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This page was generated on 2022-01-24 13:07:11 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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

CHECK results for VanillaICE on tokay2


To the developers/maintainers of the VanillaICE package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2035/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VanillaICE 1.56.3  (landing page)
R.B. Scharpf
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/VanillaICE
git_branch: RELEASE_3_14
git_last_commit: 65bbda3
git_last_commit_date: 2021-12-05 08:54:51 -0500 (Sun, 05 Dec 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: VanillaICE
Version: 1.56.3
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VanillaICE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings VanillaICE_1.56.3.tar.gz
StartedAt: 2022-01-24 04:04:27 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 04:10:33 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 365.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VanillaICE.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:VanillaICE.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings VanillaICE_1.56.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VanillaICE/DESCRIPTION' ... OK
* this is package 'VanillaICE' version '1.56.3'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
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 ... WARNING
checkRd: (5) VanillaICE.Rd:0-7: Must have a \description
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/VanillaICE/libs/i386/VanillaICE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/VanillaICE/libs/x64/VanillaICE.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'doRUnit.R'
 OK
** running tests for arch 'x64' ...
  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: 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.Rcheck/00check.log'
for details.



Installation output

VanillaICE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/VanillaICE_1.56.3.tar.gz && rm -rf VanillaICE.buildbin-libdir && mkdir VanillaICE.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=VanillaICE.buildbin-libdir VanillaICE_1.56.3.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL VanillaICE_1.56.3.zip && rm VanillaICE_1.56.3.tar.gz VanillaICE_1.56.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1100k  100 1100k    0     0  2701k      0 --:--:-- --:--:-- --:--:-- 2710k

install for i386

* installing *source* package 'VanillaICE' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rinit.c -o rinit.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c viterbi.c -o viterbi.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o VanillaICE.dll tmp.def rinit.o viterbi.o -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.buildbin-libdir/00LOCK-VanillaICE/00new/VanillaICE/libs/i386
** 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
  converting help for package 'VanillaICE'
    finding HTML links ... done
    ArrayViews-class                        html  
    CopyNumScanParams                       html  
    finding level-2 HTML links ... done

    EmissionParam-methods                   html  
    FilterParam-class                       html  
    HMM                                     html  
    HMMList-class                           html  
    HMMList                                 html  
    HmmGRanges-methods                      html  
    HmmParam                                html  
    HmmTrellisParam                         html  
    IO                                      html  
    IdiogramParam-class                     html  
    IdiogramParams-class                    html  
    LogLik-class                            html  
    LogLik                                  html  
    LowLevelSummaries                       html  
    NA_filter                               html  
    SnpArrayExperiment-class                html  
    SnpExperiment                           html  
    SnpGRanges                              html  
    TransitionParam                         html  
    VanillaICE                              html  
    Viterbi-methods                         html  
    acf2                                    html  
    baumWelchUpdate                         html  
    calculateEmission                       html  
    cnvFilter                               html  
    doUpdate                                html  
    dropDuplicatedMapLocs                   html  
    dropSexChrom                            html  
    emission                                html  
    emissionParam                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.buildbin-libdir/00LOCK-VanillaICE/00new/VanillaICE/help/emissionParam.html
    filters                                 html  
    getExampleSnpExperiment                 html  
    getHmmParams                            html  
    hmm2                                    html  
    hmmResults                              html  
    isHeterozygous                          html  
    matrixOrNULL-class                      html  
    numberFeatures                          html  
    parseSourceFile                         html  
    parsedPath                              html  
    plotting                                html  
    probability                             html  
    rescale                                 html  
    robust-statistics                       html  
    segs                                    html  
    snpArrayAssays                          html  
    snp_exp                                 html  
    sourcePaths                             html  
    start-oligoSnpSet-method                html  
    state-methods                           html  
    sweepMode                               html  
    threshold                               html  
    updateHmmParams                         html  
    viewports                               html  
** 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'
** 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

install for x64

* installing *source* package 'VanillaICE' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c rinit.c -o rinit.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c viterbi.c -o viterbi.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o VanillaICE.dll tmp.def rinit.o viterbi.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.buildbin-libdir/VanillaICE/libs/x64
** testing if installed package can be loaded
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
* MD5 sums
packaged installation of 'VanillaICE' as VanillaICE_1.56.3.zip
* DONE (VanillaICE)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'VanillaICE' successfully unpacked and MD5 sums checked

Tests output

VanillaICE.Rcheck/tests_i386/doRUnit.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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]$", sep="" ),
+                                      rngKind="Mersenne-Twister")
+     } else {
+         testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+                                      testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+                                      dirs=path ,
+                                      rngKind="Mersenne-Twister")
+     }
+     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] "C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.Rcheck/tests_i386"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/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, 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.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 1.56.3
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 1.56.0


Executing test function test_ArrayViews  ...  done successfully.



Executing test function test_columnSubset  ... Writing parsed files to C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp6NusMO
 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 1.52.0

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 -- Mon Jan 24 04:09:57 2022 
*********************************************** 
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 
  20.50    1.84   22.37 

VanillaICE.Rcheck/tests_x64/doRUnit.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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]$", sep="" ),
+                                      rngKind="Mersenne-Twister")
+     } else {
+         testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+                                      testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+                                      dirs=path ,
+                                      rngKind="Mersenne-Twister")
+     }
+     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] "C:/Users/biocbuild/bbs-3.14-bioc/meat/VanillaICE.Rcheck/tests_x64"

$pathToUnitTests
[1] "C:/Users/biocbuild/bbs-3.14-bioc/R/library/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, 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.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

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 1.56.3
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 1.56.0


Executing test function test_ArrayViews  ...  done successfully.



Executing test function test_columnSubset  ... Writing parsed files to C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\Rtmp61WkrN
 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 1.52.0

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 -- Mon Jan 24 04:10:22 2022 
*********************************************** 
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 
  23.60    0.75   24.36 

Example timings

VanillaICE.Rcheck/examples_i386/VanillaICE-Ex.timings

nameusersystemelapsed
ArrayViews-class3.250.224.05
CopyNumScanParams0.020.000.01
EmissionParam-methods000
FilterParam-class0.020.000.01
HMM0.520.070.60
HMMList-class1.920.442.36
HmmParam000
IO0.010.020.03
IdiogramParams-class0.110.090.20
SnpArrayExperiment-class0.190.080.26
SnpExperiment0.230.030.27
SnpGRanges0.100.000.09
TransitionParam000
cnvFilter1.950.001.96
dropDuplicatedMapLocs0.130.000.12
emissionParam000
getExampleSnpExperiment000
getHmmParams0.010.000.02
hmm21.300.001.29
isHeterozygous0.420.040.55
parseSourceFile0.660.211.81
plotting1.330.031.36
robust-statistics000
snpArrayAssays0.030.000.03
sourcePaths0.020.000.01
sweepMode0.310.000.32
threshold000
viewports000

VanillaICE.Rcheck/examples_x64/VanillaICE-Ex.timings

nameusersystemelapsed
ArrayViews-class3.000.083.07
CopyNumScanParams0.020.000.02
EmissionParam-methods0.010.000.01
FilterParam-class000
HMM0.380.010.40
HMMList-class1.200.081.28
HmmParam0.020.000.01
IO000
IdiogramParams-class0.130.000.12
SnpArrayExperiment-class0.120.000.13
SnpExperiment1.050.001.04
SnpGRanges0.090.000.10
TransitionParam000
cnvFilter2.330.002.33
dropDuplicatedMapLocs0.130.000.12
emissionParam000
getExampleSnpExperiment000
getHmmParams0.010.000.01
hmm21.810.001.82
isHeterozygous0.320.010.32
parseSourceFile0.390.020.41
plotting1.090.031.12
robust-statistics000
snpArrayAssays0.010.000.02
sourcePaths0.020.000.01
sweepMode0.330.000.33
threshold000
viewports000