Re: $$e not set on import --> import of .Rnw (knitr) fails
On Sat, Oct 20, 2012 at 6:17 PM, Yihui Xie wrote: > I think it should be easy to ignore the encoding argument if it does > not exist, but the problem that confuses me is why importing Rnw is > involved with lyxsweave.R or lyxknitr.R. I mean Rnw should be treated > as a normal TeX document (the R code should not be executed through > Sweave or knitr), except that the code chunks (between <<>>= and @) > should be treated differently, e.g. as ERT. You're right. Now I understand what JMarc was saying -- this converter should not be used for importing. This is the problem. Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
I think it should be easy to ignore the encoding argument if it does not exist, but the problem that confuses me is why importing Rnw is involved with lyxsweave.R or lyxknitr.R. I mean Rnw should be treated as a normal TeX document (the R code should not be executed through Sweave or knitr), except that the code chunks (between <<>>= and @) should be treated differently, e.g. as ERT. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Sat, Oct 20, 2012 at 11:13 AM, Scott Kostyshak wrote: > On Fri, Oct 19, 2012 at 5:11 AM, Jean-Marc Lasgouttes > wrote: >> Le 18/10/2012 16:19, Scott Kostyshak a écrit : >> >>> The unchangedConverter.log is here (error): >>> http://paste.debian.net/201557/ >> >> >> So the error happens on export to latex because the encoding is not >> specified. > > The error happens when importing the Rnw in LyX, which from what I > understand currently calls the Rnw -> LaTeX (plain) converter and then > run tex2lyx. > >> I think I do not understand what you do exactly. Does the same happen with >> Sweave (I do not have knitr here)? > > Yes, the same happens with Sweave because the converter Sweave -> > LaTeX (plain) has a $$e and that string is set to empty because of the > following code: > command = subst(command, token_encoding, buffer ? > buffer->params().encoding().iconvName() : string()); > >> Could you send me an example file and a >> step by step description of what you actually do? > > Yes. I've been using the example file that comes with LyX but I think > that the same error would occur with trying to import any .Rnw file > via Sweave or knitr. > > 1. Start a clean LyX instance from current master branch (although I > have the same problem in branch. I wonder if importing a .Rnw has > worked at some point?). > 2. File > Open > Examples button > sweave.lyx > 3. File > Export > Export As > [tempfolder]/sweaveexample.Rnw (select > the Sweave (.Rnw) format) > 4. Close the current document (the sweave.lyx file) just to make sure > that it's not involved with the import probem. > 5. File > Import > Sweave... > [tempfolder]/sweaveexample.Rnw > 6. At this point I get an error. > > Here are steps to show that (1) it is indeed the Sweave -> LaTeX > (plain) converter that is being used and (2) that setting the $$e > variable improves things: > 7. Close the error box from (6). > 8. Go to Tools > Preferences > File Handling > Converters > select > Sweave -> LaTeX (plain) and in the Converter text box manually delete > "$$e" and insert in it's place "ISO-8859-15" so that the converter is > now: > Rscript --verbose --no-save --no-restore $$s/scripts/lyxsweave.R > $$p$$i $$p$$o ISO-8859-15 $$r > 9. Click the Modify button. > 10. Click the Save button. > 11. Repeat step (5). > 12. The .Rnw is now partly imported. There will be other problems in > the import process which I think are due to tex2lyx, but these > problems are different from the Rnw -> tex problem I am reporting > here. > > Is the solution to modify lyxsweave.R and lyxknitr.R so that if they > are not passed an encoding they should just not change the encoding > from the default R one? This would be easy to do. > > Thanks, > > Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
On Fri, Oct 19, 2012 at 5:11 AM, Jean-Marc Lasgouttes wrote: > Le 18/10/2012 16:19, Scott Kostyshak a écrit : > >> The unchangedConverter.log is here (error): >> http://paste.debian.net/201557/ > > > So the error happens on export to latex because the encoding is not > specified. The error happens when importing the Rnw in LyX, which from what I understand currently calls the Rnw -> LaTeX (plain) converter and then run tex2lyx. > I think I do not understand what you do exactly. Does the same happen with > Sweave (I do not have knitr here)? Yes, the same happens with Sweave because the converter Sweave -> LaTeX (plain) has a $$e and that string is set to empty because of the following code: command = subst(command, token_encoding, buffer ? buffer->params().encoding().iconvName() : string()); > Could you send me an example file and a > step by step description of what you actually do? Yes. I've been using the example file that comes with LyX but I think that the same error would occur with trying to import any .Rnw file via Sweave or knitr. 1. Start a clean LyX instance from current master branch (although I have the same problem in branch. I wonder if importing a .Rnw has worked at some point?). 2. File > Open > Examples button > sweave.lyx 3. File > Export > Export As > [tempfolder]/sweaveexample.Rnw (select the Sweave (.Rnw) format) 4. Close the current document (the sweave.lyx file) just to make sure that it's not involved with the import probem. 5. File > Import > Sweave... > [tempfolder]/sweaveexample.Rnw 6. At this point I get an error. Here are steps to show that (1) it is indeed the Sweave -> LaTeX (plain) converter that is being used and (2) that setting the $$e variable improves things: 7. Close the error box from (6). 8. Go to Tools > Preferences > File Handling > Converters > select Sweave -> LaTeX (plain) and in the Converter text box manually delete "$$e" and insert in it's place "ISO-8859-15" so that the converter is now: Rscript --verbose --no-save --no-restore $$s/scripts/lyxsweave.R $$p$$i $$p$$o ISO-8859-15 $$r 9. Click the Modify button. 10. Click the Save button. 11. Repeat step (5). 12. The .Rnw is now partly imported. There will be other problems in the import process which I think are due to tex2lyx, but these problems are different from the Rnw -> tex problem I am reporting here. Is the solution to modify lyxsweave.R and lyxknitr.R so that if they are not passed an encoding they should just not change the encoding from the default R one? This would be easy to do. Thanks, Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
I can put some time into this next week. Yes, I noticed (and very much appreciate) that you don't need to use CTRL-return anymore. Best regards, Kayvan On Oct 19, 2012, at 2:00, Jean-Marc Lasgouttes wrote: > Le 18/10/2012 15:57, Kayvan Sylvan a écrit : >> The [[foo]] notation is noweb syntax for a reference to something that >> is defined elsewhere. By putting it in an ERT we ensure that it ends >> up in the noweb file unaltered. > > I was wondering whether this could clash with Sweave documents, which do > not use such syntax AFAIK. > > BTW, Kayvan, it would be nice to update the Noweb For LyX documentation > to explain how to use the noweb module instead of the specific > literate-* classes. Actually, I would like to get rid of these classes ASAP. > > Note also that it is not necessary anymore to use Ctrl-Return at the end > of scrap lines. > > JMarc
Re: $$e not set on import --> import of .Rnw (knitr) fails
Le 18/10/2012 16:19, Scott Kostyshak a écrit : The unchangedConverter.log is here (error): http://paste.debian.net/201557/ So the error happens on export to latex because the encoding is not specified. I think I do not understand what you do exactly. Does the same happen with Sweave (I do not have knitr here)? Could you send me an example file and a step by step description of what you actually do? JMarc
Re: $$e not set on import --> import of .Rnw (knitr) fails
Le 18/10/2012 15:57, Kayvan Sylvan a écrit : The [[foo]] notation is noweb syntax for a reference to something that is defined elsewhere. By putting it in an ERT we ensure that it ends up in the noweb file unaltered. I was wondering whether this could clash with Sweave documents, which do not use such syntax AFAIK. BTW, Kayvan, it would be nice to update the Noweb For LyX documentation to explain how to use the noweb module instead of the specific literate-* classes. Actually, I would like to get rid of these classes ASAP. Note also that it is not necessary anymore to use Ctrl-Return at the end of scrap lines. JMarc
Re: $$e not set on import --> import of .Rnw (knitr) fails
Le 18/10/2012 19:11, Yihui Xie a écrit : Import Rnw is something I was asked long time ago but have not figured out how it works. It seems the Sweave/knitr module is called but really should not be, because these modules are only responsible for Rnw-->TeX, not for Rnw-->LyX. Or should they? Ideally LyX should be able to handle the TeX part, and for the R code chunks (<<>>= and @), they can be imported to ERT, but I do not know how to do that. Assuming we can fix tex2lyx for our different uses, it would be easier if knitr used a file extension different from Sweave's Rnw. This way we could define a different knitr>lyx import filter. JMarc
Re: $$e not set on import --> import of .Rnw (knitr) fails
Import Rnw is something I was asked long time ago but have not figured out how it works. It seems the Sweave/knitr module is called but really should not be, because these modules are only responsible for Rnw-->TeX, not for Rnw-->LyX. Or should they? Ideally LyX should be able to handle the TeX part, and for the R code chunks (<<>>= and @), they can be imported to ERT, but I do not know how to do that. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Thu, Oct 18, 2012 at 5:02 AM, Scott Kostyshak wrote: > On Thu, Oct 18, 2012 at 3:46 AM, Jean-Marc Lasgouttes > wrote: >> Le 18/10/12 01:49, Scott Kostyshak a écrit : >> Stupid question; where is importation of knitr files defined in converters? >>> >>> >>> Rnw (knitr) -> latex (plain) >>> The converter is currently: >>> Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i >>> $$p$$o $$e $$r >>> When I change this to the following, import works: >>> Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i >>> $$p$$o ISO-8859-15 $$r >> >> >> But this is a converter for export, not import. > > Ah, then I don't understand how LyX handles imports. The Customization > manual does not talk about importing. Doesn't LyX use the converters > to convert the file to LaTeX and then use tex2lyx to import the tex > file? > >> What is the difference between the Rnw files when you do this change? > > No difference. In the recipe for reproducing, steps (1) and (2) are > the same. To get it to import I only substitute for $$e before step > (3) (importing). > > Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
On Thu, Oct 18, 2012 at 9:11 AM, Jean-Marc Lasgouttes wrote: > Le 18/10/2012 14:55, Scott Kostyshak a écrit : > >>> The old way this "noweb mode" works is >>> 1/ ensure that the class name is literate-something (now it would be >>> ensure >>> that some module is loaded and the module name should be passed to >>> tex2lyx) >>> >>> 2/ when a layout starts with <<, change it to a layout with name "Scrap". >>> This could be OK because the Sweave/knitr modules declare Scrap as a >>> synonym >>> for Chunk. >>> >>> 3/ transform [[something]] to ERT. I do not know what this is good for, >>> presumably a noweb-only thing. >> >> >> OK, thanks for the explanation. > > > So my point is that we should fix 1/ and get rid of the literate-xx classes > if they are still there. Ah, now I see why importing these types of files is different -- because they depend on modules. I didn't think about that. > > >> Yes, the only thing that changes is what I have as the Converter for >> Rnw (knitr) to LaTeX (plain). Is there some other output that I can >> send? Any -dbg flag that I can set to give more information on this? > > > Try "-dbg files". The unchangedConverter.log is here (error): http://paste.debian.net/201557/ And the changedConverter.log is here (no error): http://paste.debian.net/201558/ Thanks, Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
The [[foo]] notation is noweb syntax for a reference to something that is defined elsewhere. By putting it in an ERT we ensure that it ends up in the noweb file unaltered. On Oct 18, 2012, at 5:18, Jean-Marc Lasgouttes wrote: > Le 18/10/2012 14:02, Scott Kostyshak a écrit : >> Ah, then I don't understand how LyX handles imports. The Customization >> manual does not talk about importing. Doesn't LyX use the converters >> to convert the file to LaTeX and then use tex2lyx to import the tex >> file? > > Normally, the importation is done by tex2lyx using the -n flag, but I > think that this support needs to be updated to the new world of module > based literate programming. > > The old way this "noweb mode" works is > 1/ ensure that the class name is literate-something (now it would be > ensure that some module is loaded and the module name should be passed > to tex2lyx) > > 2/ when a layout starts with <<, change it to a layout with name > "Scrap". This could be OK because the Sweave/knitr modules declare Scrap > as a synonym for Chunk. > > 3/ transform [[something]] to ERT. I do not know what this is good for, > presumably a noweb-only thing. >> >>> What is the difference between the Rnw files when you do this change? >> >> No difference. In the recipe for reproducing, steps (1) and (2) are >> the same. > > You mean that the Rnw files are the same in the two cases? This is weird. > > JMarc >
Re: $$e not set on import --> import of .Rnw (knitr) fails
Le 18/10/2012 14:55, Scott Kostyshak a écrit : The old way this "noweb mode" works is 1/ ensure that the class name is literate-something (now it would be ensure that some module is loaded and the module name should be passed to tex2lyx) 2/ when a layout starts with <<, change it to a layout with name "Scrap". This could be OK because the Sweave/knitr modules declare Scrap as a synonym for Chunk. 3/ transform [[something]] to ERT. I do not know what this is good for, presumably a noweb-only thing. OK, thanks for the explanation. So my point is that we should fix 1/ and get rid of the literate-xx classes if they are still there. Yes, the only thing that changes is what I have as the Converter for Rnw (knitr) to LaTeX (plain). Is there some other output that I can send? Any -dbg flag that I can set to give more information on this? Try "-dbg files". JMarc
Re: $$e not set on import --> import of .Rnw (knitr) fails
On Thu, Oct 18, 2012 at 8:18 AM, Jean-Marc Lasgouttes wrote: > Le 18/10/2012 14:02, Scott Kostyshak a écrit : > >> Ah, then I don't understand how LyX handles imports. The Customization >> manual does not talk about importing. Doesn't LyX use the converters >> to convert the file to LaTeX and then use tex2lyx to import the tex >> file? > > > Normally, the importation is done by tex2lyx using the -n flag, but I think > that this support needs to be updated to the new world of module based > literate programming. > > The old way this "noweb mode" works is > 1/ ensure that the class name is literate-something (now it would be ensure > that some module is loaded and the module name should be passed to tex2lyx) > > 2/ when a layout starts with <<, change it to a layout with name "Scrap". > This could be OK because the Sweave/knitr modules declare Scrap as a synonym > for Chunk. > > 3/ transform [[something]] to ERT. I do not know what this is good for, > presumably a noweb-only thing. OK, thanks for the explanation. >> >>> What is the difference between the Rnw files when you do this change? >> >> >> No difference. In the recipe for reproducing, steps (1) and (2) are >> the same. > > > You mean that the Rnw files are the same in the two cases? This is weird. Yes, the only thing that changes is what I have as the Converter for Rnw (knitr) to LaTeX (plain). Is there some other output that I can send? Any -dbg flag that I can set to give more information on this? Thanks, Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
Le 18/10/2012 14:02, Scott Kostyshak a écrit : Ah, then I don't understand how LyX handles imports. The Customization manual does not talk about importing. Doesn't LyX use the converters to convert the file to LaTeX and then use tex2lyx to import the tex file? Normally, the importation is done by tex2lyx using the -n flag, but I think that this support needs to be updated to the new world of module based literate programming. The old way this "noweb mode" works is 1/ ensure that the class name is literate-something (now it would be ensure that some module is loaded and the module name should be passed to tex2lyx) 2/ when a layout starts with <<, change it to a layout with name "Scrap". This could be OK because the Sweave/knitr modules declare Scrap as a synonym for Chunk. 3/ transform [[something]] to ERT. I do not know what this is good for, presumably a noweb-only thing. What is the difference between the Rnw files when you do this change? No difference. In the recipe for reproducing, steps (1) and (2) are the same. You mean that the Rnw files are the same in the two cases? This is weird. JMarc
Re: $$e not set on import --> import of .Rnw (knitr) fails
On Thu, Oct 18, 2012 at 3:46 AM, Jean-Marc Lasgouttes wrote: > Le 18/10/12 01:49, Scott Kostyshak a écrit : > >>> Stupid question; where is importation of knitr files defined in >>> converters? >> >> >> Rnw (knitr) -> latex (plain) >> The converter is currently: >> Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i >> $$p$$o $$e $$r >> When I change this to the following, import works: >> Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i >> $$p$$o ISO-8859-15 $$r > > > But this is a converter for export, not import. Ah, then I don't understand how LyX handles imports. The Customization manual does not talk about importing. Doesn't LyX use the converters to convert the file to LaTeX and then use tex2lyx to import the tex file? > What is the difference between the Rnw files when you do this change? No difference. In the recipe for reproducing, steps (1) and (2) are the same. To get it to import I only substitute for $$e before step (3) (importing). Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
Le 18/10/12 01:49, Scott Kostyshak a écrit : Stupid question; where is importation of knitr files defined in converters? Rnw (knitr) -> latex (plain) The converter is currently: Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r When I change this to the following, import works: Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o ISO-8859-15 $$r But this is a converter for export, not import. What is the difference between the Rnw files when you do this change? JMarc
Re: $$e not set on import --> import of .Rnw (knitr) fails
On Wed, Oct 17, 2012 at 6:52 PM, Jean-Marc Lasgouttes wrote: > Le 17/10/12 06:09, Scott Kostyshak a écrit : > >> I have this problem on master and 2.0.x. >> >> An empty $$e variable is being passed to the converter script on >> import because the document is not open yet: >> command = subst(command, token_encoding, buffer ? >> buffer->params().encoding().iconvName() : string()); >> >> Should $$e be set to the default encoding of a new document? >> >> Or is this something that the converter script should deal with? >> >> To reproduce: >> 1. Open examples/knitr.lyx >> 2. Export to Rnw (knitr) >> 3. Import the Rnw (knitr) file >> >> I get an error after (3) because lyxknitr.R is expecting a non-empty >> $$e argument. > > > Stupid question; where is importation of knitr files defined in converters? Rnw (knitr) -> latex (plain) The converter is currently: Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r When I change this to the following, import works: Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R $$p$$i $$p$$o ISO-8859-15 $$r Scott
Re: $$e not set on import --> import of .Rnw (knitr) fails
Le 17/10/12 06:09, Scott Kostyshak a écrit : I have this problem on master and 2.0.x. An empty $$e variable is being passed to the converter script on import because the document is not open yet: command = subst(command, token_encoding, buffer ? buffer->params().encoding().iconvName() : string()); Should $$e be set to the default encoding of a new document? Or is this something that the converter script should deal with? To reproduce: 1. Open examples/knitr.lyx 2. Export to Rnw (knitr) 3. Import the Rnw (knitr) file I get an error after (3) because lyxknitr.R is expecting a non-empty $$e argument. Stupid question; where is importation of knitr files defined in converters? JMarc
$$e not set on import --> import of .Rnw (knitr) fails
I have this problem on master and 2.0.x. An empty $$e variable is being passed to the converter script on import because the document is not open yet: command = subst(command, token_encoding, buffer ? buffer->params().encoding().iconvName() : string()); Should $$e be set to the default encoding of a new document? Or is this something that the converter script should deal with? To reproduce: 1. Open examples/knitr.lyx 2. Export to Rnw (knitr) 3. Import the Rnw (knitr) file I get an error after (3) because lyxknitr.R is expecting a non-empty $$e argument.
