Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:04 -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 2233/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VanillaICE 1.68.0 (landing page) Robert Scharpf
| 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 VanillaICE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VanillaICE.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: VanillaICE |
Version: 1.68.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings VanillaICE_1.68.0.tar.gz |
StartedAt: 2024-12-20 06:27:26 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:32:12 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 286.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: VanillaICE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings VanillaICE_1.68.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/VanillaICE.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 ‘VanillaICE/DESCRIPTION’ ... OK * this is package ‘VanillaICE’ version ‘1.68.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'doMPI', 'doRedis' * 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 ‘VanillaICE’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 loading without being on the library search path ... 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 Namespaces in Imports field not imported from: ‘BSgenome.Hsapiens.UCSC.hg18’ ‘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 ... OK * checking Rd files ... NOTE checkRd: (-1) TransitionParam.Rd:27: Lost braces; missing escapes or markup? 27 | computed as e^{-2*d/taup}, where d is the distance between markers | ^ * 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/VanillaICE.Rcheck/00check.log’ for details.
VanillaICE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL VanillaICE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘VanillaICE’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rinit.c -o rinit.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c viterbi.c -o viterbi.o gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-VanillaICE/00new/VanillaICE/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ Creating a new generic function for ‘distance’ in package ‘VanillaICE’ ** 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’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location No methods found in package ‘oligoClasses’ for request: ‘mean’ when loading ‘crlmm’ ** testing if installed package keeps a record of temporary installation path * DONE (VanillaICE)
VanillaICE.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-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. > ## from xmapcore package > if( require( "RUnit", quietly=TRUE ) ) { + pkg <- "VanillaICE" + + 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=2 ) + + ## 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" ), + rngKind="Mersenne-Twister", + dirs=path, + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" )) + } else { + ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path ) + testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ), + rngKind="Mersenne-Twister", + testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", 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] "VanillaICE" $getwd [1] "/home/biocbuild/bbs-3.20-bioc/meat/VanillaICE.Rcheck/tests" $pathToUnitTests [1] "/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpLZg8fg/RLIBS_1624ee6e8b370/VanillaICE/unitTests" 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 Loading required package: BSgenome.Hsapiens.UCSC.hg18 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 Loading required package: data.table 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 Loading required package: foreach Loading required package: oligoClasses Welcome to oligoClasses version 1.68.0 Executing test function test_ArrayViews ... done successfully. Executing test function test_columnSubset ... Writing parsed files to /home/biocbuild/bbs-3.20-bioc/tmpdir/Rtmp2zoOwp done successfully. Executing test function test_FilterParam ... done successfully. Executing test function test_EmissionParam ... done successfully. Executing test function test_SnpArrayExperiment ... Error : unable to find an inherited method for function 'SnpDataFrame' for signature 'x = "numeric"' Error in VanillaICE:::SnpDataFrame(DataFrame(x = 3)) : isSnp must be specified Error in .local(object, isSnp, ...) : isSnp must be specified Error in validObject(.Object) : invalid class "RangedSummarizedExperiment" object: 'x@assays' is not parallel to 'x' Error in SnpArrayExperiment(x, y, rowRanges = rowranges) : isSnp must be the same length as rowRanges done successfully. Executing test function test_SnpArrayExperiment2 ... done successfully. Executing test function test_SnpGRanges ... done successfully. Executing test function test_acf2 ... done successfully. Executing test function test_hmm_cnset ... Loading required package: crlmm Loading required package: preprocessCore Welcome to crlmm version 1.64.0 Attaching package: 'crlmm' The following object is masked from 'package:VanillaICE': genotypes done successfully. Executing test function test_state4 ... done successfully. Executing test function test_rowMAD ... done successfully. Executing test function test_scaleBy ... done successfully. Executing test function test_duplicatedMapLocs ... done successfully. Executing test function test_sweepMode.R ... done successfully. Executing test function test_Viterbi ... done successfully. Executing test function test_baf_emission ... done successfully. Executing test function test_cn_NAs ... done successfully. Executing test function test_emission_for_list ... done successfully. Executing test function test_emission_update ... done successfully. Executing test function test_multiple_chromosomes ... done successfully. Executing test function test_null_assignment ... done successfully. Executing test function test_oligoset_comparison ... done successfully. Executing test function test_summarized_exp ... done successfully. Executing test function test_updating ... done successfully. ------------------- UNIT TEST SUMMARY --------------------- RUNIT TEST PROTOCOL -- Fri Dec 20 06:31:32 2024 *********************************************** Number of test functions: 24 Number of errors: 0 Number of failures: 0 1 Test Suite : VanillaICE unit testing - 24 test functions, 0 errors, 0 failures > > proc.time() user system elapsed 19.320 0.673 19.944
VanillaICE.Rcheck/VanillaICE-Ex.timings
name | user | system | elapsed | |
ArrayViews-class | 3.452 | 0.094 | 3.548 | |
CopyNumScanParams | 0.003 | 0.000 | 0.002 | |
EmissionParam-methods | 0.006 | 0.000 | 0.005 | |
FilterParam-class | 0.002 | 0.000 | 0.001 | |
HMM | 0.227 | 0.027 | 0.253 | |
HMMList-class | 1.688 | 0.033 | 1.721 | |
HmmParam | 0.003 | 0.000 | 0.002 | |
IO | 0.008 | 0.000 | 0.008 | |
IdiogramParams-class | 0.124 | 0.012 | 0.136 | |
SnpArrayExperiment-class | 0.066 | 0.011 | 0.076 | |
SnpExperiment | 0.105 | 0.014 | 0.120 | |
SnpGRanges | 0.043 | 0.014 | 0.058 | |
TransitionParam | 0.001 | 0.000 | 0.001 | |
cnvFilter | 1.335 | 0.146 | 1.481 | |
dropDuplicatedMapLocs | 0.107 | 0.000 | 0.107 | |
emissionParam | 0.003 | 0.000 | 0.003 | |
getExampleSnpExperiment | 0 | 0 | 0 | |
getHmmParams | 0.008 | 0.000 | 0.009 | |
hmm2 | 0.918 | 0.001 | 0.919 | |
isHeterozygous | 0.211 | 0.009 | 0.215 | |
parseSourceFile | 0.383 | 0.016 | 0.359 | |
plotting | 0.760 | 0.037 | 0.797 | |
robust-statistics | 0.001 | 0.000 | 0.001 | |
snpArrayAssays | 0.009 | 0.002 | 0.012 | |
sourcePaths | 0.007 | 0.000 | 0.007 | |
sweepMode | 0.198 | 0.000 | 0.198 | |
threshold | 0 | 0 | 0 | |
viewports | 0.001 | 0.000 | 0.000 | |