Re: including a Sweave/R code chunk in a LyX table cell
Hi!
Rob Oakes wrote:
This is clearly either a problem in the way that R installs itself, or
the way that LaTeX installs itself. I'm not actually sure which though
and I don't know where to file the bug report.
It Sweave.sty is required by LaTeX only when used with R, who must we
take care of the correct installation of the style file? Sorry, I don't
know LaTeX as for being able to answer this question!
When I just checked, I was not able to find a "sweave" package for R,
nor was I able to find one for TeXLive 2009 (don't know about MikTeX).
But I've experienced a similar problem on Mac OS X and on Linux, which
provides some evidence that it's not getting packaged.
As far as I can find, Sweave is included with R at least as of R 2.4.1
In R, ...
help("Sweave", package="utils")
Read this from http://tinyurl.com/346jrnu ...
"Unfortunately, Sweave hard-codes the absolute path to its style files
in its LaTeX output. The path to the style files depends on where R was
installed on the local system. This means that while an Sweave document
may be portable, the LaTeX file it produces is not. If you receive a
LaTeX document produced by Sweave on someone else's computer, you will
need to edit the path inside the \usepackage statement so that it points
to the Sweave style file location on your computer. If you want to give
your LaTeX file to someone who does not have R, you can delete the
reference to Sweave and paste in the contents of the Sweave.sty file. "
Because out of the box support for Sweave is one of LyX 2's newest (and
IMHO, killer) features, it might make sense to include a copy of
Sweave.sty with the installation script and have it installed at the
time of LyX configuration. LyX already does this with a few specialty
document classes anyway (broadway, hollywood).
As Sweave.sty file will be only required by people not running R, I
think it must be "maintained" by LyX and/or LaTeX bundles.
But I'm just a newbie here! Please, any insight will be extremely
welcome! Thanks!
Greetings,
Ricardo
--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
Hi! I've been trying to learn a bit more about LyX, LaTeX, R and Sweave to better understand this issue :-) Jean-Marc LASGOUTTES wrote: It is expected (by me at least) that either: 1/ the installation of R installs Sweave.sty at the right place (was MaxTeX already installed when you installed R?) Yes, MacTex was installed when I installed R. Please, what does it mean? Must I get a different result if MacTex was not installed before R installation? or 2/ Sweave is set up in such a way that it puts the full path to the Sweave.sty file in the \usepackage command. The point is that there is no Sweave.sty in the system. Neither before R installation, nor before after it. As far as I understand, and read, it is expected that R copy Sweave.sty on my system although I don't know yet if I must also expect that the texmf tree is modified with the same installation or the user must customize the installation on his/her own. Actually, with the new LyX 2.0 releases, I don't know if Sweave.sty is required by LyX at all! Sorry, I am still a bit puzzle with this issue! Thanks! Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
This is clearly either a problem in the way that R installs itself, or the way that LaTeX installs itself. I'm not actually sure which though and I don't know where to file the bug report. When I just checked, I was not able to find a "sweave" package for R, nor was I able to find one for TeXLive 2009 (don't know about MikTeX). But I've experienced a similar problem on Mac OS X and on Linux, which provides some evidence that it's not getting packaged. Because out of the box support for Sweave is one of LyX 2's newest (and IMHO, killer) features, it might make sense to include a copy of Sweave.sty with the installation script and have it installed at the time of LyX configuration. LyX already does this with a few specialty document classes anyway (broadway, hollywood). Cheers, Rob
Re: including a Sweave/R code chunk in a LyX table cell
"[Ricardo Rodriguez] eBioTIC." writes: > *3.* If I try to compile a new document including S/R expressions, > compilation fails throwing the following error: > > ! LaTeX Error: File `Sweave.sty' not found. > > Here the full stack to further reference: > > http://xen.net/onLyX/lyxSweaveStyNotFound.html > Please, provided its module is loaded, must Sweave work out of the box > in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I > guess a warning will be required some where to avoid the problem we > are facing here! Thanks! It is expected (by me at least) that either: 1/ the installation of R installs Sweave.sty at the right place (was MaxTeX already installed when you installed R?) or 2/ Sweave is set up in such a way that it puts the full path to the Sweave.sty file in the \usepackage command. If neither of those two conditions are fulfilled, I think this is a bug in the way R installs itself... JMarc
Re: including a Sweave/R code chunk in a LyX table cell
Hi! lyx-de...@oak-tree.us wrote: Hi JMarc, Reasonably sure. I was having the problems back in November. And there were two separate issues. The first was getting LyX 2 to work, the second was related to getting R + Sweave to work. The problems that eventually required Sweave.sty were related to getting documents to compile correctly. Without it, the compilation would simply terminate with "There was an R error" or some such. After placing Sweave.sty in the tex path, this resolved itself. Being truth what I've said before and what JMarc said about LyX checking R availability to load Sweave module, I'm facing the same problem Rob describes when trying to compile a new document including S/R expressions. I will try to describe the situation: *1.* A LyX 2.0.0 alpha2 installation crashes when trying to load Sweave module if R is not installed in the same box. In this case, I guess it will be advisable to trigger a warning saying that R is required instead of causing an exception that crashes LyX. I'm sure developers are consciences of this and the only problem here is time to make the required changes! :-) *2. *Once R is installed, Sweave module loads without a glitch. *3.* If I try to compile a new document including S/R expressions, compilation fails throwing the following error: ! LaTeX Error: File `Sweave.sty' not found. Here the full stack to further reference: http://xen.net/onLyX/lyxSweaveStyNotFound.html As stated in a previous message, the LaTeX environment here was created as per... http://www.tug.org/mactex/2009/ [ approximately 1.3G - 12 March 2010 ] MacTeX-2009.mpkg MacTeX.mpkg.zip *4. *Until I copy Sweave.sty to the TeX path and reconfigure LyX, compilation fails. I copied Sweave.sty from a older box with a running LyX 1.6.5/Sweave/R installation. GMXUX-Ricardo-Rodriguez:~ rrodriguez$ kpsewhich Sweave.sty /Users/rrodriguez/Library/texmf/tex/latex/R/Sweave.sty Please, provided its module is loaded, must Sweave work out of the box in LyX 2.0? Is it expected that Sweave.sty is included with LaTeX? I guess a warning will be required some where to avoid the problem we are facing here! Thanks! Let me know if I can be of any further help! Greetings, Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
"[Ricardo Rodriguez] eBioTIC." writes: > Sorry, I replied to Rob's message before reading this one! That's what > I've found here: Sweave.sty as is is not longer in the path and LyX > looks for R libraries instead. Is it ok this interpretation? Thanks! Yes. But still it should not crash... JMarc
Re: including a Sweave/R code chunk in a LyX table cell
Hi JMarc, Reasonably sure. I was having the problems back in November. And there were two separate issues. The first was getting LyX 2 to work, the second was related to getting R + Sweave to work. The problems that eventually required Sweave.sty were related to getting documents to compile correctly. Without it, the compilation would simply terminate with "There was an R error" or some such. After placing Sweave.sty in the tex path, this resolved itself. But then, I haven't really spent much time working on the Mac since then. Problems with PyQt (related to work stuff) have forced me over to my Linux laptop, and that's what I've mostly been working with for the last seven months. It wasn't till this morning that sat down again to take a look at the problem. About the same time that it was reported solved ;) If I have any problems, I'll be sure to file a bug report/send an email to the developer list. Cheers, Rob > Rob Oakes writes: >> Just one thought, make sure that there is a copy of Sweave.sty installed >> in your LaTeX path (and make sure that LyX can find it). I was having >> some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is >> what ultimately fixed it. > > Are you sure? It should not be necessary on 2.0. What is needed though > is to have R installed and available in the path. The module tests the > availability of a Rnw>tex converter (aka R CMD Sweave). > > JMarc >
Re: including a Sweave/R code chunk in a LyX table cell
Oops! Jean-Marc LASGOUTTES wrote: Rob Oakes writes: Just one thought, make sure that there is a copy of Sweave.sty installed in your LaTeX path (and make sure that LyX can find it). I was having some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is what ultimately fixed it. Are you sure? It should not be necessary on 2.0. What is needed though is to have R installed and available in the path. The module tests the availability of a Rnw>tex converter (aka R CMD Sweave). Sorry, I replied to Rob's message before reading this one! That's what I've found here: Sweave.sty as is is not longer in the path and LyX looks for R libraries instead. Is it ok this interpretation? Thanks! Greetings, Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
Hi Rob! Rob Oakes wrote: Hi Ricardo, Just one thought, make sure that there is a copy of Sweave.sty installed in your LaTeX path (and make sure that LyX can find it). I was having some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is what ultimately fixed it. Nope, it is not! In fact Sweave.sty is no where in the path. It seems it looks for R! R was not installed in this box! Shame on me! Once installed, LyX 2.0 no longer crashes while loading Sweave module. Thanks for your help! But, to be honest, I haven't really played with LyX 2.0 on my Mac recently. I've been on a book deadline and it just felt to unstable to any real work. On Linux, though, it's been very reliable. I will keep an eye on new releases and maintain this experimental installation on the MacPro running Mac OS X 10.6.3 and at the same time keep running a stable a 1.6.5 release in a 10.5.8 MacBook Pro. I have not two available boxes with the same SO. Please, let me know if I can be of any further help to debug this or any other issue. Thanks! Greetings, Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
Rob Oakes writes: > Just one thought, make sure that there is a copy of Sweave.sty installed > in your LaTeX path (and make sure that LyX can find it). I was having > some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is > what ultimately fixed it. Are you sure? It should not be necessary on 2.0. What is needed though is to have R installed and available in the path. The module tests the availability of a Rnw>tex converter (aka R CMD Sweave). JMarc
Re: including a Sweave/R code chunk in a LyX table cell
Hi Ricardo, Just one thought, make sure that there is a copy of Sweave.sty installed in your LaTeX path (and make sure that LyX can find it). I was having some troubles with Sweave and LyX 2.0 on Mac a while ago, and this is what ultimately fixed it. But, to be honest, I haven't really played with LyX 2.0 on my Mac recently. I've been on a book deadline and it just felt to unstable to any real work. On Linux, though, it's been very reliable. Cheers, Rob On Tue, 2010-05-11 at 00:13 +0200, [Ricardo Rodriguez] eBioTIC. wrote: > Hi! > > Jean-Marc LASGOUTTES wrote: > > > Without doing any other step, if I create a new document and go to > > > Document>Settings>Modules and try to add Sweave module, LyX crashes. I > > > am nevertheless able to add other modules like Braille or EndNote. > > > > > > > This is bad. However, I do not see where it comes from. Do you have > > messages in the console (launch Console.app and look for messages that > > may come from LyX). > > > > > > Sorry, I've not been able to regain access to the concerned box until > late in the afternoon. Here what I've found: > > These are the lines recorded in the console log each time LyX crashes > after trying to load Sweave module: > > * > 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] terminate called > after throwing an instance of 'lyx::support::ExceptionMessage' > 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] what(): Package > not available > 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] The module sweave > requires a package that is > 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] not available in > your LaTeX installation. LaTeX output > 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] may not be possible. > 5/10/10 7:06:09 PM com.apple.launchd.peruser.501[121] > ([0x0-0x57057].org.lyx.lyx[685]) Job appears to have crashed: Abort > trap > 5/10/10 7:06:09 PM ReportCrash[907] Saved crash report for lyx[685] > version 2.0.0alpha2 (???) > to > /Users/rrodriguez/Library/Logs/DiagnosticReports/lyx_2010-05-10-190609_Ricardo-Rodriguezs-Mac-Pro.crash > * > > For easier reference... > > http://xen.net/onLyX/lyxCrashConsoleMessages.html > > The full report generated by Mac OS X is available here... > > http://xen.net/onLyX/lyxCrashProbReport.html > > The box has a fresh and fully updated Mac OS X 10.6.3 (10D573) > > I've installed MacTeX (as per section 2.2 at > http://www.lyx.org/Download) prior to install LyX 1.6.5, then to > install LyX 2.0.0 alpha2 > > The link at the LyX download page drove me to... > http://www.tug.org/mactex/2009/ > [ approximately 1.3G - 12 March 2010 ] > MacTeX-2009.mpkg > MacTeX.mpkg.zip > > Please, does this make any sense for you? Let me know how I can be of > any further help. Thanks! > > Cheers, > > Ricardo > -- > Ricardo Rodríguez > CTO > eBiotic. > Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
Hi! Jean-Marc LASGOUTTES wrote: Without doing any other step, if I create a new document and go to Document>Settings>Modules and try to add Sweave module, LyX crashes. I am nevertheless able to add other modules like Braille or EndNote. This is bad. However, I do not see where it comes from. Do you have messages in the console (launch Console.app and look for messages that may come from LyX). Sorry, I've not been able to regain access to the concerned box until late in the afternoon. Here what I've found: These are the lines recorded in the console log each time LyX crashes after trying to load Sweave module: * 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] terminate called after throwing an instance of 'lyx::support::ExceptionMessage' 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] what(): Package not available 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] The module sweave requires a package that is 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] not available in your LaTeX installation. LaTeX output 5/10/10 7:06:09 PM [0x0-0x57057].org.lyx.lyx[685] may not be possible. 5/10/10 7:06:09 PM com.apple.launchd.peruser.501[121] ([0x0-0x57057].org.lyx.lyx[685]) Job appears to have crashed: Abort trap 5/10/10 7:06:09 PM ReportCrash[907] Saved crash report for lyx[685] version 2.0.0alpha2 (???) to /Users/rrodriguez/Library/Logs/DiagnosticReports/lyx_2010-05-10-190609_Ricardo-Rodriguezs-Mac-Pro.crash * For easier reference... http://xen.net/onLyX/lyxCrashConsoleMessages.html The full report generated by Mac OS X is available here... http://xen.net/onLyX/lyxCrashProbReport.html The box has a fresh and fully updated Mac OS X 10.6.3 (10D573) I've installed MacTeX (as per section 2.2 at http://www.lyx.org/Download) prior to install LyX 1.6.5, then to install LyX 2.0.0 alpha2 The link at the LyX download page drove me to... http://www.tug.org/mactex/2009/ [ approximately 1.3G - 12 March 2010 ] MacTeX-2009.mpkg MacTeX.mpkg.zip Please, does this make any sense for you? Let me know how I can be of any further help. Thanks! Cheers, Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
"[Ricardo Rodriguez] eBioTIC." writes: > I'm afraid I am facing some kind of problem here. I've downloaded the > 2.0 alfa release and installed in on an MacPro running Mac OS X 10.6.3 > and on top of a LyX 1.6.5 installation running fine. > > First of all, please, after copying the new LyX to Applications, must > I perform some new action before using the new release? I am afraid I > am missing some basic step due to my lack of understanding of the > whole system. The new *.dmg doesn't content any install file to > configure LyX on a per user basis. The maintainer of the mac version has changed, so I cannot say for sure what changes he did the the packaging. In any case, you could try to run LyX>Reconfigure, which should not hurt... > Without doing any other step, if I create a new document and go to > Document>Settings>Modules and try to add Sweave module, LyX crashes. I > am nevertheless able to add other modules like Braille or EndNote. This is bad. However, I do not see where it comes from. Do you have messages in the console (launch Console.app and look for messages that may come from LyX). JMarc
Re: including a Sweave/R code chunk in a LyX table cell
Thanks Julien and Rob, Rob Oakes wrote: Hi Ricardo, Sweave in LyX 2.0 works a little different. Instead of being relegated to a single document class, it has instead been implemented as a module. The upside is that you can now use Sweave with any document class and with any LaTeX variant (my personal favorite class is the Tufte Handout). This wasn't possible in LyX 1.6 (or, I should say, it was possible but much more difficult). But before you can use the module, you need to add it to your document. This is done from the Document->Settings->Modules pane. Once the pane is loaded, simply scroll down to Sweave and add it to your dodcument. Then click on "Ok" or "Apply". Once you have done this, a couple of new inset options should appear in the Inset->Custom menu. If you have any problems, go ahead and shoot me an email. I'm afraid I am facing some kind of problem here. I've downloaded the 2.0 alfa release and installed in on an MacPro running Mac OS X 10.6.3 and on top of a LyX 1.6.5 installation running fine. First of all, please, after copying the new LyX to Applications, must I perform some new action before using the new release? I am afraid I am missing some basic step due to my lack of understanding of the whole system. The new *.dmg doesn't content any install file to configure LyX on a per user basis. Without doing any other step, if I create a new document and go to Document>Settings>Modules and try to add Sweave module, LyX crashes. I am nevertheless able to add other modules like Braille or EndNote. Please, does this make any sense for you? Thanks! All the best, Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
Hi Ricardo, Sweave in LyX 2.0 works a little different. Instead of being relegated to a single document class, it has instead been implemented as a module. The upside is that you can now use Sweave with any document class and with any LaTeX variant (my personal favorite class is the Tufte Handout). This wasn't possible in LyX 1.6 (or, I should say, it was possible but much more difficult). But before you can use the module, you need to add it to your document. This is done from the Document->Settings->Modules pane. Once the pane is loaded, simply scroll down to Sweave and add it to your dodcument. Then click on "Ok" or "Apply". Once you have done this, a couple of new inset options should appear in the Inset->Custom menu. If you have any problems, go ahead and shoot me an email. Cheers, Rob On Sun, 2010-05-09 at 23:15 +0200, [Ricardo Rodriguez] eBioTIC. wrote: > Rob, > > > > > Rob Oakes wrote: > > > >> If the code chunk is short, you can also use S/R expression insets. > >> (Not sure if this is available in LyX 1.6.5. From LyX 2.0, go to > >> Insert->Custom Inserts->S/R expression). > > I've just installed LyX-2.0.0alpha2.dmg and I don't find the S/R > expression option in Insert>Custom Insets. > > Must it be available out of the box? > > Thanks! > > Ricardo >
Re: including a Sweave/R code chunk in a LyX table cell
On 09/05/2010 5:15 PM, [Ricardo Rodriguez] eBioTIC. wrote: I've just installed LyX-2.0.0alpha2.dmg and I don't find the S/R expression option in Insert>Custom Insets. Must it be available out of the box? Thanks! Ricardo The sweave module should be there out of the box. Once you add it to your document (Under Document > Settings > Modules), the custom inset should become available from the menu. Cheers, Julien
Re: including a Sweave/R code chunk in a LyX table cell
Rob, Rob Oakes wrote: If the code chunk is short, you can also use S/R expression insets. (Not sure if this is available in LyX 1.6.5. From LyX 2.0, go to Insert->Custom Inserts->S/R expression). I've just installed LyX-2.0.0alpha2.dmg and I don't find the S/R expression option in Insert>Custom Insets. Must it be available out of the box? Thanks! Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
Thanks, Rob! Rob Oakes wrote: Hi Ricardo, <> For reasons I do not really understand, R code within tables (or figure floats) can be very fragile. LyX 2.0 makes this better through the Sweave module, but it is still not perfect. The best way I have found for overcoming the fragility is to place it within a minipage. You can do this by clicking on Insert->Box, and then placing the code within there. This works fine! By putting an ERT within the minipage problems are solved! If the code chunk is short, you can also use S/R expression insets. (Not sure if this is available in LyX 1.6.5. From LyX 2.0, go to Insert->Custom Inserts->S/R expression). No Custom Insert is available out of the box with LyX 1.6.5. I guess LyX 2.0 is in beta stage (I found some spare references to it in latex-community.org). I don't know why but I've not access to LyX website right now, I'll check it asap and move ahead to this release. I'm currently in an entry stage of my work with LyX, thus it is a perfect time for experimentation! BTW, I see that your message has been sent to lyx-de...@oak-tree.us as well as to lyx-us...@lists.lux.org. Just to be polite and to respect the rules, is is expected that I reply to the list? Just to the sender? Thanks for your help and advice! Greetings, Ricardo -- Ricardo Rodríguez CTO eBiotic. Life Sciences, Data Modeling and Information Management Systems
Re: including a Sweave/R code chunk in a LyX table cell
Hi Ricardo, <> For reasons I do not really understand, R code within tables (or figure floats) can be very fragile. LyX 2.0 makes this better through the Sweave module, but it is still not perfect. The best way I have found for overcoming the fragility is to place it within a minipage. You can do this by clicking on Insert->Box, and then placing the code within there. If the code chunk is short, you can also use S/R expression insets. (Not sure if this is available in LyX 1.6.5. From LyX 2.0, go to Insert->Custom Inserts->S/R expression). Cheers, Rob Oakes
including a Sweave/R code chunk in a LyX table cell
Hi all,
I've posted this same message yesterday evening at
http://www.latex-community.org LyX forum. Please, accept my apologies
for cross-posting! I'm new to this LyX world and trying to identify the
best way of getting/providing help! Here the issue:
I've successfully installed R 2.11.0 and LyX 1.6.5 in a MacBook Pro
running Mac OS X 10.5.8. Some examples including more or less complex R
code chunks run without a glitch.
But I am not able to include a R code chuck within a table.
This works fine:
% Preview source code for paragraph 10
<>=
qs=1
@
But this doesn't work:
% Preview source code for paragraph 11
\begin{tabular}{|c|}
\hline
<>=
pot=2
@
\tabularnewline
\hline
\end{tabular}
The LyX literate errors window gives this information:
*
Errors:
LaTeX Error: Something's wrong--perhaps a missing \item.
LaTeX Error: Something's wrong--perhaps a missing \item.
LaTeX Error: Something's wrong--perhaps a missing \item.
LaTeX Error: Something's wrong--perhaps a missing \item.
Description:
\begin{Sinput}
Try typing to proceed.
If that doesn't work, type X to quit.
*
This proposal by gmedina at http://www.latex-community.org LyX forum,
avoids the error, but the result is a table with those lines in the
table, not with the R results.
Please, where am I wrong? Is it not possible to include R code chunks in
LyX tables?
Thanks for your help!
Ricardo
--
Ricardo Rodríguez
CTO
eBiotic.
Life Sciences, Data Modeling and Information Management Systems
