Re: Knitr (Rnw) Rscript error log
On 10/1/12 12:15 AM, Yihui Xie wrote: > If you are using the German translation of the GUI, you can set the > interface language option to be Default in the preferences. Otherwise > you have to wait for LyX 2.0.5 for the bug fix. > My interpretation was wrong then. I thought the workaround was to explicitly use the "Default" language option if I had been using the German GUI. My OS is set to American language, so "Default" for me led to US GUI and the C locale. Setting the user interface language to German solves it. I could have thought this far... Thanks yet again. On 10/1/12 10:36 PM, Jean-Marc Lasgouttes wrote: What do you mean exactly? Is it just that the US GUI is not convenient to you? You do not need the German UI to input German documents. Quite the contrary, I prefer the US GUI. The last sentence is exactly why I thought my German document has to work using the the US GUI. I thought that setting the document language leads to Rscript picking up the correct locale - it did not occur to me that the locale is influenced by the GUI language setting.
Re: Knitr (Rnw) Rscript error log
That is something confused me as well. Here is a screenshot of what I was talking about: http://i.imgur.com/vkLhP.png It only sets the language of the GUI and will not affect the document itself. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Mon, Oct 1, 2012 at 3:36 PM, Jean-Marc Lasgouttes wrote: > Le 01/10/12 21:37, Michael Bach a écrit : >> I am using an American locale and GUI, so interface language default >> does not work. > > > What do you mean exactly? Is it just that the US GUI is not convenient to > you? You do not need the German UI to input German documents. > > JMarc
Re: Knitr (Rnw) Rscript error log
Le 01/10/12 21:37, Michael Bach a écrit : On 10/1/12 12:15 AM, Yihui Xie wrote: I am using an American locale and GUI, so interface language default does not work. What do you mean exactly? Is it just that the US GUI is not convenient to you? You do not need the German UI to input German documents. JMarc
Re: Knitr (Rnw) Rscript error log
On 10/1/12 12:15 AM, Yihui Xie wrote: Wonderful. That is the root of the problem. The locale should not be C. This bug has been biting us: http://www.lyx.org/trac/ticket/7741 If you are using the German translation of the GUI, you can set the interface language option to be Default in the preferences. Otherwise you have to wait for LyX 2.0.5 for the bug fix. Thanks for your help on investigation and the bug link! I am using an American locale and GUI, so interface language default does not work. Anyway, I am preparing statistics lectures involving R as the main tool, so I might get into compiling LyX myself if I can find my way around on the (new) OS X - switched two weeks ago... Best Regards, Michael
Re: Knitr (Rnw) Rscript error log
Wonderful. That is the root of the problem. The locale should not be C. This bug has been biting us: http://www.lyx.org/trac/ticket/7741 If you are using the German translation of the GUI, you can set the interface language option to be Default in the preferences. Otherwise you have to wait for LyX 2.0.5 for the bug fix. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Sun, Sep 30, 2012 at 5:06 PM, Michael Bach wrote: > On 9/30/12 10:51 PM, Yihui Xie wrote: >> >> You can make a copy of that document, delete everything in it, and >> only put a code chunk >> >> <<>>= >> sessionInfo() >> @ >> >> there and compile it. Then show us the results from sessionInfo(). >> > > Good idea, it is as I suspected: > > sessionInfo() > ## R version 2.15.1 (2012-06-22) > ## Platform: i386-apple-darwin9.8.0/i386 (32-bit) > ## > ## locale: > ## [1] C > ## > ## attached base packages: > ## [1] stats graphics grDevices utils datasets base > ## > ## other attached packages: > ## [1] knitr_0.8 > ## > ## loaded via a namespace (and not attached): > ## [1] digest_0.5.2 evaluate_0.4.2 formatR_0.6plyr_1.7.1 > ## [5] stringr_0.6.1 tools_2.15.1 > > The R started from Terminal picks up the utf-8 locale, Rscript does not. > How/where best to look next? > > Michael
Re: Knitr (Rnw) Rscript error log
On 9/30/12 10:51 PM, Yihui Xie wrote: You can make a copy of that document, delete everything in it, and only put a code chunk <<>>= sessionInfo() @ there and compile it. Then show us the results from sessionInfo(). Good idea, it is as I suspected: sessionInfo() ## R version 2.15.1 (2012-06-22) ## Platform: i386-apple-darwin9.8.0/i386 (32-bit) ## ## locale: ## [1] C ## ## attached base packages: ## [1] stats graphics grDevices utils datasets base ## ## other attached packages: ## [1] knitr_0.8 ## ## loaded via a namespace (and not attached): ## [1] digest_0.5.2 evaluate_0.4.2 formatR_0.6plyr_1.7.1 ## [5] stringr_0.6.1 tools_2.15.1 The R started from Terminal picks up the utf-8 locale, Rscript does not. How/where best to look next? Michael
Re: Knitr (Rnw) Rscript error log
You can make a copy of that document, delete everything in it, and only put a code chunk <<>>= sessionInfo() @ there and compile it. Then show us the results from sessionInfo(). Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Sun, Sep 30, 2012 at 2:11 PM, Michael Bach wrote: > I found the error source, but have no clue for a fix yet. The resulting .tex > document after a LyX-caused knit() is cut off exactly at the first > occurrence of a German diacritic o, i.e. the character ö. This is also in > line with the fact that the knitr-minimal example runs fine since it is > written in English... > > As I wrote earlier, a manual knit() from an R session on the .Rnw file > succeeds. So I guess there is something wrong with the UTF-8 part in the > Rscript call by the knitr(Rnw) module(?). > > For reference: > > >> 12:13:14.353: Rscript --verbose --no-save --no-restore >> "/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R" >> >> "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.Rnw" >> >> "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""tex" >> UTF-8 "/Users/XYZ/Documents/..." > > R and Terminal locale are set correctly as mentioned in a previous post. > > @Yihui: > > Do you remember any similar issues when updating knitr.module and > lyxknitr.R? > > @Scott: > > I will try your attached files if that could help now as the error is > obvious. > > Michael
Re: Knitr (Rnw) Rscript error log
I found the error source, but have no clue for a fix yet. The resulting .tex document after a LyX-caused knit() is cut off exactly at the first occurrence of a German diacritic o, i.e. the character ö. This is also in line with the fact that the knitr-minimal example runs fine since it is written in English... As I wrote earlier, a manual knit() from an R session on the .Rnw file succeeds. So I guess there is something wrong with the UTF-8 part in the Rscript call by the knitr(Rnw) module(?). For reference: > 12:13:14.353: Rscript --verbose --no-save --no-restore > "/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R" > "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.Rnw" > "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""tex" > UTF-8 "/Users/XYZ/Documents/..." R and Terminal locale are set correctly as mentioned in a previous post. @Yihui: Do you remember any similar issues when updating knitr.module and lyxknitr.R? @Scott: I will try your attached files if that could help now as the error is obvious. Michael
Re: Knitr (Rnw) Rscript error log
On 9/29/12 11:43 PM, Yihui Xie wrote: He sent me the message log without cc'ing the list, and I saw Sorry about that, I am using a Newsgroup Account under Thunderbird and am posting to gmane. There is a predefined "Newsgroup" field that I use, that posts to gmane, and thus later also to the LyX list, or so I thought. This field apparently does not get transmitted in the email header, so I will now try to also cc the list. Sorry in advance for eventual double-posts because of this... 12:13:14.353: Rscript --verbose --no-save --no-restore "/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.Rnw" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""tex" UTF-8 "/Users/XYZ/Documents/..." I think that is Mac OS, although in the first email it was Windows 7. Sorry about the confusion! The error occurs only on Mac OS X 10.8.2 Mountain Lion. The problem I think is related to the fact that I work on the same code base from both Windows 7 and Mac OS X using a git repository. To handle end-of-line characters differently, there is an option in git to always commit unix-style line endings, but check out files with OS-native line endings respectively. Now I wondered whether end-of-line issues lead to the error, but then again the .tex gets cut off some lines after \begin{document}. Michael
Re: Knitr (Rnw) Rscript error log
On Sat, Sep 29, 2012 at 5:43 PM, Yihui Xie wrote: > He sent me the message log without cc'ing the list, and I saw > > 12:13:14.353: Rscript --verbose --no-save --no-restore > "/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R" > "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.Rnw" > "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""tex" > UTF-8 "/Users/XYZ/Documents/..." > > I think that is Mac OS, although in the first email it was Windows 7. Ah, yes I think I thought the same thing when I saw that. Glad I'm not the only one that was confused. Scott
Re: Knitr (Rnw) Rscript error log
He sent me the message log without cc'ing the list, and I saw 12:13:14.353: Rscript --verbose --no-save --no-restore "/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.Rnw" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""tex" UTF-8 "/Users/XYZ/Documents/..." I think that is Mac OS, although in the first email it was Windows 7. 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, Sep 29, 2012 at 4:39 PM, Scott Kostyshak wrote: > > I misunderstood. In his original email he stated that he is using Windows 7. > Sorry for the confusion. > > Scott
Re: Knitr (Rnw) Rscript error log
On Sat, Sep 29, 2012 at 5:34 PM, Yihui Xie wrote: > I think this indicated the problem in your log: > > 12:13:14.670: Warning in readLines(input, warn = FALSE) : > 12:13:14.673: invalid input found on input connection 'skryptum.Rnw' > > But without a reproducible example, I'm afraid I cannot do anything, > especially I do not have Mac OS to test with. I misunderstood. In his original email he stated that he is using Windows 7. Sorry for the confusion. Scott
Re: Knitr (Rnw) Rscript error log
I think this indicated the problem in your log: 12:13:14.670: Warning in readLines(input, warn = FALSE) : 12:13:14.673: invalid input found on input connection 'skryptum.Rnw' But without a reproducible example, I'm afraid I cannot do anything, especially I do not have Mac OS to test with. 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, Sep 29, 2012 at 10:52 AM, Michael Bach wrote: > Just a quick follow-up. > > I gather from the log that R reads the file as UTF-8. I checked my System > > $ locale > > and the R > >> Sys.getlocale() > > Both are correctly set up as en_US.UTF-8. Just to rule that one out(?)... >
Re: Knitr (Rnw) Rscript error log
Does the knitr example file work? I forget how to get to example files on MacOS. Mabye Yihui will have an idea of what's going on, but in the meantime if you want to try something, you can try with the newest version of LyX's knitr module that Yihui sent in a couple of days ago. To do this, you can either (1) apply the attached diff. It should succeed on 2.0.4 with a hunk offset. or (2) copy the other two files attached, to the correct places. Don't forget to back up the original files. Scott On Sat, Sep 29, 2012 at 11:52 AM, Michael Bach wrote: > Just a quick follow-up. > > I gather from the log that R reads the file as UTF-8. I checked my System > > $ locale > > and the R > >> Sys.getlocale() > > Both are correctly set up as en_US.UTF-8. Just to rule that one out(?)... > diff --git a/lib/examples/knitr.lyx b/lib/examples/knitr.lyx index ddbfe01..feab161 100644 --- a/lib/examples/knitr.lyx +++ b/lib/examples/knitr.lyx @@ -182,7 +182,7 @@ status collapsed \begin_layout Plain Layout -http://yihui.github.com/knitr +http://yihui.name/knitr \end_layout \end_inset diff --git a/lib/layouts/knitr.module b/lib/layouts/knitr.module index 694ae77..fe64359 100644 --- a/lib/layouts/knitr.module +++ b/lib/layouts/knitr.module @@ -1,7 +1,7 @@ #\DeclareLyXModule[knitr->latex]{Rnw (knitr)} #DescriptionBegin #Uses the knitr package in R for dynamic report generation. This R package has to be installed for this module to work: install.packages('knitr'). Note it depends on R >= 2.14.1. -#For more info see http://yihui.github.com/knitr +#For more info see http://yihui.name/knitr #DescriptionEnd #Category: literate #Excludes: lilypond | sweave diff --git a/lib/scripts/lyxknitr.R b/lib/scripts/lyxknitr.R index 03150f2..7c029ea 100644 --- a/lib/scripts/lyxknitr.R +++ b/lib/scripts/lyxknitr.R @@ -11,7 +11,7 @@ ## author Yihui Xie ## knitr is an alternative package to Sweave, and has more features -## and flexibility; see https://yihui.github.com/knitr +## and flexibility; see https://yihui.name/knitr ## Rscript $$s/scripts/lyxknitr.R $$p$$i $$p$$o $$e $$r ## $$p the path of the output (temp dir) @@ -31,18 +31,7 @@ options(encoding = .cmdargs[3]) ## can put your data files there and functions like read.table() can ## work correctly without specifying the full path setwd(.cmdargs[4]) +opts_knit$set(root.dir = getwd()) -## copy the Rnw file to the current working directory if it does not exist -.tmp.file = tempfile(); .rnw.file = basename(.cmdargs[1]) -.rnw.exists = file.exists(.rnw.file) -if (.rnw.exists) file.rename(.rnw.file, .tmp.file) -file.copy(.cmdargs[1], '.') ## run knit() to get .tex or .R -knit(.rnw.file, tangle = 'tangle' %in% .cmdargs) - -setwd(.cmdargs[4]) -## remove the copied .Rnw if it did not exist, otherwise move the original one back -if (.rnw.exists) file.rename(.tmp.file, .rnw.file) else unlink(.rnw.file) -file.rename(basename(.cmdargs[2]), .cmdargs[2]) # move .tex to the temp dir -rm(.tmp.file, .rnw.file, .rnw.exists) # clean up these variables - +knit(.cmdargs[1], output = .cmdargs[2], tangle = 'tangle' %in% .cmdargs) knitr.module Description: Binary data lyxknitr.R Description: Binary data
Re: Knitr (Rnw) Rscript error log
Just a quick follow-up. I gather from the log that R reads the file as UTF-8. I checked my System $ locale and the R > Sys.getlocale() Both are correctly set up as en_US.UTF-8. Just to rule that one out(?)...
Re: Knitr (Rnw) Rscript error log
On 9/26/12 6:25 PM, Yihui Xie wrote: The first place to look at is View-->View Messages, as described in the troubleshooting section in Sweave manual (which applies to knitr as well): https://github.com/downloads/yihui/lyx/sweave.pdf Very good to know, thanks. I enabled that and tried again. It seems that there is an invalid input found by R(?). Please see also the complete log at the end of this post. I investigated the .tex file and found it was cut off in the middle of the abstract environment. I then opened an R session in the temp directory and ran knit("skryptum.Rnw") which produces a skryptum.tex file that can be tex'ed correctly and contains the \Sepr{} parts. Also, the .Rnw file is complete, i.e. not cut off like the .tex file. So I guess the Rscript call messes things up? I tried the hint by Scott on setting an error hook, but to no avail. How to debug further? -- 12:13:14.051: Previewing ... 12:13:14.085: (buffer-view: ⌘R) 12:13:14.353: Rscript --verbose --no-save --no-restore "/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.Rnw" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.tex" UTF-8 "/Users/XYZ/Documents/Vorlesung/Theorie der Simulationstechnik/src/" 12:13:14.373: running 12:13:14.381: '/Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R --slave --no-restore --no-save --no-restore --file=/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R --args /var/folders/yx/ 12:13:14.383: tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/skryptum.Rnw /var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/skryptum.tex UTF-8' 12:13:14.384: Running: Rscript --verbose --no-save --no-restore "/Applications/LyX.app/Contents/Resources/scripts/lyxknitr.R" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.Rnw" "/var/folders/yx/tvnzczfx7c31c68jrddvlqgrgn/T/lyx_tmpdir.xJL523/lyx_tmpbuf3/""skryptum.tex" UTF-8 "/Users/XYZ/Documents/Vorlesung/Theorie der Simulationstechnik/src/" 12:13:14.663: [1] TRUE 12:13:14.670: Warning in readLines(input, warn = FALSE) : 12:13:14.673: invalid input found on input connection 'skryptum.Rnw' 12:13:14.925: 12:13:14.925: 12:13:14.927: processing file: skryptum.Rnw 12:13:14.942: | | | 0% | 12:13:14.943: |>| 100% 12:13:14.944: ordinary text without R code 12:13:14.944: 12:13:14.947: 12:13:14.948: output file: /Users/.../Documents/Vorlesung/Theorie der Simulationstechnik/src/skryptum.tex 12:13:14.949: 12:13:14.949: [1] "skryptum.tex" 12:13:14.951: [1] TRUE 12:13:14.965: pdflatex "skryptum.tex" Running: pdflatex "skryptum.tex" > /dev/null 12:13:15.211: This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012) 12:13:15.212: restricted \write18 enabled. 12:13:15.227: entering extended mode 12:13:15.229: (./skryptum.tex 12:13:15.230: LaTeX2e <2011/06/27> 12:13:15.230: Babel and hyphenation patterns for english, dumylang, nohyphenation, ge 12:13:15.231: rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi 12:13:15.232: c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis 12:13:15.232: h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic, farsi, finnis 12:13:15.233: h, french, friulan, galician, german, ngerman, swissgerman, monogreek, greek, h 12:13:15.233: ungarian, icelandic, assamese, bengali, gujarati, hindi, kannada, malayalam, ma 12:13:15.234: rathi, oriya, panjabi, tamil, telugu, indonesian, interlingua, irish, italian, 12:13:15.234: kurmanji, latin, latvian, lithuanian, mongolian, mongolianlmc, bokmal, nynorsk, 12:13:15.235: polish, portuguese, romanian, romansh, russian, sanskrit, serbian, serbianc, s 12:13:15.236: lovak, slovenian, spanish, swedish, turkish, turkmen, ukrainian, uppersorbian, 12:13:15.236: welsh, loaded. 12:13:15.237: 12:13:16.309: pdflatex "skryptum.tex" 12:13:16.503: This is pdfTeX, Version 3.1415926-2.4-1.40.13 (TeX Live 2012) 12:13:16.504: restricted \write18 enabled. /Users/Shared/LyX/lyx-2.0.4/src/support/Systemcall.cpp(273): Systemcall: 'pdflatex "skryptum.tex"' finished with exit code 1 Running: pdflatex "skryptum.tex" > /dev/null 12:13:16.520: entering extended mode 12:13:16.521: (./skryptum.tex 12:13:16.521: LaTeX2e <2011/06/27> 12:13:16.522: Babel and hyphenation patterns for english, dumylang, nohyphenation, ge 12:13:16.523: rman-x-2012-05-30, ngerman-x-2012-05-30, afrikaans, ancientgreek, ibycus, arabi 12:13:16.523: c, armenian, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danis 12:13:16.523: h, dutch, ukenglish, usenglishmax, esperanto, estonian, ethiopic
Re: Knitr (Rnw) Rscript error log
On Wed, Sep 26, 2012 at 12:25 PM, Yihui Xie wrote: > The first place to look at is View-->View Messages, as described in > the troubleshooting section in Sweave manual (which applies to knitr > as well): https://github.com/downloads/yihui/lyx/sweave.pdf Michael, You might also be interested in setting an error hook (a command that is run when an error occurs). Otherwise if your document exports fine you might not realize that there could be an error (knitr will print the error message to your latex document but it will appear to compile just fine). For example, knit_hooks$set(error = function(x, options) stop(x)) Scott
Re: Knitr (Rnw) Rscript error log
The first place to look at is View-->View Messages, as described in the troubleshooting section in Sweave manual (which applies to knitr as well): https://github.com/downloads/yihui/lyx/sweave.pdf Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Wed, Sep 26, 2012 at 10:16 AM, Michael Bach wrote: > Hi Scott, > > Thanks for responses. > >> Look in the terminal output. It might give you the error. >> > > I cannot find a terminal output view in LyX - checked all toolbars and View > menu. > >> You could alternatively do File > Export > R/S code and then run/debug >> the resulting file in R. >> > > I tried this and after checking each line interactively in the R console and > commenting out some things in LyX files, e.g. packages that are not available > in > R2.15.1, it runs through, but the LyX called Rscript does not. > >> Also note that since version 0.7 : >> >> - when `opts_knit$get('verbose')` is TRUE, logs (messages, warnings and >> errors) along with the corresponding R code will be printed after `knit()` >> is done; this might help users figure out possible problems in R code >> quickly (#276) >> > > This is a good hint, I set it with: > opts_knit$set(verbose = TRUE) > > inside the first code chunk, but I assume this prints to the R console if > knit() > is called interactively, doesn't it? Anyway, I do not get any feedback on > where > the error comes from > > Michael > > > >
Re: Knitr (Rnw) Rscript error log
Hi Scott, Thanks for responses. > Look in the terminal output. It might give you the error. > I cannot find a terminal output view in LyX - checked all toolbars and View menu. > You could alternatively do File > Export > R/S code and then run/debug > the resulting file in R. > I tried this and after checking each line interactively in the R console and commenting out some things in LyX files, e.g. packages that are not available in R2.15.1, it runs through, but the LyX called Rscript does not. > Also note that since version 0.7 : > > - when `opts_knit$get('verbose')` is TRUE, logs (messages, warnings and > errors) along with the corresponding R code will be printed after `knit()` > is done; this might help users figure out possible problems in R code > quickly (#276) > This is a good hint, I set it with: opts_knit$set(verbose = TRUE) inside the first code chunk, but I assume this prints to the R console if knit() is called interactively, doesn't it? Anyway, I do not get any feedback on where the error comes from Michael
Re: Knitr (Rnw) Rscript error log
On Wed, Sep 26, 2012 at 5:54 AM, Michael Bach wrote: > Dear LyX Developers and Users, > > I am using LyX 2.0.4 on Windows 7 with the knitr (Rnw) module. I successfully > compiled the knitr-minimal.lyx example file and moved on to the > knitr-manual.lyx. I then get an error message that Rscript failed. > > Can someone give me a hint on how to get a debug log of a failed Rscript call > to > investigate? I am pretty sure my R environment is not set up correctly... Look in the terminal output. It might give you the error. You could alternatively do File > Export > R/S code and then run/debug the resulting file in R. Also note that since version 0.7 : - when `opts_knit$get('verbose')` is TRUE, logs (messages, warnings and errors) along with the corresponding R code will be printed after `knit()` is done; this might help users figure out possible problems in R code quickly (#276) Scott
Knitr (Rnw) Rscript error log
Dear LyX Developers and Users, I am using LyX 2.0.4 on Windows 7 with the knitr (Rnw) module. I successfully compiled the knitr-minimal.lyx example file and moved on to the knitr-manual.lyx. I then get an error message that Rscript failed. Can someone give me a hint on how to get a debug log of a failed Rscript call to investigate? I am pretty sure my R environment is not set up correctly... Best Regards, Michael