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demo.R
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## load "pander" package
## http://rapporter.github.com/pander/
library(pander)
## "brew" the below file to Pandoc's markdown
Pandoc.brew('example.brew')
## or convert to HTML at one go
## NOTE: `pandoc` is needed for the conversion
Pandoc.brew('example.brew', output = tempfile(), convert = 'html')
## or pdf/docx/odt
Pandoc.brew('example.brew', output = tempfile(), convert = 'pdf')
Pandoc.brew('example.brew', output = tempfile(), convert = 'docx')
Pandoc.brew('example.brew', output = tempfile(), convert = 'odt')
example.brew
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# Doc header 1
Some text explaining the analysis we are doing
<%=
summary(cars)# a summary table
%>
Images should be in separate chunks not to be handles as inline image:
<%=
plot(cars) # a plot
%>
And a model at last:
<%=
fit <- lm(dist~speed, data = cars)
fit
%>
example.txt
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# Doc header 1
 
Some text explaining the analysis we are doing
 
----------------------------------
&nbsp; speed dist
------ ------------ --------------
**** Min. : 4.0 Min. : 2.00
 
**** 1st Qu.:12.0 1st Qu.: 26.00
 
**** Median :15.0 Median : 36.00
 
**** Mean :15.4 Mean : 42.98
 
**** 3rd Qu.:19.0 3rd Qu.: 56.00
 
**** Max. :25.0 Max. :120.00
----------------------------------
 
Images should be in separate chunks not to be handles as inline image:
![](/tmp/RtmpD3QXAs/plots/4304da6127c.png)
 
And a model at last:
 
--------------------------------------------------------------
&nbsp; Estimate Std. Error t value Pr(>|t|)
----------------- ---------- ------------ --------- ----------
**(Intercept)** -17.58 6.758 -2.601 0.01232
 
**speed** 3.932 0.4155 9.464 1.49e-12
--------------------------------------------------------------
 
Table: Fitting linear model: dist ~ speed

Daroczig,

I'm new to the R/markdown/pandoc/knitr continuum and used your example to try to learn how to convert R Markdown files into MS-Word files. (Why would I want to do that, you ask? Well, my colleagues insist on using Word.) However, I ran into an error. The command Pandoc.brew('example.brew') ran just fine. But all of the next commands specifying output to html, docx, etc. produced the following error in the
R console:

Error in gsub(sprintf("]\\(%s/", basedir), "]\\(", res) :
invalid regular expression ']\(/var/folders/Yq/YqZGRlFzE9yM-RL+qDXd0U+++TI/-Tmp-//RtmpTWO4zs/',
reason 'Invalid use of repetition operators'

I get the same error even if the 'example.brew' file contains just a single sentence of plain text. I'm hoping you might know what's causing the problem. In case it might help, here's my R sessionInfo:

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
stats, graphics, grDevices, utils, datasets, methods and base
other attached packages:
knitr_1.1, pander_0.3.1, stringr_0.6.2, foreign_0.8-52, reshape2_1.2.2, car_2.0-16, nnet_7.3-5, MASS_7.3-23 and slidify_0.3.3
loaded via a namespace (and not attached):
digest_0.6.3, evaluate_0.4.3, formatR_0.7, markdown_0.5.4, plyr_1.8, tools_2.15.1, whisker_0.1 and yaml_2.1.7

Thanks for any suggestions you might have.

eipi10

Thanks @eipi10 for the bug report, that's definitely a bug in pander it seems. There is a command in Pandoc.brew [L134] where I try to remove absolute path from the generated image tags and your pretty strange basedir produces a screwed up regular expression there. BTW is it normal to have a folder like /var/folders/Yq/YqZGRlFzE9yM-RL+qDXd0U+++TI/-Tmp-//RtmpTWO4zs/ on OSX?

Anyway, I will fix that on the GitHub version soon (in 24 hours), I promise. Thanks again!

Thanks for the quick reply @Daroczig. The weird directory is (AFAIK) a temporary (hidden) folder that OS-X creates in some download situations. I don't really know the details, but it does that in a wide range of situations, such as when installing an R package. For example, here's the output of a command I just ran in the R console:

> install.packages('ggplot2')
Installing package(s) into ‘/Users/eipi10/Library/R/2.15/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.15/ggplot2_0.9.3.1.tgz'
Content type 'application/x-gzip' length 2659920 bytes (2.5 Mb)
opened URL
==================================================
downloaded 2.5 Mb


The downloaded binary packages are in
/var/folders/Yq/YqZGRlFzE9yM-RL+qDXd0U+++TI/-Tmp-//RtmpTWO4zs/downloaded_packages`

I'm not sure why it works that way and I've never had a reason to try and find anything on those weird paths, but that's the way it seems to work.

eipi10

Yeah, that's pretty normal after all it seems, I am just curious why this problem did not occurred recently.
Anyway, IMHO it's fixed in the GitHub version. Could you please verify, @eipi10?

Works fine now. Thanks very much for creating and maintaining pander!

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