CRAN Package Check Results for Package CNVassoc

Last updated on 2014-04-24 23:48:00.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.1 2.48 110.44 112.92 NOTE
r-devel-linux-x86_64-debian-gcc 2.0.1 2.52 107.44 109.96 NOTE
r-devel-linux-x86_64-fedora-clang 2.0.1 229.12 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.1 223.52 NOTE
r-devel-osx-x86_64-clang 2.0.1 174.68 NOTE
r-devel-osx-x86_64-gcc 2.0.1 WARN
r-devel-windows-ix86+x86_64 2.0.1 18.00 177.00 195.00 NOTE
r-patched-linux-x86_64 2.0.1 2.59 108.54 111.13 NOTE
r-patched-solaris-sparc 2.0.1 1291.70 NOTE
r-patched-solaris-x86 2.0.1 238.40 NOTE
r-release-linux-ix86 2.0.1 5.00 163.00 168.00 NOTE
r-release-linux-x86_64 2.0.1 2.60 109.61 112.21 NOTE
r-release-osx-x86_64-mavericks 2.0.1 WARN
r-release-windows-ix86+x86_64 2.0.1 17.00 179.00 196.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.1 18.00 178.00 196.00 NOTE

Check Details

Version: 2.0.1
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘CNVassocData’ ‘mclust’ ‘mixdist’ ‘survival’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-osx-x86_64-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.0.1
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     ‘CGHcall’ ‘CGHregions’ ‘CNVtools’
Flavors: r-devel-osx-x86_64-gcc, r-release-osx-x86_64-mavericks

Version: 2.0.1
Check: R code for possible problems
Result: NOTE
    fastCNVassoc: no visible global function definition for ‘mclapply’
    getProbs.cghCall: no visible global function definition for
     ‘featureNames’
    getProbs.cghCall: no visible global function definition for
     ‘chromosomes’
    getProbs.cghCall: no visible global function definition for ‘bpstart’
    getProbs.cghCall: no visible global function definition for ‘bpend’
    getProbs.cghCall: no visible global function definition for ‘calls’
    getProbs.cghCall: no visible global function definition for ‘probloss’
    getProbs.cghCall: no visible global function definition for ‘probnorm’
    getProbs.cghCall: no visible global function definition for ‘probgain’
    getProbs.cghCall: no visible global function definition for ‘probamp’
    plapply: no visible global function definition for ‘parLapply’
Flavors: r-devel-osx-x86_64-gcc, r-release-osx-x86_64-mavericks

Version: 2.0.1
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘CGHcall’
Flavors: r-devel-osx-x86_64-gcc, r-release-osx-x86_64-mavericks

Version: 2.0.1
Check: running R code from vignettes
Result: WARNING
    Errors in running code in vignettes:
    when running code in ‘CNVassoc_vignette.Rnw’
     ...
    > data(NeveCalled)
    
    > probs <- getProbs(NeveCalled)
    Loading required package: CGHbase
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘CGHbase’
    
     When sourcing ‘CNVassoc_vignette.R’:
    Error: unable to find required package ‘CGHbase’
    Execution halted
Flavors: r-devel-osx-x86_64-gcc, r-release-osx-x86_64-mavericks

Version: 2.0.1
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: CNVassocData
    Loading required package: mixdist
    Loading required package: mclust
    Package 'mclust' version 4.2
    Loading required package: survival
    Loading required package: splines
    Loading required package: CGHbase
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘CGHbase’
    
    Error: processing vignette 'CNVassoc_vignette.Rnw' failed with diagnostics:
     chunk 40
    Error in .requirePackage(package) :
     unable to find required package ‘CGHbase’
    Execution halted
Flavors: r-devel-osx-x86_64-gcc, r-release-osx-x86_64-mavericks

Version: 2.0.1
Check: PDF version of manual
Result: WARNING
    LaTeX errors when creating PDF version.
    This typically indicates Rd problems.
    LaTeX errors found:
    ! LaTeX Error: File `upquote.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    3cf64b/Rd2.tex:8: ==> Fatal error occurred, no output PDF file produced!
Flavor: r-release-osx-x86_64-mavericks