CRAN Package Check Results for Package MLPAstats

Last updated on 2014-08-01 17:48:27.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.5-9 1.40 20.99 22.39 NOTE
r-devel-linux-x86_64-debian-gcc 0.5-9 1.38 21.11 22.49 NOTE
r-devel-linux-x86_64-fedora-clang 0.5-9 44.68 NOTE
r-devel-linux-x86_64-fedora-gcc 0.5-9 45.23 NOTE
r-devel-osx-x86_64-clang 0.5-9 44.93 NOTE
r-devel-windows-ix86+x86_64 0.5-9 5.00 32.00 37.00 NOTE
r-patched-linux-x86_64 0.5-9 1.40 21.12 22.52 NOTE
r-patched-solaris-sparc 0.5-9 283.00 NOTE
r-patched-solaris-x86 0.5-9 73.30 NOTE
r-release-linux-ix86 0.5-9 1.76 30.80 32.56 NOTE
r-release-linux-x86_64 0.5-9 1.41 21.28 22.69 NOTE
r-release-osx-x86_64-mavericks 0.5-9 NOTE
r-release-osx-x86_64-snowleopard 0.5-9 WARN
r-release-windows-ix86+x86_64 0.5-9 8.00 48.00 56.00 NOTE
r-oldrel-windows-ix86+x86_64 0.5-9 9.00 56.00 65.00 NOTE

Check Details

Version: 0.5-9
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to tcltk which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     boot pixmap tkrplot
     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: 0.5-9
Check: R code for possible problems
Result: NOTE
    exponential.correction: warning in assign("datG", datG, env =
     .GlobalEnv): partial argument match of 'env' to 'envir'
    get.analysis.menu : call.mlpa : OnOK: warning in
     mlpa(.GlobalEnv$Ms$norm$norm.dat, method = method, band = band, alpha
     = alpha): partial argument match of 'band' to 'bands'
    
    Found the following assignments to the global environment:
    File MLPAstats/R/bootBands.R :
     assign(".inds", inds, envir = .GlobalEnv)
    File MLPAstats/R/exponential.correction.R :
     assign("datG", datG, env = .GlobalEnv)
    File MLPAstats/R/gui.filemenu.r :
     assign("fileMenu", tkmenu(.GlobalEnv$topMenu, tearoff = FALSE),
     envir = .GlobalEnv)
     assign(var, scan(fileName.win, sep = " "), envir = .GlobalEnv)
    
    Found the following calls to data() loading into the global environment:
    File MLPAstats/R/gui.filemenu.r :
     data(BRCA)
     data(MLPAvalidation)
    See section Good practice in ?data .
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 0.5-9
Check: installed files from inst/doc
Result: NOTE
    The following files are already in R: Sweave.sty
    Please remove them from your package.
    The following directories should probably not be installed:
     figures
    
    Consider the use of a .Rinstignore file: see Writing R Extensions ,
    or move the vignette sources from inst/doc to vignettes .
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-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.5-9
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in inst/doc :
     MLPAstats.Rnw
    A vignettes directory is required as from R 3.1.0
    and these will not be indexed nor checked
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-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64

Version: 0.5-9
Check: Rd line widths
Result: NOTE
    Rd file 'mlpa.Rd':
     \usage lines wider than 90 characters:
     mlpa(x, method, threshold = c(0.7, 1.33), gamma = 0.95, alpha = 0.01, id = 0.05, bands = "parametric", maxit = 100, B = 200)
    
    Rd file 'mlpaNorm.Rd':
     \usage lines wider than 90 characters:
     mlpaNorm(x, method = "sum.peaks.controls", reference.probes = TRUE, replicate = FALSE, transform = "none", sliding = 9, quadratic = TRU ... [TRUNCATED]
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.5-9
Check: R code for possible problems
Result: NOTE
    exponential.correction: warning in assign("datG", datG, env =
     .GlobalEnv): partial argument match of 'env' to 'envir'
    get.analysis.menu : call.mlpa : OnOK: warning in
     mlpa(.GlobalEnv$Ms$norm$norm.dat, method = method, band = band, alpha
     = alpha): partial argument match of 'band' to 'bands'
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.5-9
Check: dependencies in R code
Result: NOTE
    'library' or 'require' call to 'tcltk' which was already attached by Depends.
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     'boot' 'pixmap' 'tkrplot'
     These packages need to be imported from for the case 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.
Flavor: r-release-osx-x86_64-snowleopard

Version: 0.5-9
Check: examples
Result: WARNING
    checking a package with encoding 'latin1' in an ASCII locale
    
     OK
Flavor: r-release-osx-x86_64-snowleopard

Version: 0.5-9
Check: for old-style vignette sources
Result: NOTE
    Vignette sources only in 'inst/doc':
     'MLPAstats.Rnw'
    A 'vignettes' directory will be required as from R 3.1.0
Flavor: r-oldrel-windows-ix86+x86_64