CRAN Package Check Results for Package vegan

Last updated on 2014-10-01 11:48:02.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0-10 5.70 118.08 123.78 NOTE
r-devel-linux-x86_64-debian-gcc 2.0-10 5.80 118.90 124.70 NOTE
r-devel-linux-x86_64-fedora-clang 2.0-10 260.96 NOTE
r-devel-linux-x86_64-fedora-gcc 2.0-10 244.55 NOTE
r-devel-osx-x86_64-clang 2.0-10 204.10 NOTE
r-devel-windows-ix86+x86_64 2.0-10 23.00 197.00 220.00 NOTE
r-patched-linux-x86_64 2.0-10 7.65 131.05 138.70 NOTE
r-patched-solaris-sparc 2.0-10 1409.90 OK --no-build-vignettes
r-patched-solaris-x86 2.0-10 327.00 OK
r-release-linux-ix86 2.0-10 8.32 161.02 169.34 NOTE
r-release-linux-x86_64 2.0-10 6.14 130.77 136.92 NOTE
r-release-osx-x86_64-mavericks 2.0-10 NOTE
r-release-osx-x86_64-snowleopard 2.0-10 NOTE
r-release-windows-ix86+x86_64 2.0-10 22.00 211.00 233.00 OK
r-oldrel-windows-ix86+x86_64 2.0-10 21.00 228.00 249.00 OK

Check Details

Version: 2.0-10
Check: R code for possible problems
Result: NOTE
    goodness.metaMDS: no visible global function definition for ‘Shepard’
    metaMDSiter: no visible global function definition for ‘isoMDS’
    ordirgl: no visible global function definition for ‘rgl.clear’
    ordirgl: no visible global function definition for ‘rgl.points’
    ordirgl: no visible global function definition for ‘rgl.texts’
    ordirgl: no visible global function definition for ‘rgl.lines’
    ordisurf.default: no visible global function definition for ‘gam’
    orditkplot: no visible global function definition for ‘tclvalue’
    orditkplot: no visible global function definition for ‘tcl’
    orditkplot : Point: no visible global function definition for
     ‘tkcreate’
    orditkplot: no visible global function definition for ‘tktoplevel’
    orditkplot: no visible global function definition for ‘tktitle<-’
    orditkplot: no visible global function definition for ‘tkwinfo’
    orditkplot: no visible global function definition for ‘tkframe’
    orditkplot: no visible global function definition for ‘tkbutton’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkpostscript’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkgetSaveFile’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkdestroy’
    orditkplot : ordDump: no visible global function definition for
     ‘tclvalue’
    orditkplot : pDump: no visible global function definition for ‘tclVar’
    orditkplot : pDump: no visible global function definition for
     ‘tktoplevel’
    orditkplot : pDump: no visible global function definition for
     ‘tktitle<-’
    orditkplot : pDump: no visible global function definition for ‘tkentry’
    orditkplot : pDump: no visible global function definition for ‘tkgrid’
    orditkplot : pDump: no visible global function definition for ‘tklabel’
    orditkplot : pDump : isDone: no visible global function definition for
     ‘tclvalue’
    orditkplot : pDump : isDone: no visible global function definition for
     ‘tkmessageBox’
    orditkplot : pDump : isDone: no visible global function definition for
     ‘tkdestroy’
    orditkplot : pDump: no visible global function definition for ‘tkbind’
    orditkplot : pDump: no visible global function definition for ‘tkfocus’
    orditkplot : devDump: no visible global function definition for
     ‘tkgetSaveFile’
    orditkplot : devDump: no visible global function definition for
     ‘tclvalue’
    orditkplot : devDump: no visible global function definition for
     ‘tkmessageBox’
    orditkplot: no visible global function definition for ‘tkmessageBox’
    orditkplot: no visible global function definition for ‘tkdestroy’
    orditkplot : xy2usr: no visible global function definition for
     ‘tkcoords’
    orditkplot: no visible global function definition for ‘tkcanvas’
    orditkplot: no visible global function definition for ‘tkconfigure’
    orditkplot: no visible global function definition for ‘tkscrollbar’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkyview’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkset’
    orditkplot: no visible global function definition for ‘tkpack’
    orditkplot: no visible global function definition for ‘tkgrid’
    orditkplot: no visible global function definition for ‘tkcreate’
    orditkplot: no visible global function definition for ‘tclArray’
    orditkplot: no visible global function definition for ‘tkaddtag’
    orditkplot : pEnter: no visible global function definition for
     ‘tkdelete’
    orditkplot : pEnter: no visible global function definition for
     ‘tkcreate’
    orditkplot : pEnter: no visible global function definition for ‘tkbbox’
    orditkplot : pEnter: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pEnter: no visible global function definition for
     ‘tkitemraise’
    orditkplot : pLeave: no visible global function definition for
     ‘tkdelete’
    orditkplot : pDown: no visible global function definition for ‘tkdtag’
    orditkplot : pDown: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pDown: no visible global function definition for
     ‘tkitemraise’
    orditkplot : pDown: no visible global function definition for
     ‘tkcoords’
    orditkplot : pDown: no visible global function definition for ‘tkfind’
    orditkplot : pMove: no visible global function definition for ‘tkmove’
    orditkplot : pMove: no visible global function definition for
     ‘tkdelete’
    orditkplot : pMove: no visible global function definition for
     ‘tkcanvasx’
    orditkplot : pMove: no visible global function definition for
     ‘tkcanvasy’
    orditkplot : pMove: no visible global function definition for
     ‘tkcreate’
    orditkplot : pMove: no visible global function definition for ‘tkbbox’
    orditkplot : pMove: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pEdit: no visible global function definition for ‘tkdtag’
    orditkplot : pEdit: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pEdit: no visible global function definition for
     ‘tkitemraise’
    orditkplot : pEdit: no visible global function definition for ‘tkfind’
    orditkplot : pEdit: no visible global function definition for ‘tclVar’
    orditkplot : pEdit: no visible global function definition for
     ‘tktoplevel’
    orditkplot : pEdit: no visible global function definition for ‘tkentry’
    orditkplot : pEdit: no visible global function definition for ‘tkgrid’
    orditkplot : pEdit: no visible global function definition for ‘tklabel’
    orditkplot : pEdit : isDone: no visible global function definition for
     ‘tclvalue’
    orditkplot : pEdit : isDone: no visible global function definition for
     ‘tkitemconfigure’
    orditkplot : pEdit : isDone: no visible global function definition for
     ‘tkdestroy’
    orditkplot : pEdit: no visible global function definition for ‘tkbind’
    orditkplot : pRect0: no visible global function definition for
     ‘tkcanvasy’
    orditkplot : pRect: no visible global function definition for
     ‘tkdelete’
    orditkplot : pRect: no visible global function definition for
     ‘tkcanvasy’
    orditkplot : pRect: no visible global function definition for
     ‘tkcreate’
    orditkplot : pRect: no visible global function definition for
     ‘tkaddtag’
    orditkplot: no visible global function definition for ‘tkitembind’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkdtag’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkdelete’
    orditkplot: no visible global function definition for ‘tkbind’
    orglpoints: no visible global function definition for ‘rgl.points’
    orglsegments: no visible global function definition for ‘rgl.lines’
    orglspider: no visible global function definition for ‘rgl.lines’
    orgltext: no visible global function definition for ‘rgl.texts’
    plot.spantree: no visible binding for global variable ‘sammon’
    rankindex: no visible global function definition for ‘daisy’
    rgl.isomap: no visible global function definition for ‘rgl.lines’
    rgl.renyiaccum: no visible global function definition for ‘rgl.bg’
    rgl.renyiaccum: no visible global function definition for ‘rgl.surface’
    rgl.renyiaccum: no visible global function definition for ‘rgl.bbox’
    rgl.renyiaccum: no visible global function definition for ‘rgl.texts’
    stressplot.default: no visible global function definition for ‘Shepard’
    
    Found the following assignments to the global environment:
    File ‘vegan/R/orditkplot.R’:
     assign(dumpName, xy, envir = .GlobalEnv)
     assign(dumpName, xy, envir = .GlobalEnv)
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-osx-x86_64-clang

Version: 2.0-10
Check: R code for possible problems
Result: NOTE
    goodness.metaMDS: no visible global function definition for ‘Shepard’
    metaMDSiter: no visible global function definition for ‘isoMDS’
    ordirgl: no visible global function definition for ‘rgl.clear’
    ordirgl: no visible global function definition for ‘rgl.points’
    ordirgl: no visible global function definition for ‘rgl.texts’
    ordirgl: no visible global function definition for ‘rgl.lines’
    ordisurf.default: no visible global function definition for ‘gam’
    orditkplot: no visible global function definition for ‘tclvalue’
    orditkplot: no visible global function definition for ‘tcl’
    orditkplot : Point: no visible global function definition for
     ‘tkcreate’
    orditkplot: no visible global function definition for ‘tktoplevel’
    orditkplot: no visible global function definition for ‘tktitle<-’
    orditkplot: no visible global function definition for ‘tkwinfo’
    orditkplot: no visible global function definition for ‘tkframe’
    orditkplot: no visible global function definition for ‘tkbutton’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkpostscript’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkgetSaveFile’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkdestroy’
    orditkplot : ordDump: no visible global function definition for
     ‘tclvalue’
    orditkplot : pDump: no visible global function definition for ‘tclVar’
    orditkplot : pDump: no visible global function definition for
     ‘tktoplevel’
    orditkplot : pDump: no visible global function definition for
     ‘tktitle<-’
    orditkplot : pDump: no visible global function definition for ‘tkentry’
    orditkplot : pDump: no visible global function definition for ‘tkgrid’
    orditkplot : pDump: no visible global function definition for ‘tklabel’
    orditkplot : pDump : isDone: no visible global function definition for
     ‘tclvalue’
    orditkplot : pDump : isDone: no visible global function definition for
     ‘tkmessageBox’
    orditkplot : pDump : isDone: no visible global function definition for
     ‘tkdestroy’
    orditkplot : pDump: no visible global function definition for ‘tkbind’
    orditkplot : pDump: no visible global function definition for ‘tkfocus’
    orditkplot : devDump: no visible global function definition for
     ‘tkgetSaveFile’
    orditkplot : devDump: no visible global function definition for
     ‘tclvalue’
    orditkplot : devDump: no visible global function definition for
     ‘tkmessageBox’
    orditkplot: no visible global function definition for ‘tkmessageBox’
    orditkplot: no visible global function definition for ‘tkdestroy’
    orditkplot : xy2usr: no visible global function definition for
     ‘tkcoords’
    orditkplot: no visible global function definition for ‘tkcanvas’
    orditkplot: no visible global function definition for ‘tkconfigure’
    orditkplot: no visible global function definition for ‘tkscrollbar’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkyview’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkset’
    orditkplot: no visible global function definition for ‘tkpack’
    orditkplot: no visible global function definition for ‘tkgrid’
    orditkplot: no visible global function definition for ‘tkcreate’
    orditkplot: no visible global function definition for ‘tclArray’
    orditkplot: no visible global function definition for ‘tkaddtag’
    orditkplot : pEnter: no visible global function definition for
     ‘tkdelete’
    orditkplot : pEnter: no visible global function definition for
     ‘tkcreate’
    orditkplot : pEnter: no visible global function definition for ‘tkbbox’
    orditkplot : pEnter: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pEnter: no visible global function definition for
     ‘tkitemraise’
    orditkplot : pLeave: no visible global function definition for
     ‘tkdelete’
    orditkplot : pDown: no visible global function definition for ‘tkdtag’
    orditkplot : pDown: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pDown: no visible global function definition for
     ‘tkitemraise’
    orditkplot : pDown: no visible global function definition for
     ‘tkcoords’
    orditkplot : pDown: no visible global function definition for ‘tkfind’
    orditkplot : pMove: no visible global function definition for ‘tkmove’
    orditkplot : pMove: no visible global function definition for
     ‘tkdelete’
    orditkplot : pMove: no visible global function definition for
     ‘tkcanvasx’
    orditkplot : pMove: no visible global function definition for
     ‘tkcanvasy’
    orditkplot : pMove: no visible global function definition for
     ‘tkcreate’
    orditkplot : pMove: no visible global function definition for ‘tkbbox’
    orditkplot : pMove: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pEdit: no visible global function definition for ‘tkdtag’
    orditkplot : pEdit: no visible global function definition for
     ‘tkaddtag’
    orditkplot : pEdit: no visible global function definition for
     ‘tkitemraise’
    orditkplot : pEdit: no visible global function definition for ‘tkfind’
    orditkplot : pEdit: no visible global function definition for ‘tclVar’
    orditkplot : pEdit: no visible global function definition for
     ‘tktoplevel’
    orditkplot : pEdit: no visible global function definition for ‘tkentry’
    orditkplot : pEdit: no visible global function definition for ‘tkgrid’
    orditkplot : pEdit: no visible global function definition for ‘tklabel’
    orditkplot : pEdit : isDone: no visible global function definition for
     ‘tclvalue’
    orditkplot : pEdit : isDone: no visible global function definition for
     ‘tkitemconfigure’
    orditkplot : pEdit : isDone: no visible global function definition for
     ‘tkdestroy’
    orditkplot : pEdit: no visible global function definition for ‘tkbind’
    orditkplot : pRect0: no visible global function definition for
     ‘tkcanvasy’
    orditkplot : pRect: no visible global function definition for
     ‘tkdelete’
    orditkplot : pRect: no visible global function definition for
     ‘tkcanvasy’
    orditkplot : pRect: no visible global function definition for
     ‘tkcreate’
    orditkplot : pRect: no visible global function definition for
     ‘tkaddtag’
    orditkplot: no visible global function definition for ‘tkitembind’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkdtag’
    orditkplot : <anonymous>: no visible global function definition for
     ‘tkdelete’
    orditkplot: no visible global function definition for ‘tkbind’
    orglpoints: no visible global function definition for ‘rgl.points’
    orglsegments: no visible global function definition for ‘rgl.lines’
    orglspider: no visible global function definition for ‘rgl.lines’
    orgltext: no visible global function definition for ‘rgl.texts’
    plot.spantree: no visible binding for global variable ‘sammon’
    rankindex: no visible global function definition for ‘daisy’
    rgl.isomap: no visible global function definition for ‘rgl.lines’
    rgl.renyiaccum: no visible global function definition for ‘rgl.bg’
    rgl.renyiaccum: no visible global function definition for ‘rgl.surface’
    rgl.renyiaccum: no visible global function definition for ‘rgl.bbox’
    rgl.renyiaccum: no visible global function definition for ‘rgl.texts’
    stressplot.default: no visible global function definition for ‘Shepard’
Flavors: r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 2.0-10
Check: R code for possible problems
Result: NOTE
    Found the following assignments to the global environment:
    File ‘vegan/R/orditkplot.R’:
     assign(dumpName, xy, envir = .GlobalEnv)
     assign(dumpName, xy, envir = .GlobalEnv)
Flavors: r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 2.0-10
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘maptools’
Flavor: r-release-osx-x86_64-mavericks

Version: 2.0-10
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    (/usr/local/texlive/2013basic/texmf-dist/tex/latex/amsfonts/amssymb.sty
    (/usr/local/texlive/2013basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
    
    ! LaTeX Error: File `ucs.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    Enter file name:
    /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.1/vegan.Rcheck/vign_t
    est/vegan/vignettes/vegan.sty:11: Emergency stop.
    <read *>
    
    l.11 \usepackage
     [utf8x]{inputenc}^^M
    /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.1/vegan.Rcheck/vign_t
    est/vegan/vignettes/vegan.sty:11: ==> Fatal error occurred, no output PDF file
     produced!
    Transcript written on decision-vegan.log.
    /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
    /usr/bin/texi2dvi: see decision-vegan.log for errors.
    make: *** [decision-vegan.pdf] Error 1
    Error in buildVignettes(dir = "/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.1/vegan.Rcheck/vign_test/vegan") :
     running 'make' failed
    Execution halted
Flavor: r-release-osx-x86_64-mavericks

Version: 2.0-10
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: 'smacof'
Flavor: r-release-osx-x86_64-snowleopard

Version: 2.0-10
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
    (/usr/local/texlive/2012basic/texmf-dist/tex/latex/amsfonts/amssymb.sty
    (/usr/local/texlive/2012basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
    
    ! LaTeX Error: File `ucs.sty' not found.
    
    Type X to quit or <RETURN> to proceed,
    or enter new name. (Default extension: sty)
    
    Enter file name:
    /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/snowleopard-x86_64/results/3.1/
    vegan.Rcheck/vign_test/vegan/vignettes/vegan.sty:11: Emergency stop.
    <read *>
    
    l.11 \usepackage
     [utf8x]{inputenc}^^M
    /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/snowleopard-x86_64/results/3.1/
    vegan.Rcheck/vign_test/vegan/vignettes/vegan.sty:11: ==> Fatal error occurred,
     no output PDF file produced!
    Transcript written on decision-vegan.log.
    /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
    /usr/bin/texi2dvi: see decision-vegan.log for errors.
    make: *** [decision-vegan.pdf] Error 1
    Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/snowleopard-x86_64/results/3.1/vegan.Rcheck/vign_test/vegan") :
     running 'make' failed
    Execution halted
Flavor: r-release-osx-x86_64-snowleopard