CRAN Package Check Results for Package CNVassoc

Last updated on 2014-09-03 03:50:24.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0.1 2.28 100.01 102.28 NOTE
r-devel-linux-x86_64-debian-gcc 2.0.1 2.47 97.45 99.92 NOTE
r-devel-linux-x86_64-fedora-clang 2.0.1 216.43 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0.1 217.46 NOTE
r-devel-osx-x86_64-clang 2.0.1 154.71 NOTE
r-devel-windows-ix86+x86_64 2.0.1 17.00 159.00 176.00 NOTE
r-patched-linux-x86_64 2.0.1 2.62 104.48 107.10 NOTE
r-patched-solaris-sparc 2.0.1 1304.80 NOTE
r-patched-solaris-x86 2.0.1 241.00 NOTE
r-release-linux-ix86 2.0.1 3.74 131.59 135.34 NOTE
r-release-linux-x86_64 2.0.1 2.66 103.91 106.56 NOTE
r-release-osx-x86_64-mavericks 2.0.1 WARN
r-release-windows-ix86+x86_64 2.0.1 17.00 188.00 205.00 NOTE
r-oldrel-windows-ix86+x86_64 2.0.1 18.00 173.00 191.00 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-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: R code for possible problems
Result: NOTE
    CNVtest: no visible global function definition for ‘survreg’
    fastCNVassoc: no visible global function definition for ‘survreg’
    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’
    mix: no visible global function definition for ‘Mclust’
    mix: no visible global function definition for ‘mixgroup’
    mix: no visible global function definition for ‘mixparam’
    plapply: no visible global function definition for ‘parLapply’
    weibull.fit: no visible global function definition for ‘survreg’
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-windows-ix86+x86_64

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

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

Version: 2.0.1
Check: running R code from vignettes
Result: WARN
    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
Flavor: 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 4.3
    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
Flavor: r-release-osx-x86_64-mavericks