Oh, that is a good test case which I ignored. Sorry. I will fix it soon. yihui/knitr#161 Thanks!

Originally posted on 2012-03-03 16:48:18

It has been fixed in the development version: https://github.com/yihui/knitr

Originally posted on 2012-03-05 03:19:14

The syntax is <<>>= (note the equal sign in the end!). If you are a beginner, you may start with my examples: https://github.com/yihui/knitr/tree/master/inst/examples which you can also find under the directory system.file('examples', package = 'knitr')

Originally posted on 2012-05-09 18:56:06

Guest *Alan* @ 2012-05-10 09:31:46 originally posted:

Thanks for prompt reply.  I'll study the "knitr-minimal.lyx" example and work from there.
Alan

Guest *Hockeyvic06* @ 2012-09-01 23:58:37 originally posted:

 make sure the module is added... it won't stay added for every document.

knitr is an R package, so run install.packages('knitr') in R; then see https://github.com/downloads/yihui/lyx/sweave.pdf

Originally posted on 2012-06-09 19:21:21

Guest *Gfox* @ 2012-07-03 19:43:44 originally posted:

I installed knitr into R and have looked at this document, but still get this message (also on a Win7 machine). I don't see anything in this link (but may well be missing something) that tells me how to respond to this error message from Lyx. Any suggestions?

Guest *Bruce * @ 2012-07-03 22:25:59 originally posted:

 I have this issue also on win7 (I have been happily using it on OSX for the past week, and recommended it to gfox...). I need to be able to run this on win7 as well as osx if I'm to use it. At first I thought it might be an issue with LyX 2.04 (just released this week; I had a very old LyX on my pc before), but rolling back to 2.03 gives the same error. I am using MikTeX 2.9... But I assume the knitr->latex converter is part of LyX, not part of LaTeX?

As I replied to @41ac7788f92413dd3561d875e4f69c32:disqus, you need to read the manual https://github.com/downloads/yihui/lyx/sweave.pdf

That is often an indication that LyX cannot find Rscript; you need to let LyX know R's bin path and reconfigure/restart LyX.

Originally posted on 2012-07-04 00:56:50

Please see Section 1 of the manual: https://github.com/downloads/yihui/lyx/sweave.pdf

Originally posted on 2012-07-04 00:57:51

Guest *Gfox* @ 2012-07-04 03:54:49 originally posted:

I've followed these instructions. After installing Lyx 2.0.4, to a Windows 7 machine, I went to Tools:Preferences:Paths and added the location of R (as obtained from R, using  R.home('bin'). Then I ran Tools:Reconfigure and then restarted Lyx, and tried to load a lyx file (in fact, one that Bruce sent me). Now Lyx complains (1) that I need to install article.cls (hmm  . . . I have a fully working Miktex installation, and article.cls is definitely there), and then (2) still complains that I'm missing knitr ->latex. I'm not sure what else to try to get it to work.

Guest *Bruce * @ 2012-07-04 15:54:42 originally posted:

 Sorry, when I first looked at the linked file it did not appear to be about knitr, so I assumed the link was in error.

However as gfox noted, simply adding R to the path did not solve the problem. In the end, as is often the case in Win7, it turned out to be about permissions....

First, installing the development version of knitr (which I recall reading somewhere is required for proper LyX integration) seems to require running R as administrator.

Second, LyX's reconfiguration utility doesn't run properly when running as a user (I eventually found some notes about this from the last time I installed LyX...). One has to:

1. Run LyX as an administrator, adding the R path and running the Reconfigure utility. Exit LyX
2. For good measure, run LyX again as admin, creating a new document and ensuring that knitr now works. Exit LyX
3. Copy the newly generated configuration files  from [admin home][application data home]LyX2.0 to [user home][application data home]LyX2.0
   a. In a standard desktop configuration, user home will be c:usersusername, and application data home will be appdata or appdataroaming; but if, like me, you are working in a networked file system environment that was first designed under NT, you will have to find your own user home, and application data home may be something like Application Data.
   b. The configuration files may just be the .lst files; but I went ahead and copied all the files (not the subdirectories) and that seemed to work. If you upgraded from an earlier version of LyX there may be some other files that appear not to be used any more; I just deleted those and all seems well
4. Run LyX as user, and hopefully all will be working!

Guest *Gfox* @ 2012-07-04 16:51:40 originally posted:

Just tried Bruce's solution posted above, and it doesn't change anything on my installation (where I'm using all local files) -- I still get the same error messages.

Bruce's solution sounds complicated. Windows is pretty annoying in terms of permissions. Usually I install all my software packages including R and LyX in a different place (e.g. C:/Software or D:/Packages/ where I have full permission to read/write without begging Windows for permission); the default C:/Program Files has all sorts of weird permission problems.

Let's make the last attempt: uninstall R/LyX/MikTeX and reinstall them to another directory; add R's bin path to LyX's preferences of PATH and reconfigure; install knitr.

If this still does not work, we can probably try Skype/screen sharing so that I can better identify the problem.

Originally posted on 2012-07-04 19:32:51

Guest *Gfox* @ 2012-07-05 01:47:06 originally posted:

Thanks, but no thanks -- R and MikTeX work fine on my machines, and I don't think I want to mess with that. I'll just continue to use WinEdt and Sweave (which also work fine on my machines) until these kinks get worked out. I know it takes time to get these sorts of things working in many different settings, and I'm pretty impressed that knitr works so well in so many already - just not mine yet.

Fair enough. It is hard to diagnose technical problems unless I can check your computer by myself :)

WinEdt should be easier to configure than LyX: http://yihui.name/knitr/demo/editors/

Originally posted on 2012-07-05 05:09:12

Please read: https://github.com/downloads/yihui/lyx/knitr.pdf and see examples under https://github.com/yihui/lyx/tree/master/examples

Originally posted on 2012-08-16 20:52:30

Guest *Vit* @ 2012-08-17 08:47:03 originally posted:

Thanks for your fast reply!
The problem was that I didn't realize I should also read the LyX's Sweawe manual. Now I see the <<>> marks and it works fine.
One more question: I am not able to open your LyX examples (https://github.com/yihui/lyx/tree/master/examples) using LyX, which says e.g. "D:/knitr.lyx is not a readable LyX document". How are these example files intended to be used/opened?
Many thanks for knitr and for your help!

You can download the whole repository as a zip package: https://github.com/yihui/knitr/zipball/master Unzip it and you will find the lyx examples under inst/examples/

Originally posted on 2012-08-19 01:23:34

Guest *Vit* @ 2012-08-30 13:15:59 originally posted:

Many thanks! This works.

It is not trivial to import Rnw to LyX; in fact this feature does not exist at the moment (although you seemed to have succeeded, the imported lyx document may not be a really valid lyx document).

The best way is to create one by yourself following instructions in https://github.com/downloads/yihui/lyx/knitr.pdf

Or download my lyx examples from https://github.com/yihui/knitr/zipball/master or https://github.com/yihui/lyx/zipball/master

Originally posted on 2012-08-19 01:28:16

To diagnose the problem, please read https://github.com/downloads/yihui/lyx/sweave.pdf (Section 4)

Originally posted on 2012-09-02 03:23:55

Guest *Philipp_rathjen* @ 2012-11-26 23:26:34 originally posted:

Are you really sure you installed the Knitr package on R and that you are using the newest version of R?

It seems you have solved the problem, and I guess that is probably due to a missing LaTeX package?

Originally posted on 2012-11-20 19:55:53

Guest *Simon-R* @ 2012-11-26 09:37:58 originally posted:

It seems you have solved the problem>
I have the same problem then Jay. Which package do I need? THX

He was using Windows and MikTeX, and he let MikTeX install missing packages on the fly (there is an option which you can find from the start menu). I used the mathpazo package, and other packages such as geometry and hyperref should be common; take a look at the LaTeX preamble and you will see all of them.

Originally posted on 2012-11-26 18:13:15

use the chunk option echo=FALSE: http://yihui.name/knitr/options

Originally posted on 2012-11-27 00:27:13

Guest *View Alpha* @ 2012-12-04 06:57:56 originally posted:

Finally, I found that the missing of VC++ 2008 runtime library made the lyx to do a wrong work. But here, I will still thanks a lot for your effeort !

Guest *Pierre-Olivier* @ 2012-12-13 17:35:07 originally posted:

My bug is strongly related to: yihui/knitr#230
It seems that it is still a problem, it isn't?

Are you using the latest version of knitr? v0.9

And can you try the UTF-8 encoding? (Document=>Settings)

Originally posted on 2012-12-13 17:39:22

Yes, I think so. LyX 2.0.5 has solved a bug related to this, but I'm not sure if you are using 2.0.5 or not.

Originally posted on 2012-12-13 18:35:51

Guest *Pierre-Olivier* @ 2012-12-13 19:52:37 originally posted:

Yihui, thanks to answer so quickly. I update my software (Lyx 2.0.5, knitr 0.9, R 2.15.2, MacTex 2012) and change the settings to utf-8 encoding. I still get the same error. It works only when I write 'e instead of é in my article title.

can you put a code chunk sessionInfo() in LyX and see what is the locale information in the PDF output?

I do not have problems with é under Ubuntu.

Originally posted on 2012-12-14 01:30:56

Guest *Pierre-Olivier Chasset* @ 2012-12-14 07:55:56 originally posted:

Please, find below the result of sessionInfo():

R version 2.15.2 (2012-10-26)

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_0.9

loaded via a namespace (and not attached):

[1] digest_0.6.0 evaluate_0.4.3 formatR_0.7 stringr_0.6.2

[5] tools_2.15.2

So that explained the problem: the locale should not be C. It sounds like the LyX bug 7741 was not solved on Mac OS? Can you change your GUI language in Preferences to Default and see if sessionInfo() changes?

Originally posted on 2012-12-14 21:46:27

Guest *Pierre-Olivier Chasset* @ 2012-12-15 21:08:29 originally posted:

So, the LyX GUI language in Preferences was already set to default. So, I try with different languages, but I still get the same error and the locale doesn't change: 'C' for all GUI languages.

Can you post the results of this code chunk in LYX as well?

x = as.list(Sys.getenv())
x = x[grep('^L(C|A)', names(x))]
str(x)

And also the results from a normal R session.

Originally posted on 2012-12-17 03:32:47

Guest *Pierre-Olivier Chasset* @ 2012-12-17 13:55:10 originally posted:

From LyX:
List of 2
$ LANGUAGE: chr ""
$ LC_ALL : chr ""

From a normal R session:
List of 2
$ LANG : chr "fr_FR.UTF-8"
$ LC_CTYPE: chr "fr_FR.UTF-8"

Since I do not have a Mac OS to test with, I suggest you post the question to the public such as the LyX mailing list or StackOverflow: http://stackoverflow.com/questions/tagged/r

Originally posted on 2012-12-17 22:27:03

Guest *Pierre-Olivier Chasset* @ 2012-12-18 09:52:40 originally posted:

Alright. Many thanks for your time and your great work.

Sorry I have never seen such an error before. Google tells me this:

http://comments.gmane.org/gmane.editors.lyx.general/46329

Perhaps it is a MikTeX problem. I really do not know.

Originally posted on 2012-12-17 03:25:31

Guest *Maxim Kovalenko* @ 2012-12-17 17:24:13 originally posted:

Can I do anything in terms of diagnostics?

You can export the lyx file to Rnw (File=>Export), and run knitr on it in R.

library(knitr)
knit('yourfile.Rnw')

And update LyX and MikTeX if you have not done so.

Originally posted on 2012-12-17 22:09:53

Guest *Maxim Kovalenko* @ 2012-12-18 17:27:57 originally posted:

I have figured it out, maybe the solution will be useful for someone else. It appears that there are two instances of Rscript on my 64-bit Win7. One is the C:Program FilesRR-2.15.2bin, while another is in C:Program FilesRR-2.15.2binx64. Initially I have added the first one to the Lyx Path, and got the error above. Then I changed the Lyx Path to the latter, and it worked. Of course, you need to use the 64-bit program on a 64-bit system (well, at least in this case).

Thanks for your support.

Guest *KIM Musak* @ 2013-11-27 07:30:14 originally posted:

can you be more specific, which one of the many options in 'Paths' in Lyx?

Yes, and I emphasized that in http://yihui.name/knitr/options (chunk labels are supposed to be unique). And you can actually set a different figure prefix for different documents by opts_chunk$set(fig.path = 'the-desired/prefix-').

Originally posted on 2013-01-16 21:48:52

http://stackoverflow.com/q/14407576/559676

Originally posted on 2013-01-27 19:45:13

Guest *Maxim Kovalenko* @ 2013-01-28 09:17:23 originally posted:

Thank you, that works. One also has to add the option messages = FALSE to suppress the stargazer loading text. I have to tell you, knitr is very exciting, it is a beautiful writing tool.

Guest *Maxim Kovalenko* @ 2013-01-28 09:48:41 originally posted:

When I use this with real data I quite often get the following error:

Error: could not find function ".hasSlot"

This is solved by adding "require(methods)" to the chunk. This package is enabled by default in R, and therefore the code runs in the native R environment, but gives an error in Lyx.

LyX calls Rscript, which does not load methods by default; see ?Rscript in R

Originally posted on 2013-01-28 17:51:31

Guest *KarlP* @ 2013-11-06 05:30:22 originally posted:

answered my own question

"cat" instead of "print" in the above expression does the trick

library(methods)

And maybe I'm wrong, but I do not think you can use googleVis in LaTeX/PDF.

Originally posted on 2013-12-16 05:22:27

Guest *Samar Singh* @ 2013-12-16 06:35:46 originally posted:

I have tried the other conversions also with equal lack of success. I am now of the belief that possibly GoogleVis is not compatible wtih Lyx.

It is not that googleVis is not compatible with LyX. It is that LaTeX is not compatible with HTML/JavaScript/Flash. They are completely different.

Originally posted on 2013-12-16 21:20:24

Guest *samar* @ 2013-12-17 01:53:44 originally posted:

I agree. However, Lyx is a pretty high level language so I had quite some time ago requested that it be extended to compile to HTML5. The developers had originally said they would put this in for version 2.0 but it keeps getting pushed back. Can't blame them. They have done an outstanding job with the development of Lyx already and this is no trivial task.

ctex里面水有点深，我建议用XeLaTeX配合中文字体，编码UTF8，对ctex用nofonts选项：http://yihui.name/cn/2011/05/write-chinese-in-lyx/

——原帖发布于 2014-01-30 07:01:30

访客 *Young.Tao* @ 2014-02-03 03:40:42 写道：

非常感谢您的回复。按照您的提示，我修改了lyx的document settings里的设置，结果和改之前一样，生成的pdf文档中，由knitr生成的那部分内容中的中文依然是乱码，而其他部分中文正常。实在不知道是lyx的问题还是knitr的问题了。

RStudio没问题的话，那就是LyX里面什么地方有问题了，我得看消息日志：View--View Messages

你可以粘贴到pastebin.com

——原帖发布于 2014-02-03 06:23:12

访客 *Young.Tao* @ 2014-02-10 14:16:28 写道：

抱歉pastebin.com打不开，我把完整progress messages传到了
https://skydrive.live.com/?cid=2d4ed58b019b20a4#cid=2D4ED58B019B20A4&id=2D4ED58B019B20A4%21105
其中有一个warning，Warning in native_encode(text) : some characters may not work under the current locale。麻烦您看一下，谢谢。

这个警告信息是一个未修复的bug导致的：http://www.lyx.org/trac/ticket/8537#comment:19 我本以为这个早已经修复了，没想到在Mac底下仍然存在，因为我极少用Mac，所以之前没发现。不过这个警告关系不大，如果你要去掉它的话可以在~/.Rprofile里添加Sys.setlocale(,'en_US.UTF-8')，手工告诉R你的系统语言设置是UTF-8环境。

我测试过中文了，用nofonts选项并自行选择XeLaTeX中文字体（例如宋体），没有问题，能正常显示。

——原帖发布于 2014-02-23 05:50:35

Guest *Jeremy burnison* @ 2016-12-27 22:10:24 originally posted:

I am having an issue on Mac as well. I get this error when adding knitr module to my LyX document.
"The module knitr requires a package that is not available in your Latex installation, or a converter you have not installed. LaTex output may not be possible."
Any advice or insight?

Guest *Iman* @ 2016-12-28 07:53:41 originally posted:

Dear Jeremy,
Make sure that you have the package knitr installed in R, and also through document settings ->
Modules in lyx

Guest *Jeremy burnison* @ 2016-12-28 18:30:23 originally posted:

Hi, I did have it installed but I believe the Sys.setlocale had to be correct. I reconfigured lyx several times and it eventually identified the Rnd(knitr) module. Now when I try to compile a pdf or View as is done in the example video I get this Error.
Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R
"/var/folders/mz/09m3h9qj0sb8hgclltgxbc0szm70l9/T/lyx_tmpdir.TGanerR20376/lyx_…
Here's my session info
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.2

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] knitr_1.15.1