CRAN Package Check Results for Package phyclust

Last updated on 2014-10-02 01:48:23.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.1-15 15.77 29.84 45.61 NOTE
r-devel-linux-x86_64-debian-gcc 0.1-15 22.34 28.74 51.08 NOTE
r-devel-linux-x86_64-fedora-clang 0.1-15 87.96 NOTE
r-devel-linux-x86_64-fedora-gcc 0.1-15 87.95 NOTE
r-devel-osx-x86_64-clang 0.1-15 75.58 NOTE
r-devel-windows-ix86+x86_64 0.1-15 106.00 55.00 161.00 NOTE
r-patched-linux-x86_64 0.1-15 22.60 30.30 52.89 OK
r-patched-solaris-sparc 0.1-15 539.20 OK
r-patched-solaris-x86 0.1-15 136.30 OK
r-release-linux-ix86 0.1-15 28.67 39.63 68.30 OK
r-release-linux-x86_64 0.1-15 22.76 30.28 53.04 OK
r-release-osx-x86_64-mavericks 0.1-15 NOTE
r-release-osx-x86_64-snowleopard 0.1-15 ERROR
r-release-windows-ix86+x86_64 0.1-15 96.00 57.00 153.00 OK
r-oldrel-windows-ix86+x86_64 0.1-15 101.00 62.00 163.00 OK

Check Details

Version: 0.1-15
Check: R code for possible problems
Result: NOTE
    .EMControl: no visible binding for global variable ‘.init.procedure’
    .EMControl: no visible binding for global variable ‘.init.method’
    .EMControl: no visible binding for global variable
     ‘.substitution.model’
    .EMControl: no visible binding for global variable ‘.edist.model’
    .EMControl: no visible binding for global variable ‘.identifier’
    .EMControl: no visible binding for global variable ‘.code.type’
    .EMControl: no visible binding for global variable ‘.em.method’
    .EMControl: no visible binding for global variable ‘.boundary.method’
    .EMControl: no visible binding for global variable ‘.se.model’
    .show.option: no visible binding for global variable ‘.boundary.method’
    .show.option: no visible binding for global variable ‘.code.type’
    .show.option: no visible binding for global variable ‘.edist.model’
    .show.option: no visible binding for global variable ‘.em.method’
    .show.option: no visible binding for global variable ‘.identifier’
    .show.option: no visible binding for global variable ‘.init.method’
    .show.option: no visible binding for global variable ‘.init.procedure’
    .show.option: no visible binding for global variable ‘.nucleotide’
    .show.option: no visible binding for global variable ‘.snp’
    .show.option: no visible binding for global variable
     ‘.substitution.model’
    acode2aid.default: no visible binding for global variable ‘.amino.acid’
    aid2acode.default: no visible binding for global variable ‘.amino.acid’
    bootstrap.merge.seq: no visible binding for global variable
     ‘.code.type’
    check.label: no visible binding for global variable ‘.label.method’
    cid2aid.default: no visible binding for global variable ‘.genetic.code’
    cid2aid.default: no visible binding for global variable ‘.amino.acid’
    code2nid.default: no visible binding for global variable ‘.nucleotide’
    code2nid.default: no visible binding for global variable
     ‘.missing.code’
    find.best: no visible binding for global variable ‘.EMC’
    find.best: no visible binding for global variable ‘.init.procedure’
    find.best: no visible binding for global variable ‘.init.method’
    find.consensus: no visible binding for global variable ‘.code.type’
    gen.seq.HKY: no visible binding for global variable ‘.nucleotide’
    gen.seq.SNP: no visible binding for global variable ‘.snp’
    nid2aid.default: no visible binding for global variable ‘.amino.acid’
    nid2aid.default: no visible binding for global variable ‘.nucleotide’
    nid2aid.default: no visible binding for global variable ‘.genetic.code’
    nid2aid.default : nid2aid.a.seq: no visible binding for global variable
     ‘.genetic.code’
    nid2cid.default: no visible binding for global variable ‘.nucleotide’
    nid2cid.default: no visible binding for global variable ‘.codon’
    nid2cid.default: no visible binding for global variable ‘.genetic.code’
    nid2cid.default : nid2cid.a.seq: no visible binding for global variable
     ‘.genetic.code’
    nid2code.default: no visible binding for global variable ‘.nucleotide’
    nid2code.default: no visible binding for global variable
     ‘.missing.code’
    paml.baseml: no visible binding for global variable ‘.code.type’
    phyclust: no visible binding for global variable ‘.EMC’
    phyclust.Pt: no visible binding for global variable
     ‘.substitution.model’
    phyclust.Pt: no visible binding for global variable ‘.code.type’
    phyclust.e.step: no visible binding for global variable
     ‘.substitution.model’
    phyclust.e.step: no visible binding for global variable ‘.identifier’
    phyclust.e.step: no visible binding for global variable ‘.code.type’
    phyclust.edist: no visible binding for global variable ‘.edist.model’
    phyclust.em.step: no visible binding for global variable
     ‘.substitution.model’
    phyclust.em.step: no visible binding for global variable ‘.identifier’
    phyclust.em.step: no visible binding for global variable ‘.code.type’
    phyclust.logL: no visible binding for global variable
     ‘.substitution.model’
    phyclust.logL: no visible binding for global variable ‘.identifier’
    phyclust.logL: no visible binding for global variable ‘.code.type’
    phyclust.m.step: no visible binding for global variable
     ‘.substitution.model’
    phyclust.m.step: no visible binding for global variable ‘.identifier’
    phyclust.m.step: no visible binding for global variable ‘.code.type’
    phyclust.se: no visible binding for global variable ‘.EMC’
    phyclust.se.update: no visible binding for global variable ‘.EMC’
    phyclust.update: no visible binding for global variable ‘.EMC’
    plotdots: no visible binding for global variable ‘.code.type’
    plotdots : <anonymous>: no visible binding for global variable
     ‘.missing.code’
    plotdots: no visible binding for global variable ‘.missing.code’
    plotfd: no visible binding for global variable ‘.Color’
    plotgaps: no visible binding for global variable ‘.code.type’
    plotgaps: no visible binding for global variable ‘.nucleotide’
    plotgaps: no visible binding for global variable ‘.snp’
    plothist: no visible binding for global variable ‘.Color’
    plotnj: no visible binding for global variable ‘.Color’
    plotstruct: no visible binding for global variable ‘.Color’
    print.Pt: no visible binding for global variable ‘.nucleotide’
    print.Pt: no visible binding for global variable ‘.snp’
    prune.Mu: no visible binding for global variable ‘.code.type’
    prune.Mu: no visible binding for global variable ‘.nucleotide’
    prune.Mu: no visible binding for global variable ‘.snp’
    read.fasta: no visible binding for global variable ‘.code.type’
    read.phylip: no visible binding for global variable ‘.code.type’
    read.seqgen: no visible binding for global variable ‘.code.type’
    sid2snp.default: no visible binding for global variable ‘.snp’
    sid2snp.default: no visible binding for global variable ‘.missing.code’
    snp2sid.default: no visible binding for global variable ‘.snp’
    snp2sid.default: no visible binding for global variable ‘.missing.code’
    summary.phyclust: no visible binding for global variable ‘.nucleotide’
    translate.EMC: no visible binding for global variable ‘.init.procedure’
    translate.EMC: no visible binding for global variable ‘.init.method’
    translate.EMC: no visible binding for global variable
     ‘.substitution.model’
    translate.EMC: no visible binding for global variable ‘.edist.model’
    translate.EMC: no visible binding for global variable ‘.identifier’
    translate.EMC: no visible binding for global variable ‘.code.type’
    translate.EMC: no visible binding for global variable ‘.em.method’
    translate.EMC: no visible binding for global variable
     ‘.boundary.method’
    translate.EMC.se: no visible binding for global variable
     ‘.init.procedure’
    translate.EMC.se: no visible binding for global variable ‘.init.method’
    translate.EMC.se: no visible binding for global variable
     ‘.substitution.model’
    translate.EMC.se: no visible binding for global variable ‘.edist.model’
    translate.EMC.se: no visible binding for global variable ‘.identifier’
    translate.EMC.se: no visible binding for global variable ‘.code.type’
    translate.EMC.se: no visible binding for global variable ‘.em.method’
    translate.EMC.se: no visible binding for global variable
     ‘.boundary.method’
    translate.EMC.se: no visible binding for global variable ‘.se.model’
    translate.ret: no visible binding for global variable ‘.init.procedure’
    translate.ret: no visible binding for global variable ‘.init.method’
    translate.ret: no visible binding for global variable
     ‘.substitution.model’
    translate.ret: no visible binding for global variable ‘.edist.model’
    translate.ret: no visible binding for global variable ‘.identifier’
    translate.ret: no visible binding for global variable ‘.code.type’
    translate.ret: no visible binding for global variable ‘.em.method’
    translate.ret: no visible binding for global variable
     ‘.boundary.method’
    translate.ret: no visible binding for global variable ‘.nucleotide’
    translate.ret: no visible binding for global variable ‘.snp’
    translate.ret: no visible binding for global variable ‘.label.method’
    translate.ret.se: no visible binding for global variable
     ‘.init.procedure’
    translate.ret.se: no visible binding for global variable ‘.init.method’
    translate.ret.se: no visible binding for global variable
     ‘.substitution.model’
    translate.ret.se: no visible binding for global variable ‘.edist.model’
    translate.ret.se: no visible binding for global variable ‘.identifier’
    translate.ret.se: no visible binding for global variable ‘.code.type’
    translate.ret.se: no visible binding for global variable ‘.em.method’
    translate.ret.se: no visible binding for global variable
     ‘.boundary.method’
    translate.ret.se: no visible binding for global variable ‘.nucleotide’
    translate.ret.se: no visible binding for global variable ‘.snp’
    translate.ret.se: no visible binding for global variable ‘.se.model’
    write.fasta: no visible binding for global variable ‘.code.type’
    write.paml: no visible binding for global variable ‘.code.type’
    write.phylip: no visible binding for global variable ‘.code.type’
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

Version: 0.1-15
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
     Running 'texi2dvi' on 'phyclust-guide.tex' failed.
    LaTeX errors:
    ! LaTeX Error: File `a4wide.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    ./phyclust-include/jss.cls:72: ==> Fatal error occurred, no output PDF file pr
    oduced!
    Calls: buildVignettes -> texi2pdf -> texi2dvi
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 0.1-15
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-release-osx-x86_64-snowleopard