Robert Scharpf
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/VanillaICE |
| Branch: RELEASE_3_11 |
| Last Commit: 5b04c40 |
| Last Changed Date: 2020-04-27 14:15:46 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:51 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE VanillaICE PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1862/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| VanillaICE 1.50.0 Robert Scharpf
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | NA | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK | |
| Package: VanillaICE |
| Version: 1.50.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VanillaICE_1.50.0.tar.gz |
| StartedAt: 2020-10-17 06:11:34 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:17:06 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 332.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VanillaICE.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:VanillaICE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings VanillaICE_1.50.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/VanillaICE.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘VanillaICE/DESCRIPTION’ ... OK * this is package ‘VanillaICE’ version ‘1.50.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Packages which this enhances but not available for checking: 'doMC', '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 * 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 R 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BSgenome.Hsapiens.UCSC.hg18’ 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 ... 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 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 sizes of PDF files under ‘inst/doc’ ... OK * 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.11-bioc/meat/VanillaICE.Rcheck/00check.log’ for details.
VanillaICE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL VanillaICE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘VanillaICE’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rinit.c -o rinit.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c viterbi.c -o viterbi.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o VanillaICE.so rinit.o viterbi.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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" ),
+ 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] "VanillaICE"
$getwd
[1] "/Users/biocbuild/bbs-3.11-bioc/meat/VanillaICE.Rcheck/tests"
$pathToUnitTests
[1] "/Library/Frameworks/R.framework/Versions/4.0/Resources/library/VanillaICE/unitTests"
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, 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, setdiff, sort, table,
tapply, union, unique, unsplit, which, 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:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
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")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to VanillaICE version 1.50.0
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: rtracklayer
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 1.50.4
Executing test function test_ArrayViews ... done successfully.
Executing test function test_columnSubset ... Writing parsed files to /tmp/Rtmpg65AH6
done successfully.
Executing test function test_FilterParam ... done successfully.
Executing test function test_EmissionParam ... done successfully.
Executing test function test_SnpArrayExperiment ... Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'SnpDataFrame' for signature '"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 1.46.0
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 -- Sat Oct 17 06:16:56 2020
***********************************************
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
28.056 1.410 29.495
VanillaICE.Rcheck/VanillaICE-Ex.timings
| name | user | system | elapsed | |
| ArrayViews-class | 4.440 | 0.098 | 4.548 | |
| CopyNumScanParams | 0.004 | 0.001 | 0.004 | |
| EmissionParam-methods | 0.014 | 0.002 | 0.016 | |
| FilterParam-class | 0.003 | 0.001 | 0.004 | |
| HMM | 0.476 | 0.023 | 0.499 | |
| HMMList-class | 2.244 | 0.105 | 2.359 | |
| HmmParam | 0.005 | 0.001 | 0.007 | |
| IO | 0.016 | 0.003 | 0.019 | |
| IdiogramParams-class | 0.198 | 0.022 | 0.219 | |
| SnpArrayExperiment-class | 0.117 | 0.014 | 0.132 | |
| SnpExperiment | 0.197 | 0.021 | 0.217 | |
| SnpGRanges | 0.087 | 0.010 | 0.098 | |
| TransitionParam | 0.001 | 0.000 | 0.002 | |
| cnvFilter | 2.327 | 0.030 | 2.363 | |
| dropDuplicatedMapLocs | 0.191 | 0.004 | 0.195 | |
| emissionParam | 0.007 | 0.000 | 0.007 | |
| getExampleSnpExperiment | 0.000 | 0.000 | 0.001 | |
| getHmmParams | 0.015 | 0.001 | 0.016 | |
| hmm2 | 1.632 | 0.013 | 1.645 | |
| isHeterozygous | 0.383 | 0.013 | 0.399 | |
| parseSourceFile | 0.512 | 0.034 | 0.561 | |
| plotting | 1.258 | 0.063 | 1.322 | |
| robust-statistics | 0.001 | 0.001 | 0.001 | |
| snpArrayAssays | 0.028 | 0.001 | 0.030 | |
| sourcePaths | 0.016 | 0.000 | 0.016 | |
| sweepMode | 0.385 | 0.016 | 0.401 | |
| threshold | 0.001 | 0.001 | 0.001 | |
| viewports | 0.001 | 0.000 | 0.001 | |