CRAN Package Check Results for Package FunCluster

Last updated on 2018-09-23 22:46:56 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.09 27.25 102.97 130.22 NOTE
r-devel-linux-x86_64-debian-gcc 1.09 27.70 82.80 110.50 NOTE
r-devel-linux-x86_64-fedora-clang 1.09 163.16 NOTE
r-devel-linux-x86_64-fedora-gcc 1.09 158.48 NOTE
r-devel-windows-ix86+x86_64 1.09 60.00 141.00 201.00 WARN
r-patched-linux-x86_64 1.09 25.97 88.03 114.00 NOTE
r-patched-solaris-x86 1.09 235.70 NOTE
r-release-linux-x86_64 1.09 29.39 87.91 117.30 NOTE
r-release-windows-ix86+x86_64 1.09 43.00 131.00 174.00 WARN
r-release-osx-x86_64 1.09 NOTE
r-oldrel-windows-ix86+x86_64 1.09 39.00 144.00 183.00 NOTE
r-oldrel-osx-x86_64 1.09 NOTE

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    NB: .First.lib is obsolete and will not be used in R 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-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.09
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64