Version 1.0.6

.gitignore

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+.DS_Store

ChangeLog

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+commit 90eca3594203c1f5fefc286040958a8d57441b5f
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date:   Wed Apr 28 17:46:04 2010 -0600
+
+    Incorporating changes from Yihui Xie which preserves comments in echo'd code when keep.source=F
+
+ R/pgfSweaveDriver.R |   78 +++++++++++++++++++++++++++++++++++++++++++++++++-
+ 1 files changed, 76 insertions(+), 2 deletions(-)
+
+commit d8ec8642a7296225877f14a40098fdb43cf92cb8
+Author: cameronbracken <cameron.bracken@gmail.com>
+Date:   Thu Apr 8 13:02:12 2010 -0600
+
+    Try using predefined R_HOME in Makevars and no GNU Make requirement
+
+    Add binary attribute to pdf files to avoid merging, rebuild vignette to test
+
+ .gitattributes                            |    1 +
+ ChangeLog                                 |   36 +++++++++++++++++++++++++++++
+ DESCRIPTION                               |    2 +-
+ inst/doc/figs/fig-normalSweave.pdf        |  Bin 3056 -> 3140 bytes
+ inst/doc/figs/fig-pgfSweave-hist.pdf      |  Bin 17639 -> 17643 bytes
+ inst/doc/figs/fig-pgfSweave-tikz-hist.pdf |  Bin 28915 -> 28962 bytes
+ inst/doc/pgfSweave-example.pdf            |  Bin 88353 -> 88361 bytes
+ inst/doc/pgfSweave.pdf                    |  Bin 293971 -> 294117 bytes
+ src/Makevars                              |    4 ---
+ 9 files changed, 38 insertions(+), 5 deletions(-)
+
 commit a6c2600e7df9b9137c0ef1c0caf6d002df33e36e
 Author: cameronbracken <cameron.bracken@gmail.com>
 Date:   Tue Apr 6 18:29:32 2010 -0600

DESCRIPTION

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 Package: pgfSweave
 Type: Package
 Title: Quality speedy graphics compilation with Sweave
-Version: 1.0.5
-Date: 2010-01-23
+Version: 1.0.6
+Date: 2010-08-06
 Author: Cameron Bracken <cameron.bracken@gmail.com> and Charlie Sharpsteen <source@sharpsteen.net>
 Maintainer: Cameron Bracken <cameron.bracken@gmail.com> 
 Depends: stashR, filehash, tikzDevice, cacheSweave, getopt

NEWS

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-Please see the README directory for development info
+Please see the README.md file for development info
+
+--------------------------
+Version 1.0.6 - 2010-08-06
+--------------------------
+* Incorporated changes from Yihui Xie which preserves comments in echo'd code
+  when keep.source=F
 
 --------------------------
 Version 1.0.5 - 2010-04-04

README.md

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+#pgfSweave README
+##ABOUT
+
+The pgfSweave package provides capabilities for "caching" graphics 
+generated with Sweave.  Using pgfSweave, figure labels are converted to 
+LaTeX strings so not only do they match the style of the document but math 
+can be put in labels. pgfSweave provides a new driver for Sweave 
+(pgfSweaveDriver) and new chunk options pgf and external on top of the 
+cache option provided by cacheSweave. This package is built upon 
+cacheSweave and therefore also Sweave.
+
+
+##TODO
+
+* Add option to copy Sweave.sty to the local directory, circumventing path 
+  issues on windows
+
+* Add options to access the noae and nogin options in Sweave.sty.  The 
+  logical thing for pgfSweave is to set nogin by default i.e. 
+  `\usepackage[nogin]{Sweave}`.
+
+
+##BUGS
+* If java does not exist the compilation is reported as successful though 
+  the pgf file did not properly get created. 
+
+* A stray Rplots.pdf gets generated using caching. Not sure if this a 
+  cacheSweave or Sweave or a pgfSweave problem.  When using a gui 
+  interface a plotting window opens up.
+
+
+##ISSUES:
+
+* `external=T` only works if a single plot is generated with a single code 
+  chunk.  This is an issue with Sweave as well. The offered fix in Sweave 
+  is to `cat()` your own includegraphics commands.
+
+* Not all latex commands work in labels for example `\scshape` works but 
+  `\textsc{}` does not
+
+* Changing the width and height of a figure ONLY but not the code chunk 
+  does not register as a change and thus the code chunk will not 
+  recompile.
+
+
+##POSSIBLE NEW FEATURES
+
+* chunk dependency checking like weaver using codetools. 
+
+* Scrap Sweave.sty completely (since it is so short) just copy the few 
+  lines of LaTeX defining the Sweave environments into the tex file. 
+
+* Nicer LaTeX number formatting.
+
+* Follow `\input` and `\include` statements. 
+
+* Automatically add the `\pgfrealjobname` command if it is not already in 
+  the file like the Sweave style file is added when `stylepath=TRUE`.
+
+* When a pgf/TikZ graphic is included manually (not in a code chunk) add 
+  the commands to externalize into the graphics into the shell script that 
+  is created. This may need to be a separate function that gives the tex 
+  file a once over and checks if the pdf file exists corresponding to the 
+  name in `\beginpgfgraphicnamed{name}` or the corresponding TikZ 
+  externalization command. There are already scripts available on example 
+  to do stuff like this so maybe integration of one of those may be 
+  possible. 
+
+* Add support for TikZ externalization.  TikZ externalization library is
+  more elegant and could provide more advanced options.  For example the 
+  option to create a make file would be really awesome since it would take 
+  care of most of the checking for graphics changes on the part of 
+  pgfSweave.  This would be a substantial change, requring alot of 
+  rewriting of internal code. 
+
+
+## RESOLVED (resolution in brackets)
+* latex/pdflatex is not found when using R.app (Mac OS X) unless path to 
+  pdflatex is hardcoded (but pgfSweave <file> works)
+  [put path to latex distro in .Rprofile (see vignette faq)]
+
+* Package currently generates a bash shell script to compile external 
+  graphics, which will not work in windows.
+  [This actually does work on windows if Rtools and MiKTeX are installed]
+
+* Using the 'pdf' option and 'external' option will conflict suggest using 
+  one or the other or possibly have a default when this is the case
+  [If pgf is TRUE it supercedes everything else]
+
+* output pdf size when included in document is refined by textwidth by 
+  default, need a feature to add the 'width' and 'height' and possibly and 
+  other option 'scale' the `\includegraphics[width=,height=,scale=]{file}`
+  [Use `\usepackage[nogin]{Sweave}`]
+
+* Vignette does not compile with R CMD {check,build,install} because file 
+  is not normal Sweave (Solution for the final document may just be to 
+  save images separately and create a standard Sweave file). For now 
+  vignette moved to `inst/doc/src`.
+  [Elaborate make file created in `inst/misc/vignette-source`, run make then 
+  make cleanforbuild before uploading]
+
+
+##DONE (old TODO items):
+
+* pgf graphics device.
+  [Started tikzDevice on r-forge]
+
+* Figure out how to fill the environment variable $R_HOME in 
+  exec/pgfSweave
+  [Irrelevant now, see next item]
+
+* Figure out how to call the script exec/pgfSweave when using R CMD 
+  pgfSweave
+  [Used a Makevars file to create symlink in $RHOME/bin, basically 
+  a much simplified version of Charlie's method]
+
+* Documentation has a boatload of warnings under R CMD check.
+
+* Figure out how to call eps2pgf.jar with the rJava package 
+  [scrapped for now, write a pgf graphics device!]
+
+* Determine the limitations R CMD pgfSweave.
+  [shell script pgfSweave in exec/ will do the same but using R CMD is not 
+  possible withoud a rewrite of the Rcmd script]
+
+* Determine if pgf 2.00 contains the external capabilities so that can be 
+  stated in the vignette and the documentation.
+  [must use at least pgf 2.00]