Re: [Rd] * creating vignettes ... ERROR
Achim Zeileis a crit : Philippe, I just talked to Uwe to properly understand the problem. Is it correct that the vignette gets correctly compiled to a pdf and that only the R CMD build script claims that there has been an error and then terminates? Could you please try the following: go into the inst/doc directory of your e1071 copy and try there R Sweave(svmdoc.Rnw) R texi2dvi(svmdoc.tex, pdf = TRUE) Does that work properly? Thanks all of you for your answer. running Sweave and texi2dvi directly in R leads to the same error: ALGARVE Sweave(svmdoc.Rnw) Writing to file svmdoc.tex Processing code chunks ... 1 : echo term verbatim 2 : echo term verbatim 3 : echo term verbatim 4 : echo term verbatim 5 : term tex 6 : echo term verbatim 7 : term tex You can now run LaTeX on svmdoc.tex ALGARVE texi2dvi(svmdoc.tex, pdf = TRUE) /usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting. /usr/lib/R/bin/texi2dvi: see svmdoc.log for errors. Error in texi2dvi(svmdoc.tex, pdf = TRUE) : running texi2dvi on svmdoc.tex failed ALGARVE The tex file is well generated. Running latex on this file (Sweave.sty is in my latex path) build the dvi file correctly. Philippe Also, please send me the .log file that didn't come through on R-devel. If we can track down the problem precisely, I'll talk directly to Kurt about it. Best, Z . -- Philippe Hup UMR 144 - Service Bioinformatique Institut Curie Laboratoire de Transfert (4me tage) 26 rue d'Ulm 75005 Paris - France Email : [EMAIL PROTECTED] Tl : +33 (0)1 44 32 42 75 Fax :+33 (0)1 42 34 65 28 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] * creating vignettes ... ERROR
Is the error here perchance /tmp/svmdoc.tex:87: LaTeX Error: File `svm' not found? in svmdoc.log? If so, the problem is in graphics inclusion paths. On my system both pdflatex and pdfelatex work, but you do have to be careful with etex paths. On Mon, 24 Jan 2005, [UTF-8] Philippe Hup wrote: Achim Zeileis a crit : Philippe, I just talked to Uwe to properly understand the problem. Is it correct that the vignette gets correctly compiled to a pdf and that only the R CMD build script claims that there has been an error and then terminates? Could you please try the following: go into the inst/doc directory of your e1071 copy and try there R Sweave(svmdoc.Rnw) R texi2dvi(svmdoc.tex, pdf = TRUE) Does that work properly? Thanks all of you for your answer. running Sweave and texi2dvi directly in R leads to the same error: ALGARVE Sweave(svmdoc.Rnw) Writing to file svmdoc.tex Processing code chunks ... 1 : echo term verbatim 2 : echo term verbatim 3 : echo term verbatim 4 : echo term verbatim 5 : term tex 6 : echo term verbatim 7 : term tex You can now run LaTeX on svmdoc.tex ALGARVE texi2dvi(svmdoc.tex, pdf = TRUE) /usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting. /usr/lib/R/bin/texi2dvi: see svmdoc.log for errors. Error in texi2dvi(svmdoc.tex, pdf = TRUE) : running texi2dvi on svmdoc.tex failed ALGARVE The tex file is well generated. Running latex on this file (Sweave.sty is in my latex path) build the dvi file correctly. Well, it should not as svm.pdf is not a valid graphics files for .dvi. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] * creating vignettes ... ERROR
Dear R developers, I had some problem when building package: for exemple when building the package e1071 available from CRAN, I get the following message error: * checking for file 'e1071/DESCRIPTION' ... OK * preparing 'e1071': * cleaning src * running cleanup * creating vignettes ... ERROR /usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting. /usr/lib/R/bin/texi2dvi: see svmdoc.log for errors. Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet = quiet) : running texi2dvi on svmdoc.tex failed Execution halted The system I use is: R2.0.1 under Debian Linux (testing) with kernel 2.6.9-1-686 The pdflatex version is: pdfeTeX (Web2C 7.4.5) 3.14159-1.10b-2.1 kpathsea version 3.4.5 Copyright (C) 1997-2003 The NTS Team (eTeX)/Han The Thanh (pdfTeX). Kpathsea is copyright (C) 1997-2003 Free Software Foundation, Inc. There is NO warranty. Redistribution of this software is covered by the terms of both the pdfeTeX copyright and the GNU General Public License. For more information about these matters, see the files named COPYING and the pdfeTeX source. Primary author of pdfeTeX: The NTS Team (eTeX)/Han The Thanh (pdfTeX). Kpathsea written by Karl Berry and others. I attached the log file svmdoc.log. I have a quick look on the perl script build and it seem there is a grep for error. In the log file there is a line with the following: file:line:error style messages enabled it is just the summary of the option used when running pdflatex and then an error is systematically reported. If you have any idea where the problem comes from? Thanks, Philippe -- Philippe Hupé UMR 144 - Service Bioinformatique Institut Curie Laboratoire de Transfert (4ème étage) 26 rue d'Ulm 75005 Paris - France Email : [EMAIL PROTECTED] Tél :+33 (0)1 44 32 42 75 Fax :+33 (0)1 42 34 65 28 __ R-devel@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] * creating vignettes ... ERROR
On Fri, 21 Jan 2005 17:33:25 +0100 Philippe Hupé wrote:
Dear R developers,
I had some problem when building package: for exemple when building
the package e1071 available from CRAN, I get the following message
error:
* checking for file 'e1071/DESCRIPTION' ... OK
* preparing 'e1071':
* cleaning src
* running cleanup
* creating vignettes ... ERROR
/usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting.
/usr/lib/R/bin/texi2dvi: see svmdoc.log for errors.
Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
quiet) :
running texi2dvi on svmdoc.tex failed
Execution halted
works for me
The system I use is:
R2.0.1 under Debian Linux (testing) with kernel 2.6.9-1-686
The pdflatex version is:
pdfeTeX (Web2C 7.4.5) 3.14159-1.10b-2.1
kpathsea version 3.4.5
Copyright (C) 1997-2003 The NTS Team (eTeX)/Han The Thanh (pdfTeX).
Kpathsea is copyright (C) 1997-2003 Free Software Foundation, Inc.
There is NO warranty. Redistribution of this software is
covered by the terms of both the pdfeTeX copyright and
the GNU General Public License.
For more information about these matters, see the files
named COPYING and the pdfeTeX source.
Primary author of pdfeTeX: The NTS Team (eTeX)/Han The Thanh (pdfTeX).
Kpathsea written by Karl Berry and others.
I attached the log file svmdoc.log.
That did not come true. But my guess is that running LaTeX is what fails
(and that the problem is neither in R nor in the Per script).
From looking briefly at svmdoc.Rnw, it has a
\usepackage{Sweave}
so it expects that Sweave.sty is somewhere in your search path. Is that
the case?
Furthermore, the R code in vignettes should always run, but compiling
the resulting .tex file just has to work at build time. So there are
vignettes (at least in my packages) that depend on local sty/bib/bst
files not included in the package and thus cannot be (easily) compiled
by other people.
Z
I have a quick look on the perl script build and it seem there is a
grep for error.
In the log file there is a line with the following:
file:line:error style messages enabled
it is just the summary of the option used when running pdflatex and
then an error is systematically reported.
If you have any idea where the problem comes from?
Thanks,
Philippe
--
Philippe Hupé
UMR 144 - Service Bioinformatique
Institut Curie
Laboratoire de Transfert (4ème étage)
26 rue d'Ulm
75005 Paris - France
Email : [EMAIL PROTECTED]
Tél : +33 (0)1 44 32 42 75
Fax : +33 (0)1 42 34 65 28
__
R-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] * creating vignettes ... ERROR
Achim Zeileis wrote:
On Fri, 21 Jan 2005 17:33:25 +0100 Philippe Hupé wrote:
Dear R developers,
I had some problem when building package: for exemple when building
the package e1071 available from CRAN, I get the following message
error:
* checking for file 'e1071/DESCRIPTION' ... OK
* preparing 'e1071':
* cleaning src
* running cleanup
* creating vignettes ... ERROR
/usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting.
/usr/lib/R/bin/texi2dvi: see svmdoc.log for errors.
Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
quiet) :
running texi2dvi on svmdoc.tex failed
Execution halted
works for me
The system I use is:
R2.0.1 under Debian Linux (testing) with kernel 2.6.9-1-686
The pdflatex version is:
pdfeTeX (Web2C 7.4.5) 3.14159-1.10b-2.1
kpathsea version 3.4.5
Copyright (C) 1997-2003 The NTS Team (eTeX)/Han The Thanh (pdfTeX).
Kpathsea is copyright (C) 1997-2003 Free Software Foundation, Inc.
There is NO warranty. Redistribution of this software is
covered by the terms of both the pdfeTeX copyright and
the GNU General Public License.
For more information about these matters, see the files
named COPYING and the pdfeTeX source.
Primary author of pdfeTeX: The NTS Team (eTeX)/Han The Thanh (pdfTeX).
Kpathsea written by Karl Berry and others.
I attached the log file svmdoc.log.
That did not come true. But my guess is that running LaTeX is what fails
(and that the problem is neither in R nor in the Per script).
From looking briefly at svmdoc.Rnw, it has a
\usepackage{Sweave}
so it expects that Sweave.sty is somewhere in your search path. Is that
the case?
Furthermore, the R code in vignettes should always run, but compiling
the resulting .tex file just has to work at build time. So there are
vignettes (at least in my packages) that depend on local sty/bib/bst
files not included in the package and thus cannot be (easily) compiled
by other people.
Z
Philippe is right. I have seen the log file and it causes the problem.
It was me who suggested to write to r-devel. The relevant lines in the
log file were:
This is pdfeTeXk, Version 3.14159-1.10b-2.1 (Web2C 7.4.5)
(format=pdflatex 2005.1.5) 19 JAN 2005 17:37
entering extended mode
file:line:error style messages enabled.
**\nonstopmode \input /home/phupe/tmp/e1071/inst/doc/svmdoc.tex
[SNIP]
Output written on svmdoc.pdf (7 pages, 186335 bytes).
Note, this is a very modern version of pdf*e*TeX!
I don't know whether R is supposed to support it. If so, this is a bug.
Uwe Ligges
I have a quick look on the perl script build and it seem there is a
grep for error.
In the log file there is a line with the following:
file:line:error style messages enabled
it is just the summary of the option used when running pdflatex and
then an error is systematically reported.
If you have any idea where the problem comes from?
Thanks,
Philippe
--
Philippe Hupé
UMR 144 - Service Bioinformatique
Institut Curie
Laboratoire de Transfert (4ème étage)
26 rue d'Ulm
75005 Paris - France
Email : [EMAIL PROTECTED]
Tél :+33 (0)1 44 32 42 75
Fax :+33 (0)1 42 34 65 28
__
R-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] * creating vignettes ... ERROR
On Fri, 21 Jan 2005, Uwe Ligges wrote:
Achim Zeileis wrote:
On Fri, 21 Jan 2005 17:33:25 +0100 Philippe Hupé wrote:
I had some problem when building package: for exemple when building
the package e1071 available from CRAN, I get the following message
error:
*Why* are you building someone else's package?
* checking for file 'e1071/DESCRIPTION' ... OK
* preparing 'e1071':
* cleaning src
* running cleanup
* creating vignettes ... ERROR
/usr/lib/R/bin/texi2dvi: pdflatex exited with bad status, quitting.
/usr/lib/R/bin/texi2dvi: see svmdoc.log for errors.
Error in texi2dvi(file = bft, pdf = TRUE, clean = FALSE, quiet =
quiet) :
running texi2dvi on svmdoc.tex failed
Execution halted
works for me
The system I use is:
R2.0.1 under Debian Linux (testing) with kernel 2.6.9-1-686
The pdflatex version is:
pdfeTeX (Web2C 7.4.5) 3.14159-1.10b-2.1
kpathsea version 3.4.5
Copyright (C) 1997-2003 The NTS Team (eTeX)/Han The Thanh (pdfTeX).
Kpathsea is copyright (C) 1997-2003 Free Software Foundation, Inc.
There is NO warranty. Redistribution of this software is
covered by the terms of both the pdfeTeX copyright and
the GNU General Public License.
For more information about these matters, see the files
named COPYING and the pdfeTeX source.
Primary author of pdfeTeX: The NTS Team (eTeX)/Han The Thanh (pdfTeX).
Kpathsea written by Karl Berry and others.
I attached the log file svmdoc.log.
That did not come true. But my guess is that running LaTeX is what fails
(and that the problem is neither in R nor in the Per script).
From looking briefly at svmdoc.Rnw, it has a
\usepackage{Sweave}
so it expects that Sweave.sty is somewhere in your search path. Is that
the case?
Furthermore, the R code in vignettes should always run, but compiling
the resulting .tex file just has to work at build time. So there are
vignettes (at least in my packages) that depend on local sty/bib/bst
files not included in the package and thus cannot be (easily) compiled
by other people.
Z
Philippe is right. I have seen the log file and it causes the problem. It was
me who suggested to write to r-devel. The relevant lines in the log file
were:
Except there is no error in those lines!
This is pdfeTeXk, Version 3.14159-1.10b-2.1 (Web2C 7.4.5) (format=pdflatex
2005.1.5) 19 JAN 2005 17:37
entering extended mode
file:line:error style messages enabled.
**\nonstopmode \input /home/phupe/tmp/e1071/inst/doc/svmdoc.tex
[SNIP]
Output written on svmdoc.pdf (7 pages, 186335 bytes).
Note, this is a very modern version of pdf*e*TeX!
I don't know whether R is supposed to support it. If so, this is a bug.
Well as I understand it for 1.10b (not at all very modern), pdflatex is
supposed to be built from pdftex: it is with the current 1.20b that
pdfetex is used. As I got a TeTeX upgrade this very morning and mine does
run R CMD check e1071, I think the problem may well be in Philippe's
setup.
gannet% pdflatex --version
pdfTeX (Web2C 7.4.5) 3.14159-1.10b
kpathsea version 3.4.5
...
gannet% pdfelatex --version
pdfeTeX (Web2C 7.4.5) 3.14159-1.10b-2.1
kpathsea version 3.4.5
Perhaps if we get to see the error message we might know what is going on.
Meanwhile I suggest using the current teTeX.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
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https://stat.ethz.ch/mailman/listinfo/r-devel
