From ross at biostat.ucsf.edu  Thu May 22 19:59:25 2003
From: ross at biostat.ucsf.edu (Ross Boylan)
Date: Thu May 22 20:59:28 2003
Subject: [Rd] Possible R CMD check problem (PR#3070)
In-Reply-To: <16076.44026.665412.70300@galadriel.ci.tuwien.ac.at>
References: <200305211918.h4LJIA2b007276@pubhealth.ku.dk>
	<16076.44026.665412.70300@galadriel.ci.tuwien.ac.at>
Message-ID: <1053629847.1219.20.camel@epibiosun115-4>

On Thu, 2003-05-22 at 03:52, Friedrich.Leisch@ci.tuwien.ac.at wrote:
> Why do you think there is a bug in R rather than in your package? (I
> assume that it is a package of yours, at least it's not on CRAN).

Well, I did say "possible" problem.  The reason I think so is that part
of the error message (Could not create DVI version) is wrong (a dvi file
was produced) and part of it (This typically indicates Rd problems) is
misleading.  There is also some chance that the problems are deeper than
that.

> 
> How should we be able to track this problem for you? You don't specify
> your computing platform and give us no examples we could try to
> reproduce.

I'm happy to try to isolate it here.  I'm running on Solaris 2.8.  I can
send the files if that would help.

> 
> Does running latex on parcv-manual.tex in a shell work?
> 
Yes (once I found out how to tell it where Rd.sty was).  However, there
is an error in the tex log, also visible (now that I look!) in the
original run.  It seems to indicate some problem with my font setup:
-----------------------------------
(/usr/local/teTeX/share/texmf/tex/latex/base/t1enc.def)kpathsea: Running
mktextfm  ecrm1000
mkdir: Failed to make directory "/usr/local/teTeXfonts/tfm"; Permission
denied
kpsestat: /usr/local/teTeXfonts/tfm/..: No such file or directory
usage:  chmod [-fR] <absolute-mode> file ...
        chmod [-fR] <symbolic-mode-list> file ...
where   <symbolic-mode-list> is a comma-separated list of
        [ugoa]{+|-|=}[rwxXlstugo]
mkdir: Failed to make directory "/usr/local/teTeXfonts/tfm/jknappen"; No
such file or directory
kpsestat: /usr/local/teTeXfonts/tfm/jknappen/..: No such file or
directory
usage:  chmod [-fR] <absolute-mode> file ...
        chmod [-fR] <symbolic-mode-list> file ...
where   <symbolic-mode-list> is a comma-separated list of
        [ugoa]{+|-|=}[rwxXlstugo]
mkdir: Failed to make directory "/usr/local/teTeXfonts/tfm/jknappen/ec";
No such file or directory
kpsestat: /usr/local/teTeXfonts/tfm/jknappen/ec/..: No such file or
directory
usage:  chmod [-fR] <absolute-mode> file ...
        chmod [-fR] <symbolic-mode-list> file ...
where   <symbolic-mode-list> is a comma-separated list of
        [ugoa]{+|-|=}[rwxXlstugo]
mktextfm: mktexdir /usr/local/teTeXfonts/tfm/jknappen/ec failed.
kpathsea: Appending font creation commands to missfont.log.

! Font T1/cmr/m/n/10=ecrm1000 at 10.0pt not loadable: Metric (TFM) file
not fou
nd.
<to be read again> 
                   relax 
l.96 \fontencoding\encodingdefault\selectfont
                                             
? 
) (/usr/local/teTeX/share/texmf/tex/latex/ae/ae.sty
(/usr/local/teTeX/share/texmf/tex/latex/base/fontenc.sty
(/usr/local ....
--------------------------------------

So here's my theory:
latex runs into the problem above, which appears to be with our local
TeX setup, and returns an error code.
R thinks the code means TeX has failed to produce the dvi file.  And
then it emits the error message.

Does this seem a plausible diagnosis?

If that's correct, the undesirable behavior on R's part just relates to
the error handling and reporting.

> fritz leisch
> 
> 
> >>>>> On Wed, 21 May 2003 21:18:10 +0200 (MET DST),
> >>>>> ross  (r) wrote:
> 
>   > Using R 1.7.0 I get 
>   > * checking parcv-manual.tex ... ERROR
>   > Could not create DVI version.
> 
>   > Although there is no apparent error.  The dvi file exists.
>   > Possibly there is some problem with my TeX setup, but the following
>   > messages don't suggest that either.
> 
>   > Here's the full log, which does show some documentation issues:
>   > sheep:~$R CMD check --library=.R/library/ src/parcv
>   > * checking for working latex ... OK
>   > * using log directory '/space/home/ross/parcv.Rcheck'
>   > * checking for file 'parcv/DESCRIPTION' ... OK
>   > * checking if this is a source package ... OK
> 
>   > * Installing *source* package 'parcv' ...
>   > ** R
>   > ** demo
>   > ** inst
>   > ** help
>   >>>> Building/Updating help pages for package 'parcv'
>   >      Formats: text html latex example
>   > * DONE (parcv)
> 
>   > * DONE (INSTALL)
> 
>   > * checking package directory ... OK
>   > * checking for sufficient/correct file permissions ... OK
>   > * checking DESCRIPTION meta-information ... OK
>   > * checking package dependencies ... OK
>   > * checking index information ... WARNING
>   > Demos with missing or empty index information:
>   > [1] "parDemo1"
>   > See the information on INDEX files and package subdirectories in
>   > * section
>   > 'Creating R packages' of the 'Writing R Extensions' manual.
>   > * checking package subdirectories ... OK
>   > * checking R files for syntax errors ... OK
>   > * checking R files for library.dynam ... OK
>   > * checking generic/method consistency ... OK
>   > * checking for assignment functions with final arg not named 'value'
>   > * ... OK
>   > * checking Rd files ... WARNING
>   > Rd files without 'alias':
>   >   man/parcv-internal.Rd
>   > These tags are required in an Rd file.
>   > See chapter 'Writing R documentation' in manual 'Writing R
>   > Extensions'.
>   > * checking for undocumented objects ... WARNING
>   > Undocumented code objects:
>   > [1] "crossval.fit"      "crossval.outerfit" "crossval.setup"
>   > [4] "gcv"
>   > * checking for code/documentation mismatches ... OK
>   > * checking for undocumented arguments in \usage ... OK
>   > * creating parcv-Ex.R ... OK
>   > * checking examples ... OK
>   > * creating parcv-manual.tex ... OK
>   > * checking parcv-manual.tex ... ERROR
>   > Could not create DVI version.
>   > This typically indicates Rd problems.
> 
>   > ______________________________________________
>   > R-devel@stat.math.ethz.ch mailing list
>   > https://www.stat.math.ethz.ch/mailman/listinfo/r-devel
-- 
Ross Boylan <ross@biostat.ucsf.edu>              wk: (415) 502-4031
University of California, San Francisco         fax: (415) 476-9856
Dept of Epidemiology and Biostatistics           hm: (415) 550-1062
530 Parnassus Avenue (Library) rm 115-4
San Francisco, CA 94143-0840


[Rd] Possible R CMD check problem (PR#3070)
Ross Boylan