Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-03 11:41 -0400 (Wed, 03 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4693 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4413 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4407 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4356 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
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 495/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DAPAR 1.37.0 (landing page) Samuel Wieczorek
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: 1.37.0 |
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_1.37.0.tar.gz |
StartedAt: 2024-07-02 19:46:54 -0400 (Tue, 02 Jul 2024) |
EndedAt: 2024-07-02 19:53:40 -0400 (Tue, 02 Jul 2024) |
EllapsedTime: 406.4 seconds |
RetCode: 1 |
Status: ERROR |
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_1.37.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/DAPAR.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DAPAR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DAPAR’ version ‘1.37.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... 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 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 ... ERROR Running examples in ‘DAPAR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compute.selection.table > ### Title: Applies an FDR threshold on a table of adjusted p-values and > ### summarizes the results > ### Aliases: compute.selection.table > > ### ** Examples > > data(Exp1_R25_prot, package='DAPARdata') > exdata <- Exp1_R25_prot[1:5,] > adjpvaltab <- globalAdjPval(testAnovaModels(applyAnovasOnProteins(exdata), "TukeyHSD")$P_Value) Error in FUN(X[[i]], ...) : Please install cp4p: BiocManager::install('cp4p') Calls: globalAdjPval -> pkgs.require -> lapply -> FUN Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-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/4.4-x86_64/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/tests/testthat.Rout
R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 1.37.0. 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 33.370 1.595 35.163
DAPAR.Rcheck/DAPAR-Ex.timings
name | user | system | elapsed | |
AggregateMetacell | 0.419 | 0.010 | 0.431 | |
BuildAdjacencyMatrix | 0.303 | 0.006 | 0.311 | |
BuildColumnToProteinDataset | 0.402 | 0.007 | 0.412 | |
BuildMetaCell | 0.655 | 0.030 | 0.692 | |
CVDistD_HC | 3.071 | 0.172 | 3.269 | |
Children | 0.006 | 0.001 | 0.005 | |
CountPep | 0.350 | 0.005 | 0.358 | |
ExtendPalette | 0.031 | 0.001 | 0.033 | |
GOAnalysisSave | 0 | 0 | 0 | |
GetCC | 2.329 | 0.024 | 2.364 | |
GetColorsForConditions | 0.301 | 0.004 | 0.307 | |
GetDetailedNbPeptides | 0.322 | 0.005 | 0.332 | |
GetDetailedNbPeptidesUsed | 0.000 | 0.001 | 0.001 | |
GetIndices_BasedOnConditions | 0.325 | 0.004 | 0.333 | |
GetIndices_MetacellFiltering | 0.322 | 0.004 | 0.328 | |
GetIndices_WholeLine | 0.315 | 0.004 | 0.322 | |
GetIndices_WholeMatrix | 0.322 | 0.005 | 0.328 | |
GetKeyId | 0.298 | 0.004 | 0.303 | |
GetMatAdj | 0.363 | 0.005 | 0.371 | |
GetMetacell | 0 | 0 | 0 | |
GetMetacellTags | 0.321 | 0.006 | 0.329 | |
GetNbPeptidesUsed | 0.313 | 0.006 | 0.321 | |
GetNbTags | 0 | 0 | 0 | |
GetSoftAvailables | 0.001 | 0.000 | 0.001 | |
GetTypeofData | 0.292 | 0.005 | 0.298 | |
Get_AllComparisons | 0.229 | 0.006 | 0.237 | |
GlobalQuantileAlignment | 0.337 | 0.014 | 0.354 | |
GraphPepProt | 0.323 | 0.005 | 0.332 | |
LH0 | 0 | 0 | 0 | |
LH0.lm | 0.000 | 0.000 | 0.001 | |
LH1 | 0 | 0 | 0 | |
LH1.lm | 0 | 0 | 0 | |
LOESS | 0.969 | 0.014 | 0.987 | |
MeanCentering | 0.273 | 0.005 | 0.279 | |
MetaCellFiltering | 0.500 | 0.006 | 0.510 | |
MetacellFilteringScope | 0 | 0 | 0 | |
Metacell_DIA_NN | 0.579 | 0.023 | 0.605 | |
Metacell_generic | 0.483 | 0.013 | 0.499 | |
Metacell_maxquant | 0.495 | 0.011 | 0.508 | |
Metacell_proline | 0.559 | 0.022 | 0.589 | |
NumericalFiltering | 0.336 | 0.005 | 0.343 | |
NumericalgetIndicesOfLinesToRemove | 0.308 | 0.004 | 0.315 | |
OWAnova | 0.006 | 0.000 | 0.007 | |
QuantileCentering | 0.283 | 0.005 | 0.290 | |
SetCC | 2.122 | 0.021 | 2.153 | |
SetMatAdj | 0.331 | 0.004 | 0.337 | |
Set_POV_MEC_tags | 0.308 | 0.004 | 0.313 | |
StringBasedFiltering | 0.363 | 0.005 | 0.371 | |
StringBasedFiltering2 | 0.307 | 0.004 | 0.313 | |
SumByColumns | 1.249 | 0.026 | 1.284 | |
SymFilteringOperators | 0 | 0 | 0 | |
UpdateMetacellAfterImputation | 0.300 | 0.004 | 0.305 | |
aggregateIter | 0.460 | 0.006 | 0.469 | |
aggregateIterParallel | 0.000 | 0.000 | 0.001 | |
aggregateMean | 0.368 | 0.005 | 0.376 | |
aggregateSum | 0.431 | 0.007 | 0.441 | |
aggregateTopn | 0.362 | 0.005 | 0.369 | |
applyAnovasOnProteins | 0.089 | 0.003 | 0.092 | |
averageIntensities | 0.624 | 0.141 | 0.770 | |
barplotEnrichGO_HC | 9.098 | 2.104 | 11.289 | |
barplotGroupGO_HC | 6.867 | 0.905 | 7.945 | |
boxPlotD_HC | 0.232 | 0.092 | 0.325 | |
buildGraph | 1.501 | 0.035 | 1.542 | |
check.conditions | 0.282 | 0.004 | 0.287 | |
check.design | 0.294 | 0.004 | 0.298 | |
checkClusterability | 4.040 | 2.420 | 6.416 | |
classic1wayAnova | 0.000 | 0.001 | 0.000 | |
compareNormalizationD_HC | 0.128 | 0.069 | 0.203 | |