CRAN Package Check Results for Package clValid

Last updated on 2020-01-20 01:50:17 CET.

Check Details

Version: 0.6-6
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls in package code:
     'Biobase' 'GO.db' 'annotate' 'kohonen' 'mclust'
     Please use :: or requireNamespace() instead.
     See section 'Suggested packages' in 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-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.6-6
Check: R code for possible problems
Result: NOTE
    BHI: no visible global function definition for 'getGO'
    BHI: no visible binding for global variable 'dropECode'
    BSI: no visible global function definition for 'xtabs'
    BSI: no visible global function definition for 'getGO'
    BSI: no visible binding for global variable 'dropECode'
    clValid: no visible global function definition for 'as.dist'
    clValid: no visible global function definition for 'cor'
    clValid: no visible global function definition for 'dist'
    connectivity: no visible global function definition for 'dist'
    dist.fn: no visible global function definition for 'cor'
    dunn: no visible global function definition for 'dist'
    mysilhouette: no visible global function definition for 'dist'
    plot.sota: no visible global function definition for 'par'
    plot.sota: no visible global function definition for 'legend'
    plot.sota: no visible global function definition for 'lines'
    stability: no visible global function definition for 'xtabs'
    stability: no visible global function definition for 'dist'
    vClusters: no visible global function definition for 'hclust'
    vClusters: no visible global function definition for 'cutree'
    vClusters: no visible global function definition for 'kmeans'
    vClusters: no visible global function definition for 'Mclust'
    vClusters: no visible global function definition for 'som'
    vClusters: no visible global function definition for 'as.dist'
    vClusters: no visible global function definition for 'cor'
    vClusters: no visible global function definition for 'dist'
    plot,clValid-missing: no visible global function definition for 'par'
    plot,clValid-missing: no visible global function definition for
     'dev.interactive'
    plot,clValid-missing: no visible global function definition for
     'matplot'
    plot,clValid-missing: no visible global function definition for 'axis'
    summary,clValid: no visible global function definition for 'ftable'
    Undefined global functions or variables:
     Mclust as.dist axis cor cutree dev.interactive dist dropECode ftable
     getGO hclust kmeans legend lines matplot par som xtabs
    Consider adding
     importFrom("grDevices", "dev.interactive")
     importFrom("graphics", "axis", "legend", "lines", "matplot", "par")
     importFrom("stats", "as.dist", "cor", "cutree", "dist", "ftable",
     "hclust", "kmeans", "xtabs")
    to your NAMESPACE file.
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-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.6-6
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'Biobase', 'annotate', 'GO.db', 'moe430a.db'
Flavor: r-release-osx-x86_64

Version: 0.6-6
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘Biobase’
Flavor: r-release-osx-x86_64

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘clValid.Rnw’ using Sweave
    Loading required package: cluster
    Read 7 items
    Loading required package: Biobase
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘Biobase’
    Loading required package: RankAggreg
    Error: processing vignette 'clValid.Rnw' failed with diagnostics:
    Running 'texi2dvi' on 'clValid.tex' failed.
    LaTeX errors:
    !pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page
    does not exist <0>
     ==> Fatal error occurred, no output PDF file produced!
    --- failed re-building ‘clValid.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘clValid.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.6-6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘moe430a.db’
Flavor: r-oldrel-osx-x86_64

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    
     expand.grid
    
    Loading required package: XML
    
    Attaching package: ‘XML’
    
    The following object is masked from ‘package:tools’:
    
     toHTML
    
    Loading required package: GO.db
    
    Loading required package: moe430a.db
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘moe430a.db’
    Loading required package: RankAggreg
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'clValid.tex' failed.
    LaTeX errors:
    !pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page
    does not exist <0>
     ==> Fatal error occurred, no output PDF file produced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-oldrel-osx-x86_64