CRAN Package Check Results for Package clValid

Last updated on 2014-10-31 06:47:15.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.6-6 1.07 93.81 94.88 NOTE
r-devel-linux-x86_64-debian-gcc 0.6-6 1.07 91.36 92.43 NOTE
r-devel-linux-x86_64-fedora-clang 0.6-6 212.08 NOTE
r-devel-linux-x86_64-fedora-gcc 0.6-6 203.82 NOTE
r-devel-osx-x86_64-clang 0.6-6 162.07 NOTE
r-devel-windows-ix86+x86_64 0.6-6 4.00 28.00 32.00 ERROR
r-patched-linux-x86_64 0.6-6 1.09 99.69 100.78 NOTE
r-patched-solaris-sparc 0.6-6 1178.90 NOTE
r-patched-solaris-x86 0.6-6 238.50 NOTE
r-release-linux-ix86 0.6-6 1.67 121.62 123.29 OK
r-release-linux-x86_64 0.6-6 1.23 100.12 101.35 OK
r-release-osx-x86_64-mavericks 0.6-6 NOTE
r-release-osx-x86_64-snowleopard 0.6-6 NOTE
r-release-windows-ix86+x86_64 0.6-6 3.00 69.00 72.00 NOTE
r-oldrel-windows-ix86+x86_64 0.6-6 4.00 69.00 73.00 NOTE

Check Details

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-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

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: examples
Result: ERROR
    Running examples in 'clValid-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: BHI
    > ### Title: Biological Homogeneity Index
    > ### Aliases: BHI
    > ### Keywords: cluster
    >
    > ### ** Examples
    >
    > data(mouse)
    > express <- mouse[1:25,c("M1","M2","M3","NC1","NC2","NC3")]
    > rownames(express) <- mouse$ID[1:25]
    > ## hierarchical clustering
    > Dist <- dist(express,method="euclidean")
    > clusterObj <- hclust(Dist, method="average")
    > nc <- 4 ## number of clusters
    > cluster <- cutree(clusterObj,nc)
    >
    > ## first way - functional classes predetermined
    > fc <- tapply(rownames(express),mouse$FC[1:25], c)
    > fc <- fc[-match( c("EST","Unknown"), names(fc))]
    > fc <- annotationListToMatrix(fc, rownames(express))
    > BHI(cluster, fc)
    [1] 0.2345238
    >
    > ## second way - using Bioconductor
    > if(require("Biobase") && require("annotate") && require("GO.db") &&
    + require("moe430a.db")) {
    + BHI(cluster, annotation="moe430a.db", names=rownames(express), category="all")
    + }
    Loading required package: Biobase
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: 'BiocGenerics'
    
    The following objects are masked from 'package:parallel':
    
     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
     clusterExport, clusterMap, parApply, parCapply, parLapply,
     parLapplyLB, parRapply, parSapply, parSapplyLB
    
    The following object is masked from 'package:stats':
    
     xtabs
    
    The following objects are masked from 'package:base':
    
     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
    Loading required package: AnnotationDbi
    Loading required package: stats4
    Loading required package: GenomeInfoDb
    Loading required package: S4Vectors
    Loading required package: IRanges
    
    Attaching package: 'AnnotationDbi'
    
    The following object is masked from 'package:GenomeInfoDb':
    
     species
    
    Loading required package: XML
    
    Attaching package: 'annotate'
    
    The following object is masked from 'package:GenomeInfoDb':
    
     organism
    
    Loading required package: GO.db
    Loading required package: DBI
    Error : .onLoad failed in loadNamespace() for 'GO.db', details:
     call: ls(envir, all.names = TRUE)
     error: 2 arguments passed to .Internal(ls) which requires 3
    >
    >
    >
    >
    > cleanEx()
    Error in ls(envir = env, all.names = TRUE) :
     2 arguments passed to .Internal(ls) which requires 3
    Calls: cleanEx -> rm -> ls -> ls
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

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

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’
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

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

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    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
    Loading required package: gtools
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'clValid.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `relsize.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    _test/clValid/vignettes/clValid.tex:29: ==> Fatal error occurred, no output PD
    F 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: 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
    Loading required package: gtools
    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-snowleopard

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    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
    Loading required package: AnnotationDbi
    Loading required package: GenomeInfoDb
    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-3.1.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.1.1/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-release-windows-ix86+x86_64

Version: 0.6-6
Check: R code for possible problems
Result: NOTE
    Error : .onLoad failed in loadNamespace() for 'GO.db', details:
     call: match.arg(synchronous, c("off", "normal", "full"))
     error: 'arg' must be NULL or a character vector
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.6-6
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
     unlist
    
    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
    Loading required package: AnnotationDbi
    Loading required package: GO.db
    Loading required package: DBI
    Error : .onLoad failed in loadNamespace() for 'GO.db', details:
     call: match.arg(synchronous, c("off", "normal", "full"))
     error: 'arg' must be NULL or a character vector
    Loading required package: RankAggreg
    Warning: running command '"D:\compiler\texmf\miktex\bin\texi2dvi.exe" --quiet --pdf "clValid.tex" -I "D:/Rcompile/recent/R-3.0.3/share/texmf/tex/latex" -I "D:/Rcompile/recent/R-3.0.3/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/3.0/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