CRAN Package Check Results for Package FunCluster

Last updated on 2020-08-07 01:49:44 CEST.

Check Details

Version: 1.09
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     'copying'
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-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.09
Check: R code for possible problems
Result: NOTE
    NB: .First.lib is obsolete and will not be used in R >= 3.0.0
    File 'FunCluster/R/FunCluster.R':
     .First.lib calls:
     cat(paste("\nThis is FunCluster package version ", f.version, " maintained by Corneliu Henegar.\n\n", "FunCluster(wd='', org='HS', go.direct=FALSE, clusterm='cc', compare='common.correl.genes',\n", "\tcorr.met='greedy', corr.th=0.85, two.lists=TRUE, restrict=FALSE, alpha=0.05,\n", "\tlocation=FALSE, details=FALSE)\n\n", sep = ""))
    
    Package startup functions should use 'packageStartupMessage' to
     generate messages.
    See section 'Good practice' in '?.onAttach'.
    
    MiseEnFormeKegg: warning in gl(1, NbKmap, label = LL): partial argument
     match of 'label' to 'labels'
    MiseEnFormeKeggSC: warning in gl(1, NbKmap, label = LL): partial
     argument match of 'label' to 'labels'
    prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
     stepsize, len = adjustment.args$num.steps), nr =
     adjustment.args$num.steps, nc = 1): partial argument match of 'nr' to
     'nrow'
    prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
     stepsize, len = adjustment.args$num.steps), nr =
     adjustment.args$num.steps, nc = 1): partial argument match of 'nc' to
     'ncol'
    AnnotationIndirecte: no visible global function definition for
     'write.table'
    ChargerKegg: no visible global function definition for 'download.file'
    ChargerKegg: no visible global function definition for 'count.fields'
    ChargerKegg: no visible global function definition for 'read.table'
    ChargerKegg: no visible global function definition for 'write.table'
    FunCluster: no visible global function definition for 'read.table'
    GeneInfo: no visible global function definition for 'download.file'
    GeneInfo: no visible global function definition for 'read.table'
    GeneInfoSC: no visible global function definition for 'download.file'
    GeneInfoSC: no visible global function definition for 'read.table'
    Kegg: no visible global function definition for 'download.file'
    Kegg: no visible global function definition for 'read.table'
    Kegg: no visible global function definition for 'write.table'
    MakeGoHierarchy: no visible global function definition for
     'download.file'
    MakeGoHierarchy: no visible global function definition for 'read.table'
    MakeGoHierarchy: no visible global function definition for
     'write.table'
    MakeGoTerms: no visible global function definition for 'write.table'
    MakeLocusNames: no visible global function definition for 'write.table'
    MiseEnFormeKegg: no visible global function definition for
     'write.table'
    MiseEnFormeKeggSC: no visible global function definition for
     'write.table'
    TroisiemeFiltrage: no visible global function definition for
     'write.table'
    gene.correl: no visible global function definition for 'as.dist'
    gene.correl: no visible global function definition for 'hclust'
    gene.correl: no visible global function definition for 'cutree'
    goAndLL: no visible global function definition for 'download.file'
    goAndLL: no visible global function definition for 'read.table'
    pclust: no visible global function definition for 'p.adjust'
    pterm: no visible global function definition for 'p.adjust'
    pvalues: no visible global function definition for 'fisher.test'
    term.compare: no visible global function definition for 'cor.test'
    Undefined global functions or variables:
     as.dist cor.test count.fields cutree download.file fisher.test hclust
     p.adjust read.table write.table
    Consider adding
     importFrom("stats", "as.dist", "cor.test", "cutree", "fisher.test",
     "hclust", "p.adjust")
     importFrom("utils", "count.fields", "download.file", "read.table",
     "write.table")
    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-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64