[Tikzdevice-bugs] [R-Forge] tikzDevice 0.4.5
Cameron Bracken
cameron.bracken at gmail.com
Fri Aug 21 16:18:58 CEST 2009
We obviously have a bit more work to do, I will resubmit when all these
warnings are fixed. Thanks for your patience.
-Cameron
--
Cameron Bracken
Graduate Research Assistant
CADSWES
University of Colorado at Boulder
cameron.bracken at colorado.edu
Cell - 925.548.7392
Work - 303.735.1180
On Wed, Aug 19, 2009 at 1:12 PM, Kurt Hornik <Kurt.Hornik at wu.ac.at> wrote:
> >>>>> Cameron Bracken writes:
>
> > The output you show now matches what we get. I did notice one small
> > noncritical typo giving the "* checking Rd \usage sections" warning.
> > This can be easily fixed. Otherwise, despite our best attempts we have
> > not been able to resolve the other warnings. We have tested on
> > windows mac and linux and have not observed any unsatisfactory
> > behavior. Otherwise all the other steps before submitting have been
> > completed successfully (such as running R CMD Rd2dvi).
>
> I am not sure about the "no unsatisfactory behavior" part: there should
> be no warnings (or errors) when running R CMD check.
>
> Some of the warnings occur because loading the package produces output
> which can not be suppressed. More precisely:
>
> R> suppressWarnings(system(paste(Sys.getenv("R_LATEXCMD"), "--version")))
> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> kpathsea version 3.5.6
> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> There is NO warranty. Redistribution of this software is
> covered by the terms of both the pdfTeX using libpoppler copyright and
> the Lesser GNU General Public License.
> For more information about these matters, see the file
> named COPYING and the pdfTeX using libpoppler source.
> Primary author of pdfTeX using libpoppler: Peter Breitenlohner (eTeX)/Han
> The Thanh (pdfTeX).
> Kpathsea written by Karl Berry, Olaf Weber, and others.
>
> Compiled with libpng 1.2.35; using libpng 1.2.38
> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> Compiled with libpoppler version 0.10.5
>
> because latex && friends have --version write to stdout (and return 0).
>
> You either need to suppress output (not using sink(): use the equiv of
> latex --version > /dev/null) or come up with a better test. In fact, I
> am not quite sure what you are trying to achieve using the latex
> --version test: in principle any GNU coding standard compliant program
> will honor --version and return 0 when called with --version. Hence, I
> think you could simply use Sys.which() to find the appropriate LaTeX
> executable from the candidates.
>
> Redirecting leaves
>
> * checking Rd files ... WARNING
> Warning: ./man/tikz.Rd:87: Unnecessary braces at ‘{\code{tikzLatex}}’
> Warning: ./man/tikz.Rd:87: Unnecessary braces at ‘{ Specifies the location
> of the LaTeX compiler to be used by \pkg{tikzDevice}. Setting this option
> may help the package locate a missing compiler. The default is searched for
> when the package is loaded, otherwise it can be set manually. This option
> may be set as follows: \code{options( tikzLatex = '/path/to/latex/compiler'
> )}.}’
> Warning: ./man/tikz.Rd:89: Unnecessary braces at
> ‘{\code{tikzMetricsDictionary}}’
> Warning: ./man/tikz.Rd:89: Unnecessary braces at ‘{ When using the graphics
> device provided by \pkg{tikzDevice}, you may notice that \R\ appears to
> ``lag" or ``hang" when commands such as \code{plot()} are executed. This is
> because the device must query the LaTeX compiler for string widths and font
> metrics. For a normal plot, this may happen dozens or hundreds of times-
> hence \R\ becomes unresponsive for a while. The good news is that the
> \code{tikz()} code is designed to cache the results of these computations so
> they need only be performed once for each string or character. By default,
> these values are stored in a temporary cache file which is deleted when \R\
> is shut down. A location for a permanent cache file may be specified by
> setting the value of \code{tikzMetricsDictionary} in \code{.Rprofile} with
> \code{options( tikzMetricsDictionary = '/path/to/dictionary/location' )}.}’
> Warning: ./man/tikz.Rd:91: Unnecessary braces at
> ‘{\code{tikzDocumentDeclaration}}’
> Warning: ./man/tikz.Rd:91-96: Unnecessary braces at ‘{A string. The
> documentclass declaration when \code{standAlone == TRUE} as well. as when
> font metrics are calculated. The default value is:
> \preformatted{
> options( tikzDocumentDeclaration = "\documentclass{article}" )
>
>
> }}’
> Warning: ./man/tikz.Rd:98: Unnecessary braces at ‘{\code{tikzFooter}}’
> Warning: ./man/tikz.Rd:98-103: Unnecessary braces at ‘{A character vector.
> The footer to be used only when \code{standAlone==TRUE}. The default value
> is:
> \preformatted{
> options( tikzFooter = c( "\end{document}" ) )
>
>
> }}’
> Warning: ./man/tikz.Rd:105: Unnecessary braces at
> ‘{\code{tikzLatexPackages}}’
> Warning: ./man/tikz.Rd:105-115: Unnecessary braces at ‘{ A character
> vector. These are the packages which are included when using the
> \code{standAlone} option as well as when font metric are calculated. The
> default value is:
> \preformatted{
> options( tikzLatexPackagesDefault = c(
> "\usepackage{tikz}",
> "\usepackage[active,tightpage]{preview}",
> "\PreviewEnvironment{pgfpicture}",
> "\setlength\PreviewBorder{0pt}") )
>
>
> }
> }’
> Warning: ./man/tikz.Rd:117: Unnecessary braces at
> ‘{\code{tikzMetricPackages}}’
> Warning: ./man/tikz.Rd:117-125: Unnecessary braces at ‘{ A character
> vector. These are the packages which are additionally loaded when doing font
> metric calculations. As you see below, the font encoding is set to Type 1.
> This is very important so that character codes of LaTeX and \R\ match up.
> The default value is:
> \preformatted{
> options( tikzMetricPackages = c(
> "\usepackage[utf8]{inputenc}",
> "\usepackage[T1]{fontenc}",
> "\usetikzlibrary{calc}"))
>
>
> }}’
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... WARNING
> Bad \usage lines found in documentation object 'tikz':
> tikz(file = "Rplots.tex", width = 7, height = 7,
> bg="white", fg="black", standAlone = FALSE, bareBones = FALSE,
> documentDeclaration = getOption("tikzDocumentDeclaration"),
> packages = getOption("tikzLatexPackages"),
> footer = getOption("tikzFooter")))
>
> Functions with \usage entries need to have the appropriate \alias entries,
> and all their arguments documented.
> The \usage entries must correspond to syntactically valid R code.
> See the chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
>
> * checking package vignettes in 'inst/doc' ... NOTE
> This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6)
> %&-line parsing enabled.
> entering extended mode
> ! I can't write on file `texput.log'.
> Please type another transcript file name>
> * checking PDF version of manual ... OK
>
>
> (and I have no idea about the texput.log message.)
>
> -k
>
>
>
>
> > -Cameron
>
>
>
> > On Mon, Aug 10, 2009 at 8:10 AM, Kurt Hornik <Kurt.Hornik at wu.ac.at>
> wrote:
>
> >> >>>>> Cameron Bracken writes:
> >>
> >> > I do not get this error, nor is this present on R-forge. I strongly
> >> suspect
> >> > that it is a problem with missing LaTeX packages when building the
> >> vignette.
> >> > I cannot tell exactly which one because the errors are very
> >> > cryptic. The LaTeX packages on which out vignette depends are:
> >> > couriers
> >> > hyperref
> >> > ulem
> >> > tikz (version 2.00)
> >> > parskip
> >> > geometry
> >> > epigraph
> >> > multicol
> >> > graphicx
> >> > float
> >> > natbib
> >>
> >> I rechecked with r-release, with basically the same results, see below.
> >>
> >> You're saying you're not getting the warnings?
> >>
> >> -k
> >>
> >> * using log directory '/home/Hornik/tmp/CRAN/ZZZ/tikzDevice.Rcheck'
> >> * using R version 2.9.1 Patched (2009-08-07 r49108)
> >> * using session charset: UTF-8
> >> * checking for file 'tikzDevice/DESCRIPTION' ... OK
> >> * checking extension type ... Package
> >> * this is package 'tikzDevice' version '0.4.5'
> >> * checking package name space information ... OK
> >> * checking package dependencies ... OK
> >> * checking if this is a source package ... OK
> >> * checking for executable files ... OK
> >> * checking whether package 'tikzDevice' can be installed ... OK
> >> * checking package directory ... OK
> >> * checking for portable file names ... OK
> >> * checking for sufficient/correct file permissions ... OK
> >> * checking DESCRIPTION meta-information ... OK
> >> * checking top-level files ... OK
> >> * checking index information ... OK
> >> * checking package subdirectories ... OK
> >> * checking R files for non-ASCII characters ... OK
> >> * checking R files for syntax errors ... OK
> >> * checking whether the package can be loaded ... OK
> >> * checking whether the package can be loaded with stated dependencies
> ...
> >> OK
> >> * checking whether the name space can be loaded with stated dependencies
> >> ... OK
> >> * checking for unstated dependencies in R code ... WARNING
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> See the information on DESCRIPTION files in the chapter 'Creating R
> >> packages' of the 'Writing R Extensions' manual.
> >> * checking S3 generic/method consistency ... WARNING
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> See section 'Generic functions and methods' of the 'Writing R
> Extensions'
> >> manual.
> >> * checking replacement functions ... WARNING
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> In R, the argument of a replacement function which corresponds to the
> right
> >> hand side must be named 'value'.
> >> * checking foreign function calls ... WARNING
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> See the chapter 'System and foreign language interfaces' of the 'Writing
> R
> >> Extensions' manual.
> >> * checking R code for possible problems ... NOTE
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> queryMetricsDictionary: no visible binding for global variable
> >> ‘dictionary’
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> * checking Rd files ... OK
> >> * checking Rd files against version 2 parser ... OK
> >> * checking Rd cross-references ... OK
> >> * checking for missing documentation entries ... WARNING
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> All user-level objects in a package should have documentation entries.
> >> See the chapter 'Writing R documentation files' in manual 'Writing R
> >> Extensions'.
> >> * checking for code/documentation mismatches ... WARNING
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> * checking Rd \usage sections ... WARNING
> >> Bad \usage lines found in documentation object 'tikz':
> >> tikz(file = "Rplots.tex", width = 7, height = 7,
> >> bg="white", fg="black", standAlone = FALSE, bareBones = FALSE,
> >> documentDeclaration = getOption("tikzDocumentDeclaration"),
> >> packages = getOption("tikzLatexPackages"),
> >> footer = getOption("tikzFooter")))
> >>
> >> Functions with \usage entries need to have the appropriate \alias
> entries,
> >> and all their arguments documented.
> >> The \usage entries must correspond to syntactically valid R code.
> >> See the chapter 'Writing R documentation files' in manual 'Writing R
> >> Extensions'.
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >>
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >>
> >> The \usage entries for S3 methods should use the \method markup and not
> >> their full name.
> >> See the chapter 'Writing R documentation files' in manual 'Writing R
> >> Extensions'.
> >> * checking line endings in C/C++/Fortran sources/headers ... OK
> >> * checking line endings in Makefiles ... OK
> >> * checking for portable use of $BLAS_LIBS ... OK
> >> * checking examples ... OK
> >> * checking package vignettes in 'inst/doc' ... NOTE
> >> pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6)
> >> kpathsea version 3.5.6
> >> Copyright 2007 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
> >> Kpathsea is copyright 2007 Karl Berry and Olaf Weber.
> >> There is NO warranty. Redistribution of this software is
> >> covered by the terms of both the pdfTeX using libpoppler copyright and
> >> the Lesser GNU General Public License.
> >> For more information about these matters, see the file
> >> named COPYING and the pdfTeX using libpoppler source.
> >> Primary author of pdfTeX using libpoppler: Peter Breitenlohner
> (eTeX)/Han
> >> The Thanh (pdfTeX).
> >> Kpathsea written by Karl Berry, Olaf Weber, and others.
> >> Compiled with libpng 1.2.35; using libpng 1.2.38
> >> Compiled with zlib 1.2.3.3; using zlib 1.2.3.3
> >> Compiled with libpoppler version 0.10.5
> >> This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6)
> >> %&-line parsing enabled.
> >> entering extended mode
> >> ! I can't write on file `texput.log'.
> >> Please type another transcript file name>
> >> * checking PDF version of manual ... OK
> >>
>
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