Re: [R] Hmisc latex function

From: Marc Schwartz <MSchwartz_at_mn.rr.com>
Date: Sat 17 Dec 2005 - 00:56:17 EST

Paul,

I believe that the bug has been fixed in the CVS version of latex(), but it has not yet made its way to an updated version of Hmisc on CRAN from what I can see.

You can get the updated version of latex() from:

http://biostat.mc.vanderbilt.edu/cgi-bin/cvsweb.cgi/Hmisc/R/latex.s

Click on the 'download' link for version 1.14 at the top of the page. You can save the updated code to a text file and then source() it into a R session for the time being.

HTH, Marc Schwartz

On Thu, 2005-12-15 at 15:53 -0600, Paul Johnson wrote:
> Does anybody suggest a work-around this problem?
>
> pj
>
> Marc Schwartz (via MN) wrote:
> > On Wed, 2005-10-12 at 08:33 -0500, Charles Dupont wrote:
> >
> >>Marc Schwartz (via MN) wrote:
> >>
> >>>On Tue, 2005-10-11 at 10:01 -0400, Rick Bilonick wrote:
> >>>
> >>>
> >>>>I'm using R 2.2.0 on an up-to-date version of Fedora Core 4 with the
> >>>>latest version of Hmisc. When I run an example from the latex function I
> >>>>get the following:
> >>>>
> >>>>
> >>>>
> >>>>>x <- matrix(1:6, nrow=2, dimnames=list(c('a','b'),c('c','d','enLine
> >>>>
> >>>>2')))
> >>>>
> >>>>
> >>>>>x
> >>>>
> >>>> c d enLine 2
> >>>>a 1 3 5
> >>>>b 2 4 6
> >>>>
> >>>>
> >>>>>latex(x) # creates x.tex in working directory
> >>>>
> >>>>sh: line 0: cd: “/tmp/Rtmpl10983”: No such file or directory
> >>>>This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
> >>>>entering extended mode
> >>>>! I can't find file `“/tmp/Rtmpl10983/file643c9869”'.
> >>>><*> “/tmp/Rtmpl10983/file643c9869”
> >>>>
> >>>>Please type another input file name: q
> >>>>(/usr/share/texmf/tex/latex/tools/q.tex
> >>>>LaTeX2e <2003/12/01>
> >>>>Babel <v3.8d> and hyphenation patterns for american, french, german,
> >>>>ngerman, b
> >>>>ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch,
> >>>>esperanto, e
> >>>>stonian, finnish, greek, icelandic, irish, italian, latin, magyar,
> >>>>norsk, polis
> >>>>h, portuges, romanian, russian, serbian, slovak, slovene, spanish,
> >>>>swedish, tur
> >>>>kish, ukrainian, nohyphenation, loaded.
> >>>>File ignored
> >>>>xdvi-motif.bin: Fatal error: /tmp/Rtmpl10983/file643c9869.dvi: No such
> >>>>file.
> >>>>
> >>>>
> >>>>How can I fix this?
> >>>>
> >>>>Rick B.
> >>>
> >>>
> >>>I get the same results, also on FC4 with R 2.2.0.
> >>>
> >>>I am cc:ing Frank here for his input, but a quick review of the code and
> >>>created files suggests that there may be conflict between the locations
> >>>of some of the resultant files during the latex system call. Some files
> >>>appear in a temporary R directory, while others appear in the current R
> >>>working directory.
> >>>
> >>>For example, if I enter the full filename:
> >>>
> >>> /tmp/RtmpC12100/file643c9869.tex
> >>>
> >>>at the latex prompt, I get:
> >>>
> >>>
> >>>
> >>>>latex(x)
> >>>
> >>>sh: line 0: cd: “/tmp/RtmpC12100”: No such file or directory
> >>>This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
> >>>entering extended mode
> >>>! I can't find file `“/tmp/RtmpC12100/file643c9869”'.
> >>><*> “/tmp/RtmpC12100/file643c9869”
> >>>
> >>>Please type another input file name: *** loading the extensions
> >>>datasource
> >>>/tmp/RtmpC12100/file643c9869.tex
> >>>(/tmp/RtmpC12100/file643c9869.tex
> >>>LaTeX2e <2003/12/01>
> >>>Babel <v3.8d> and hyphenation patterns for american, french, german,
> >>>ngerman, b
> >>>ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch,
> >>>esperanto, e
> >>>stonian, finnish, greek, icelandic, irish, italian, latin, magyar,
> >>>norsk, polis
> >>>h, portuges, romanian, russian, serbian, slovak, slovene, spanish,
> >>>swedish, tur
> >>>kish, ukrainian, nohyphenation, loaded.
> >>>(/usr/share/texmf/tex/latex/base/report.cls
> >>>Document Class: report 2004/02/16 v1.4f Standard LaTeX document class
> >>>(/usr/share/texmf/tex/latex/base/size10.clo))
> >>>(/usr/share/texmf/tex/latex/geometry/geometry.sty
> >>>(/usr/share/texmf/tex/latex/graphics/keyval.sty)
> >>>(/usr/share/texmf/tex/latex/geometry/geometry.cfg))
> >>>No file file643c9869.aux.
> >>>[1] (./file643c9869.aux) )
> >>>Output written on file643c9869.dvi (1 page, 368 bytes).
> >>>Transcript written on file643c9869.log.
> >>>xdvi-motif.bin: Fatal error: /tmp/RtmpC12100/file643c9869.dvi
> >>
> >>
> >>Hmmmm, It works for me. Interesting.
> >>
> >>It almost looks like the temp dir is not being created, but thats not
> >>possible because R does that. It might be a Unicode issue with you
> >>system shell. Can you run this statement in R
> >>
> >>sys(paste('cd',dQuote(tempdir()),";",
> >>"echo Hello BOB > test.test",
> >>";","cat test.test"))
> >>
> >>
> >>What version of Hmisc are you using? What local are you using?
> >>
> >>Charles
> >
> >
> > Hmisc version 3.0-7, Dated 2005-09-15, which is the latest according to
> > CRAN.
> >
> >
> >>sys(paste('cd',dQuote(tempdir()),";",
> >
> > + "echo Hello BOB > test.test",
> > + ";","cat test.test"))
> > sh: line 0: cd: “/tmp/RtmpGY5553”: No such file or directory
> > [1] "Hello BOB"
> >
> >
> >>From a bash console:
> >
> > $ cd /tmp/RtmpGY5553
> > $ pwd
> > /tmp/RtmpGY5553
> >
> >
> > $ locale
> > LANG=en_US.UTF-8
> > LC_CTYPE="en_US.UTF-8"
> > LC_NUMERIC="en_US.UTF-8"
> > LC_TIME="en_US.UTF-8"
> > LC_COLLATE="en_US.UTF-8"
> > LC_MONETARY="en_US.UTF-8"
> > LC_MESSAGES="en_US.UTF-8"
> > LC_PAPER="en_US.UTF-8"
> > LC_NAME="en_US.UTF-8"
> > LC_ADDRESS="en_US.UTF-8"
> > LC_TELEPHONE="en_US.UTF-8"
> > LC_MEASUREMENT="en_US.UTF-8"
> > LC_IDENTIFICATION="en_US.UTF-8"
> > LC_ALL=
> >
> >
> > On the creation of the sys() call, it looks like the backquotes are
> > causing the problem:
> >
> >
> >>paste('cd',dQuote(tempdir()))
> >
> > [1] "cd “/tmp/RtmpGY5553”"
> >
> >
> >>From a bash shell:
> >
> > $ cd “/tmp/RtmpGY5553”
> > bash: cd: “/tmp/RtmpGY5553”: No such file or directory
> > $ cd "/tmp/RtmpGY5553"
> > $ pwd
> > /tmp/RtmpGY5553
> >
> >
> > According to ?dQuote:
> >
> > By default, sQuote and dQuote provide undirectional ASCII quotation
> > style. In a UTF-8 locale (see l10n_info), the Unicode directional quotes
> > are used.
> >
> > The See Also points to "shQuote for quoting OS commands."
> >
> >
> > HTH,
> >
> > Marc
> >



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