CRAN Package Check Results for Package MLPAstats

Last updated on 2014-09-20 19:47:22.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-patched-linux-x86_64 0.5-9 1.38 26.58 27.96 NOTE
r-release-linux-ix86 0.5-9 1.91 31.56 33.47 NOTE
r-release-linux-x86_64 0.5-9 1.40 27.28 28.68 NOTE
r-release-osx-x86_64-mavericks 0.5-9 NOTE
r-release-osx-x86_64-snowleopard 0.5-9 WARN

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’ ‘tcltk’ ‘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.
Flavor: r-patched-linux-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 attach():
    File ‘MLPAstats/R/gui.function.plot.click.r’:
     attach(.GlobalEnv$plot.init$plot.config, 2, name = "plot.init$plot.config")
    See section ‘Good practice’ in ‘?attach’.
    
    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-patched-linux-x86_64, r-release-linux-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-patched-linux-x86_64, 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-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, 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 is required as from R 3.1.0
    and these will not be indexed nor checked
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

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-release-linux-ix86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks

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’.
Flavor: r-release-linux-ix86

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-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

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: WARN
    checking a package with encoding 'latin1' in an ASCII locale
    
     OK
Flavor: r-release-osx-x86_64-snowleopard