[Tikzdevice-bugs] [R-Forge] tikzDevice 0.4.5
Kurt Hornik
Kurt.Hornik at wu.ac.at
Wed Aug 19 21:12:45 CEST 2009
>>>>> 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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