015 | 0.000 | 0.014 | |
normalizeMethods.dapar | 0 | 0 | 0 | |
pepa.test | 0.452 | 0.010 | 0.462 | |
pkgs.require | 0.000 | 0.000 | 0.001 | |
plotJitter | 1.594 | 0.148 | 1.742 | |
plotJitter_rCharts | 1.470 | 0.017 | 1.487 | |
plotPCA_Eigen | 0.480 | 0.013 | 0.493 | |
plotPCA_Eigen_hc | 0.412 | 0.005 | 0.418 | |
plotPCA_Ind | 0.420 | 0.006 | 0.426 | |
plotPCA_Var | 0.414 | 0.006 | 0.420 | |
postHocTest | 0 | 0 | 0 | |
proportionConRev_HC | 0.038 | 0.008 | 0.046 | |
rbindMSnset | 0.493 | 0.012 | 0.506 | |
reIntroduceMEC | 0.450 | 0.019 | 0.470 | |
readExcel | 0 | 0 | 0 | |
removeLines | 0.444 | 0.011 | 0.455 | |
samLRT | 0 | 0 | 0 | |
saveParameters | 0.409 | 0.009 | 0.418 | |
scatterplotEnrichGO_HC | 3.817 | 0.183 | 4.006 | |
search.metacell.tags | 0.006 | 0.000 | 0.006 | |
separateAdjPval | 0.190 | 0.007 | 0.197 | |
splitAdjacencyMat | 0.443 | 0.014 | 0.457 | |
test.design | 0.429 | 0.009 | 0.438 | |
testAnovaModels | 0.134 | 0.007 | 0.141 | |
thresholdpval4fdr | 0 | 0 | 0 | |
translatedRandomBeta | 0.002 | 0.001 | 0.002 | |
univ_AnnotDbPkg | 0.101 | 0.011 | 0.112 | |
violinPlotD | 0.373 | 0.006 | 0.379 | |
visualizeClusters | 1.012 | 0.064 | 1.080 | |
vsn | 0.638 | 0.036 | 0.674 | |
wrapper.CVDistD_HC | 1.510 | 0.439 | 1.960 | |
wrapper.compareNormalizationD_HC | 33.226 | 10.935 | 44.534 | |
wrapper.corrMatrixD_HC | 0.565 | 0.015 | 0.580 | |
wrapper.dapar.impute.mi | 13.479 | 0.346 | 13.837 | |
wrapper.heatmapD | 0.615 | 0.017 | 0.633 | |
wrapper.impute.KNN | 0.440 | 0.013 | 0.453 | |
wrapper.impute.detQuant | 0.501 | 0.017 | 0.518 | |
wrapper.impute.fixedValue | 0.469 | 0.020 | 0.491 | |
wrapper.impute.mle | 0.441 | 0.024 | 0.465 | |
wrapper.impute.pa | 0.142 | 0.014 | 0.157 | |
wrapper.impute.pa2 | 0.448 | 0.015 | 0.464 | |
wrapper.impute.slsa | 0.543 | 0.030 | 0.573 | |
wrapper.mvImage | 0.163 | 0.010 | 0.173 | |
wrapper.normalizeD | 0.423 | 0.008 | 0.431 | |
wrapper.pca | 0.159 | 0.012 | 0.170 | |
wrapperCalibrationPlot | 0.199 | 0.012 | 0.211 | |
wrapperClassic1wayAnova | 0 | 0 | 0 | |
wrapperRunClustering | 1.729 | 0.196 | 1.930 | |
write.excel | 0.704 | 0.048 | 0.754 | |
writeMSnsetToCSV | 0.432 | 0.010 | 0.442 | |
writeMSnsetToExcel | 0.852 | 0.093 | 0.949 | |