Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:06 -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 1267/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MinimumDistance 1.50.0 (landing page) Robert Scharpf
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the MinimumDistance package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MinimumDistance.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: MinimumDistance |
Version: 1.50.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MinimumDistance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MinimumDistance_1.50.0.tar.gz |
StartedAt: 2024-12-20 06:04:10 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:14:33 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 622.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MinimumDistance.Rcheck |
Warnings: 4 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MinimumDistance.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MinimumDistance_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MinimumDistance.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MinimumDistance/DESCRIPTION’ ... OK * this is package ‘MinimumDistance’ version ‘1.50.0’ * 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 ‘MinimumDistance’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MinimumDistance.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 ... NOTE No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘MatrixGenerics’ 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 callDenovoSegments: no visible global function definition for ‘read.bsfiles’ combineRanges: no visible global function definition for ‘RangedData’ getRefGene: no visible global function definition for ‘RangedData’ overlapsCentromere: no visible global function definition for ‘RangedData’ pruneMD: no visible global function definition for ‘RangedDataCBS’ pruneTrioSet: no visible global function definition for ‘RangedDataList’ read.bsfiles2: no visible binding for global variable ‘read.bsfiles’ GenomeAnnotatedDataFrameFrom,character: no visible global function definition for ‘read.bsfiles’ calculateMindist,list: no visible binding for global variable ‘elt’ Undefined global functions or variables: RangedData RangedDataCBS RangedDataList elt read.bsfiles * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Functions or methods with usage in Rd file 'coercion-methods.Rd' but not in code: ‘as’ * checking Rd \usage sections ... WARNING Objects in \usage without \alias in Rd file 'coercion-methods.Rd': ‘as’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... WARNING Output for data("trioSetListExample", package = "MinimumDistance"): Warning message: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... OK * checking include directives in Makefiles ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed pedigreeGrid 5.634 0.306 6.015 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘doRUnit.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 4 WARNINGs, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/MinimumDistance.Rcheck/00check.log’ for details.
MinimumDistance.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MinimumDistance ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘MinimumDistance’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ Creating a new generic function for ‘allNames’ in package ‘MinimumDistance’ in method for ‘coerce’ with signature ‘"RangedDataCNV","GRanges"’: no definition for class “RangedDataCNV” in method for ‘todf’ with signature ‘object="TrioSet",rangeData="RangedData"’: no definition for class “RangedData” in method for ‘prune’ with signature ‘object="TrioSet",ranges="RangedDataCNV"’: no definition for class “RangedDataCNV” in method for ‘prune’ with signature ‘object="TrioSetList",ranges="RangedDataCNV"’: no definition for class “RangedDataCNV” ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ ** testing if installed package can be loaded from final location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ Warning: replacing previous import ‘ff::pattern’ by ‘grid::pattern’ when loading ‘MinimumDistance’ ** testing if installed package keeps a record of temporary installation path * DONE (MinimumDistance)
MinimumDistance.Rcheck/tests/doRUnit.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > ## from xmapcore package > if( require( "RUnit", quietly=TRUE ) ) { + pkg <- "MinimumDistance" + + if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) { + path <- file.path( getwd(), "..", "inst", "unitTests" ) + } else { + path <- system.file( package=pkg, "unitTests" ) + } + + cat( "\nRunning unit tests\n" ) + print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) ) + library( package=pkg, character.only=TRUE ) + + ##xmap.clear.cache() + + ##Fail on warnings + options( warn=1 ) + + ## Get the pattern (if there is one?) + patt <- Sys.getenv( "RUNITFILEPATTERN" ) + if( is.null( patt ) || nchar( patt ) == 0 ) { + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + dirs=path, + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" )) + } else { + ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path ) + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ), + dirs=path ) + } + tests <- runTestSuite( testSuite ) + + pathReport <- file.path( path, "report" ) + + cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" ) + printTextProtocol( tests, showDetails=FALSE ) + printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) ) + printTextProtocol( tests, showDetails=TRUE, fileName=paste( pathReport, ".txt", sep="" ) ) + + printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) ) + + tmp <- getErrors( tests ) + if( tmp$nFail > 0 | tmp$nErr > 0 ){ + stop( paste( "\n\nunit testing failed (#test failures: ", + tmp$nFail, ", #R errors: ", + tmp$nErr, ")\n\n", sep="")) + } + } else { + warning( "cannot run unit tests -- package RUnit is not available" ) + } Running unit tests $pkg [1] "MinimumDistance" $getwd [1] "/Users/biocbuild/bbs-3.20-bioc/meat/MinimumDistance.Rcheck/tests" $pathToUnitTests [1] "/private/tmp/RtmpX3lsBS/RLIBS_57583a327d0/MinimumDistance/unitTests" Loading required package: VanillaICE Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: GenomicRanges Loading required package: stats4 Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm' Welcome to VanillaICE version 1.68.0 Welcome to MinimumDistance version 1.50.0 Attaching package: 'MinimumDistance' The following object is masked from 'package:VanillaICE': acf2 Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Executing test function test_MDE ... done successfully. Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Executing test function test_Pedigree_construction ... Welcome to oligoClasses version 1.68.0 done successfully. Executing test function test_subsetPedigree ... Error in validObject(.Object) : invalid class "Pedigree" object: fatherNames can not be the same as the offspringNames In addition: Warning message: replacing previous import 'ff::pattern' by 'grid::pattern' when loading 'MinimumDistance' done successfully. Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Executing test function test_TrioSet ... done successfully. Executing test function test_TrioSetList_construction ... done successfully. Executing test function test_TrioSetListdataExamples ... done successfully. Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Executing test function test_calculateMindist ... Parallel computing support for 'oligo/crlmm': Disabled - Load 'ff' - Load and register a 'foreach' adaptor Example - Using 'multicore' for 2 cores: library(doMC) registerDoMC(2) ================================================================================ done successfully. Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Executing test function test_callDenovoSegments ... Attaching package: 'data.table' The following object is masked from 'package:SummarizedExperiment': shift The following object is masked from 'package:GenomicRanges': shift The following object is masked from 'package:IRanges': shift The following objects are masked from 'package:S4Vectors': first, second Welcome to human610quadv1bCrlmm version 1.0.3 done successfully. Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Executing test function test_MAP2 ... Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:VanillaICE': deletion The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat Analyzing: NA12891 Analyzing: NA12892 Analyzing: NA12878 Analyzing: md_NA12878 done successfully. Executing test function test_pennParam ... done successfully. Executing test function test_posteriorCalls ... done successfully. Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: Marsaglia-Multicarry has poor statistical properties Warning in RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) : RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry Executing test function test_cbsSplits ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Fri Dec 20 06:14:17 2024 *********************************************** Number of test functions: 12 Number of errors: 0 Number of failures: 0 1 Test Suite : MinimumDistance unit testing - 12 test functions, 0 errors, 0 failures > > proc.time() user system elapsed 69.172 2.640 73.862
MinimumDistance.Rcheck/MinimumDistance-Ex.timings
name | user | system | elapsed | |
DNAcopyParam | 0.025 | 0.002 | 0.028 | |
FilterParamMD | 2.994 | 0.122 | 3.143 | |
MAP2 | 0.076 | 0.011 | 0.089 | |
MDRanges-class | 0.063 | 0.006 | 0.070 | |
MinDistGRanges-class | 0.154 | 0.026 | 0.185 | |
MinDistGRanges | 0.048 | 0.002 | 0.051 | |
ParentOffspring-class | 0.001 | 0.001 | 0.003 | |
ParentOffspringList-class | 0.003 | 0.000 | 0.003 | |
Pedigree | 0.011 | 0.001 | 0.012 | |
acf2 | 0.004 | 0.000 | 0.005 | |
md_exp | 0.000 | 0.001 | 0.001 | |
pedigreeGrid | 5.634 | 0.306 | 6.015 | |
pedigreeViewports | 0.002 | 0.001 | 0.003 | |