Re: Sweave manual pdf compilation fails

2012-02-02 Thread Richard Heck
On 02/01/2012 05:47 PM, Yihui Xie wrote: I'm pretty confident with this one. It does not have specific requirements on R versions, and users do not have to upgrade R. If you and JMarc agree, it can go into 2.0.3. I know nothing about this stuff. Richard Regards, Yihui -- Yihui

Re: Sweave manual pdf compilation fails

2012-02-02 Thread Jean-Pierre Chrétien
Le 01/02/2012 20:16, Yihui Xie a écrit : The patch is pretty simple: http://www.lyx.org/trac/ticket/8019 I removed Sweave.sty from texmf-local, so that LyX cannot find it that way, applied the patch, and the Sweave manual compiles now fine from the Help menu. No failure because of write

Re: Sweave manual pdf compilation fails

2012-02-02 Thread Richard Heck
On 02/01/2012 05:47 PM, Yihui Xie wrote: I'm pretty confident with this one. It does not have specific requirements on R versions, and users do not have to upgrade R. If you and JMarc agree, it can go into 2.0.3. I know nothing about this stuff. Richard Regards, Yihui -- Yihui

Re: Sweave manual pdf compilation fails

2012-02-02 Thread Jean-Pierre Chrétien
Le 01/02/2012 20:16, Yihui Xie a écrit : The patch is pretty simple: http://www.lyx.org/trac/ticket/8019 I removed Sweave.sty from texmf-local, so that LyX cannot find it that way, applied the patch, and the Sweave manual compiles now fine from the Help menu. No failure because of write

Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Hello, I took a look to the new specific manual describing sweave with the latest 2.0.3svn. The pdf export fails on an Rscript error: cite Running: Rscript --verbose --no-save --no-restore /usr/local/share/lyx-2.0.3svn/scripts/lyxsweave.R /tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/sweave.Rnw

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
I guess you compiled the document under /usr/local/share/lyx-2.0.3svn/examples/, right? I believe the problem is that R has no write privilege to that directory, so the default pdf() device cannot be started there. You can copy sweave.lyx to a directory where you have write privilege, and see if

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Liviu Andronic
On Wed, Feb 1, 2012 at 5:15 PM, Yihui Xie x...@yihui.name wrote: I guess you compiled the document under /usr/local/share/lyx-2.0.3svn/examples/, right? I believe the problem is that R has no write privilege to that directory, so the default pdf() device cannot be started there. You can copy

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
You are right (ideally), but this is a long-lasting annoying problem with R's default graphical device which is pdf() in the non-interactive session. Unfortunately it has to create a file under the current working directory (usually named Rplots.pdf). I requested a true null device which does not

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Le 01/02/2012 17:15, Yihui Xie a écrit : I guess you compiled the document under /usr/local/share/lyx-2.0.3svn/examples/, right? I believe the problem is that R has no write privilege to that directory, so the default pdf() device cannot be started there. You can copy sweave.lyx to a directory

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
No, I do not think that is your problem :) See my second reply above. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA 2012/2/1 Jean-Pierre Chrétien

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Le 01/02/2012 17:15, Yihui Xie a écrit : I guess you compiled the document under /usr/local/share/lyx-2.0.3svn/examples/, right? I believe the problem is that R has no write privilege to that directory, so the default pdf() device cannot be started there. You can copy sweave.lyx to a directory

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
That seems like a bug of Debian; R should be able to find Sweave.sty with file.path(R.home(share), texmf, tex, latex, Sweave.sty) [1] /usr/share/R/share/texmf/tex/latex/Sweave.sty I'm using Ubuntu and R can find Sweave.sty correctly. If possible, I strongly recommend you update R to the latest

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
I think so. If you add a CRAN mirror to your software repository, Debian knows how to solve the dependencies. There is a Debian maintainer who has been working on compiling R and some R packages to Debian packages. The versions of LyX and TeXLive often have a long time lag in Debian/Ubuntu, but R

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Le 01/02/2012 18:20, Yihui Xie a écrit : If possible, I strongly recommend you update R to the latest 2.14.1 (it is pretty easy to update if you set a CRAN mirror; see instructions at http://cran.r-project.org/bin/linux/debian/). There have been many changes in Sweave since 2.11. Sure, I can

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Liviu Andronic
On Wed, Feb 1, 2012 at 5:29 PM, Yihui Xie x...@yihui.name wrote: You are right (ideally), but this is a long-lasting annoying problem with R's default graphical device which is pdf() in the non-interactive session. Unfortunately it has to create a file under the current working directory

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
The patch is pretty simple: http://www.lyx.org/trac/ticket/8019 Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Wed, Feb 1, 2012 at 12:53 PM, Liviu Andronic

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Marc Lasgouttes
Le 01/02/12 20:16, Yihui Xie a écrit : The patch is pretty simple: http://www.lyx.org/trac/ticket/8019 It looks like a reasnable thing to do, if it does what I think it does. How confident are you with this patch? Does it rely only on documented behaviour, assumed to be present in earlier R

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Marc Lasgouttes
Le 01/02/12 18:20, Yihui Xie a écrit : That seems like a bug of Debian; R should be able to find Sweave.sty with file.path(R.home(share), texmf, tex, latex, Sweave.sty) [1] /usr/share/R/share/texmf/tex/latex/Sweave.sty I'm using Ubuntu and R can find Sweave.sty correctly. If possible, I

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
I'm pretty confident with this one. It does not have specific requirements on R versions, and users do not have to upgrade R. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
Yes, that would be ideal. I will update the patch to reflect this issue. I do not remember in which version R moved Sweave.sty from texmf to texmf/tex/latex, so let's search both places. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of

Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Hello, I took a look to the new specific manual describing sweave with the latest 2.0.3svn. The pdf export fails on an Rscript error: Running: Rscript --verbose --no-save --no-restore "/usr/local/share/lyx-2.0.3svn/scripts/lyxsweave.R" "/tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/""sweave.Rnw"

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
I guess you compiled the document under /usr/local/share/lyx-2.0.3svn/examples/, right? I believe the problem is that R has no write privilege to that directory, so the default pdf() device cannot be started there. You can copy sweave.lyx to a directory where you have write privilege, and see if

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Liviu Andronic
On Wed, Feb 1, 2012 at 5:15 PM, Yihui Xie wrote: > I guess you compiled the document under > /usr/local/share/lyx-2.0.3svn/examples/, right? > > I believe the problem is that R has no write privilege to that > directory, so the default pdf() device cannot be started there. You >

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
You are right (ideally), but this is a long-lasting annoying problem with R's default graphical device which is pdf() in the non-interactive session. Unfortunately it has to create a file under the current working directory (usually named Rplots.pdf). I requested a true null device which does not

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Le 01/02/2012 17:15, Yihui Xie a écrit : I guess you compiled the document under /usr/local/share/lyx-2.0.3svn/examples/, right? I believe the problem is that R has no write privilege to that directory, so the default pdf() device cannot be started there. You can copy sweave.lyx to a directory

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
No, I do not think that is your problem :) See my second reply above. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA 2012/2/1 Jean-Pierre Chrétien

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Le 01/02/2012 17:15, Yihui Xie a écrit : I guess you compiled the document under /usr/local/share/lyx-2.0.3svn/examples/, right? I believe the problem is that R has no write privilege to that directory, so the default pdf() device cannot be started there. You can copy sweave.lyx to a directory

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
That seems like a bug of Debian; R should be able to find Sweave.sty with > file.path(R.home("share"), "texmf", "tex", "latex", "Sweave.sty") [1] "/usr/share/R/share/texmf/tex/latex/Sweave.sty" I'm using Ubuntu and R can find Sweave.sty correctly. If possible, I strongly recommend you update R

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
I think so. If you add a CRAN mirror to your software repository, Debian knows how to solve the dependencies. There is a Debian maintainer who has been working on compiling R and some R packages to Debian packages. The versions of LyX and TeXLive often have a long time lag in Debian/Ubuntu, but R

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Pierre Chrétien
Le 01/02/2012 18:20, Yihui Xie a écrit : If possible, I strongly recommend you update R to the latest 2.14.1 (it is pretty easy to update if you set a CRAN mirror; see instructions at http://cran.r-project.org/bin/linux/debian/). There have been many changes in Sweave since 2.11. Sure, I can

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Liviu Andronic
On Wed, Feb 1, 2012 at 5:29 PM, Yihui Xie wrote: > You are right (ideally), but this is a long-lasting annoying problem > with R's default graphical device which is pdf() in the > non-interactive session. Unfortunately it has to create a file under > the current working directory

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
The patch is pretty simple: http://www.lyx.org/trac/ticket/8019 Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Wed, Feb 1, 2012 at 12:53 PM, Liviu Andronic

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Marc Lasgouttes
Le 01/02/12 20:16, Yihui Xie a écrit : The patch is pretty simple: http://www.lyx.org/trac/ticket/8019 It looks like a reasnable thing to do, if it does what I think it does. How confident are you with this patch? Does it rely only on documented behaviour, assumed to be present in earlier R

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Jean-Marc Lasgouttes
Le 01/02/12 18:20, Yihui Xie a écrit : That seems like a bug of Debian; R should be able to find Sweave.sty with file.path(R.home("share"), "texmf", "tex", "latex", "Sweave.sty") [1] "/usr/share/R/share/texmf/tex/latex/Sweave.sty" I'm using Ubuntu and R can find Sweave.sty correctly. If

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
I'm pretty confident with this one. It does not have specific requirements on R versions, and users do not have to upgrade R. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA

Re: Sweave manual pdf compilation fails

2012-02-01 Thread Yihui Xie
Yes, that would be ideal. I will update the patch to reflect this issue. I do not remember in which version R moved Sweave.sty from texmf to texmf/tex/latex, so let's search both places. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of