CRAN Package Check Results for Package clValid

Last updated on 2015-08-28 12:47:47.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.6-6 1.00 96.46 97.46 NOTE
r-devel-linux-x86_64-debian-gcc 0.6-6 0.92 93.36 94.29 NOTE
r-devel-linux-x86_64-fedora-clang 0.6-6 198.88 NOTE
r-devel-linux-x86_64-fedora-gcc 0.6-6 195.74 NOTE
r-devel-osx-x86_64-clang 0.6-6 153.99 NOTE
r-devel-windows-ix86+x86_64 0.6-6 6.00 94.00 100.00 NOTE
r-patched-linux-x86_64 0.6-6 1.04 93.12 94.15 NOTE
r-patched-solaris-sparc 0.6-6 1141.10 NOTE
r-patched-solaris-x86 0.6-6 219.70 NOTE
r-release-linux-x86_64 0.6-6 1.04 94.47 95.51 NOTE
r-release-osx-x86_64-mavericks 0.6-6 NOTE
r-release-windows-ix86+x86_64 0.6-6 5.00 88.00 93.00 NOTE
r-oldrel-windows-ix86+x86_64 0.6-6 6.00 84.00 90.00 NOTE

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-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-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+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.
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

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 ‘getGO’
    BSI: no visible binding for global variable ‘dropECode’
    vClusters: no visible global function definition for ‘Mclust’
    vClusters: no visible global function definition for ‘som’
    Undefined global functions or variables:
     Mclust dropECode getGO som
Flavor: r-devel-osx-x86_64-clang

Version: 0.6-6
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'moe430a.db'
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: S4Vectors
    Loading required package: XML
    
    Attaching package: 'XML'
    
    The following object is masked from 'package:tools':
    
     toHTML
    
    Loading required package: GO.db
    Loading required package: DBI
    
    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
    Warning: running command '"D:\compiler\texmf\miktex\bin\texi2dvi.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
    Error: running 'texi2dvi' on 'clValid.tex' failed
    
    LaTeX errors:
    !pdfTeX error: pdflatex.EXE (file d:/RCompile/CRANpkg/local/3.3/clValid.Rcheck/
    vign_test/clValid/vignettes/clValid-022.pdf): PDF inclusion: required page does
     not exist <0>
     ==> Fatal error occurred, no output PDF file produced!
    Execution halted
Flavor: r-devel-windows-ix86+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 ‘getGO’
    BSI: no visible binding for global variable ‘dropECode’
    vClusters: no visible global function definition for ‘Mclust’
    vClusters: no visible global function definition for ‘som’
Flavors: r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64-mavericks, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

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

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
     eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
     mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
     rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
     unique, unlist, unsplit
    
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view with
     'browseVignettes()'. To cite Bioconductor, see
     'citation("Biobase")', and for packages 'citation("pkgname")'.
    
    Loading required package: annotate
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called ‘annotate’
    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-release-osx-x86_64-mavericks

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Loading required package: IRanges
    Loading required package: XML
    
    Attaching package: 'XML'
    
    The following object is masked from 'package:tools':
    
     toHTML
    
    Loading required package: GO.db
    Loading required package: DBI
    
    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
    Warning: running command '"D:\compiler\texmf\miktex\bin\texi2dvi.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.2/share/texmf/bibtex/bst"' had status 1
    Error: running 'texi2dvi' on 'clValid.tex' failed
    
    LaTeX errors:
    !pdfTeX error: pdflatex.EXE (file d:/RCompile/CRANpkg/local/3.2/clValid.Rcheck/
    vign_test/clValid/vignettes/clValid-022.pdf): PDF inclusion: required page does
     not exist <0>
     ==> Fatal error occurred, no output PDF file produced!
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
     toHTML
    
    
    Attaching package: 'annotate'
    
    The following object is masked from 'package:GenomeInfoDb':
    
     organism
    
    Loading required package: GO.db
    Loading required package: DBI
    
    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
    Warning: running command '"D:\compiler\texmf\miktex\bin\texi2dvi.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.1.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.1.3/share/texmf/bibtex/bst"' had status 1
    Error: running 'texi2dvi' on 'clValid.tex' failed
    
    LaTeX errors:
    !pdfTeX error: pdflatex.EXE (file d:/RCompile/CRANpkg/local/3.1/clValid.Rcheck/
    vign_test/clValid/vignettes/clValid-022.pdf): PDF inclusion: required page does
     not exist <0>
     ==> Fatal error occurred, no output PDF file produced!
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64