Re: Sweave manual pdf compilation fails
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 permission needed to access the LyX tree, nor because Sweave.sty is not found in /usr/share/R/texmf/ -- Jean-Pierre
Re: Sweave manual pdf compilation fails
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 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 4:29 PM, Jean-Marc Lasgouttes wrote: 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 versions? We do not want to force people to upgrade to latest R. JMarc
Re: Sweave manual pdf compilation fails
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 Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Wed, Feb 1, 2012 at 4:38 PM, Jean-Marc Lasgouttes wrote: > 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 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. > > > It would be nice if we could find the file even in older versions of R. My > policy is to do easy thing to support old versions, but not much more :) > > JMarc >
Re: Sweave manual pdf compilation fails
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 On Wed, Feb 1, 2012 at 4:29 PM, Jean-Marc Lasgouttes wrote: > 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 versions? We do not want to > force people to upgrade to latest R. > > JMarc >
Re: Sweave manual pdf compilation fails
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 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. It would be nice if we could find the file even in older versions of R. My policy is to do easy thing to support old versions, but not much more :) JMarc
Re: Sweave manual pdf compilation fails
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 versions? We do not want to force people to upgrade to latest R. JMarc
Re: Sweave manual pdf compilation fails
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 wrote: > 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 (usually named Rplots.pdf). I requested >> a true null device which does not write files, and it was implemented >> in R 2.14.1, but again, unfortunately it has a bug which makes this >> null device still write a file named NA. I have not got any response >> from R core yet about this bug. >> >> I can submit a simple patch to lyxsweave.R to avoid this problem by >> redirecting the default file to a temp dir, but I'm not sure if it is >> still in time. It should not break string freeze, though. >> > It would be nice, indeed. Richard, JMarc, can such a patch go in for 2.0.3? > > Liviu > > >> 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
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 (usually named Rplots.pdf). I requested > a true null device which does not write files, and it was implemented > in R 2.14.1, but again, unfortunately it has a bug which makes this > null device still write a file named NA. I have not got any response > from R core yet about this bug. > > I can submit a simple patch to lyxsweave.R to avoid this problem by > redirecting the default file to a temp dir, but I'm not sure if it is > still in time. It should not break string freeze, though. > It would be nice, indeed. Richard, JMarc, can such a patch go in for 2.0.3? Liviu > 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 10:18 AM, Liviu Andronic > wrote: >> 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 >>> can copy sweave.lyx to a directory where you have write privilege, and >>> see if it compiles correctly. >>> >> Hmm, isn't the compilation supposed to be performed in a /tmp/ dir, >> where permissions are available? >> >> Liviu -- Do you know how to read? http://www.alienetworks.com/srtest.cfm http://goodies.xfce.org/projects/applications/xfce4-dict#speed-reader Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail
Re: Sweave manual pdf compilation fails
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 make a local install of R as I do for TeXLive and LyX, but will I get dependency problems with Debian packages ? -- Jean-Pierre
Re: Sweave manual pdf compilation fails
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 gets updated pretty fast if you directly set a CRAN mirror instead of waiting for other Debian repositories. 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 : > 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 make a local install of R as I do for TeXLive and LyX, but will > I get dependency problems with Debian packages ? > > -- > Jean-Pierre
Re: Sweave manual pdf compilation fails
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 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. 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 : > 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 where you have write privilege, and >> see if it compiles correctly. > > > So I opened the example file in the compilation tree (which is under my > personal account) and the error is gone, but now it does not find > Sweave.sty. > > The doc itself says it should, but unfortunately the Debian package puts the > file in > > /usr/share/R/texmf > > instead of the documented > > /usr/share/R/texmf/tex/latex > > So I copied the file as > > /usr/local/texlive/texmf-local/tex/latex/sweave/Sweave.sty > > and ran texhash, and I get the pdf all right. > > Seems thus that the manual does not compile out of the box on Debian > Squeeze, > due to the path problem. > > -- > Jean-Pierre
Re: Sweave manual pdf compilation fails
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 where you have write privilege, and see if it compiles correctly. So I opened the example file in the compilation tree (which is under my personal account) and the error is gone, but now it does not find Sweave.sty. The doc itself says it should, but unfortunately the Debian package puts the file in /usr/share/R/texmf instead of the documented /usr/share/R/texmf/tex/latex So I copied the file as /usr/local/texlive/texmf-local/tex/latex/sweave/Sweave.sty and ran texhash, and I get the pdf all right. Seems thus that the manual does not compile out of the box on Debian Squeeze, due to the path problem. -- Jean-Pierre
Re: Sweave manual pdf compilation fails
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 : > 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 where you have write privilege, and >> see if it compiles correctly. > > > Oops, stupid of me, sorry. > > -- > Jean-Pierre
Re: Sweave manual pdf compilation fails
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 where you have write privilege, and see if it compiles correctly. Oops, stupid of me, sorry. -- Jean-Pierre
Re: Sweave manual pdf compilation fails
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 write files, and it was implemented in R 2.14.1, but again, unfortunately it has a bug which makes this null device still write a file named NA. I have not got any response from R core yet about this bug. I can submit a simple patch to lyxsweave.R to avoid this problem by redirecting the default file to a temp dir, but I'm not sure if it is still in time. It should not break string freeze, though. 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 10:18 AM, Liviu Andronic wrote: > 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 >> can copy sweave.lyx to a directory where you have write privilege, and >> see if it compiles correctly. >> > Hmm, isn't the compilation supposed to be performed in a /tmp/ dir, > where permissions are available? > > Liviu
Re: Sweave manual pdf compilation fails
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 > can copy sweave.lyx to a directory where you have write privilege, and > see if it compiles correctly. > Hmm, isn't the compilation supposed to be performed in a /tmp/ dir, where permissions are available? Liviu
Re: Sweave manual pdf compilation fails
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 it compiles correctly. 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 : > 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" > "/tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/""sweave.tex" ISO-8859-15 > "/usr/local/share/lyx-2.0.3svn/examples/" > running > '/usr/lib/R/bin/R --slave --no-restore --no-save --no-restore > --file=/usr/local/share/lyx-2.0.3svn/scripts/lyxsweave.R --args > /tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/sweave.Rnw > /tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/sweave.tex ISO-8859-15' > > [1] FALSE > Writing to file /tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/sweave.tex > Processing code chunks ... > 1 : term verbatim > 2 : echo (label=sweave-sty) > 3 : echo keep.source term verbatim (label=setup) > 4 : echo keep.source (label=sweave-manual) > 5 : echo keep.source term verbatim (label=print-integers) > 6 : echo term hide (label=hide-results) > 7 : echo term verbatim (label=calculator) > 8 : echo term verbatim (label=rnorm) > 9 : echo term verbatim (label=iris-summary) > 10 : term tex (label=xtable-demo) > Loading required package: xtable > 11 : echo term verbatim eps pdf (label=iris-pairs) > > Erreur : chunk 11 (label=iris-pairs) > Error in function (file = ifelse(onefile, "Rplots.pdf", "Rplot%03d.pdf"), : > impossible de démarrer le périphérique pdf > De plus : Messages d'avis : > 1: In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, : > there is no package called 'xtable' > 2: In function (file = ifelse(onefile, "Rplots.pdf", "Rplot%03d.pdf"), : > impossible d'ouvrir le fichier en argument de 'pdf' 'Rplots.pdf' > Exécution arrêtée > Systemcall.cpp(270): Systemcall: 'Rscript --verbose --no-save --no-restore > "/usr/local/share/lyx-2.0.3svn/scripts/lyxsweave.R" > "/tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/""sweave.Rnw" > "/tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/""sweave.tex" ISO-8859-15 > "/usr/local/share/lyx-2.0.3svn/examples/"' finished with exit code 1 > Error: Conversion du fichier impossible > > > I installed R and related packages on my Debian box (Squeeze, R version > 2.11). While updating fr.po for 2.0.3, I saw something about a requirement > for R version >=2.14. > Is that the reason of failure ? > > -- > Jean-Pierre >
Sweave manual pdf compilation fails
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" "/tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/""sweave.tex" ISO-8859-15 "/usr/local/share/lyx-2.0.3svn/examples/" running '/usr/lib/R/bin/R --slave --no-restore --no-save --no-restore --file=/usr/local/share/lyx-2.0.3svn/scripts/lyxsweave.R --args /tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/sweave.Rnw /tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/sweave.tex ISO-8859-15' [1] FALSE Writing to file /tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/sweave.tex Processing code chunks ... 1 : term verbatim 2 : echo (label=sweave-sty) 3 : echo keep.source term verbatim (label=setup) 4 : echo keep.source (label=sweave-manual) 5 : echo keep.source term verbatim (label=print-integers) 6 : echo term hide (label=hide-results) 7 : echo term verbatim (label=calculator) 8 : echo term verbatim (label=rnorm) 9 : echo term verbatim (label=iris-summary) 10 : term tex (label=xtable-demo) Loading required package: xtable 11 : echo term verbatim eps pdf (label=iris-pairs) Erreur : chunk 11 (label=iris-pairs) Error in function (file = ifelse(onefile, "Rplots.pdf", "Rplot%03d.pdf"), : impossible de démarrer le périphérique pdf De plus : Messages d'avis : 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'xtable' 2: In function (file = ifelse(onefile, "Rplots.pdf", "Rplot%03d.pdf"), : impossible d'ouvrir le fichier en argument de 'pdf' 'Rplots.pdf' Exécution arrêtée Systemcall.cpp(270): Systemcall: 'Rscript --verbose --no-save --no-restore "/usr/local/share/lyx-2.0.3svn/scripts/lyxsweave.R" "/tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/""sweave.Rnw" "/tmp/lyx_tmpdir.T21839/lyx_tmpbuf2/""sweave.tex" ISO-8859-15 "/usr/local/share/lyx-2.0.3svn/examples/"' finished with exit code 1 Error: Conversion du fichier impossible I installed R and related packages on my Debian box (Squeeze, R version 2.11). While updating fr.po for 2.0.3, I saw something about a requirement for R version >=2.14. Is that the reason of failure ? -- Jean-Pierre