[Pgfsweave-commits] r17 - in pkg: . R inst/doc inst/doc/figs
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Aug 6 18:45:11 CEST 2010
Author: cameronbracken
Date: 2010-08-06 18:45:11 +0200 (Fri, 06 Aug 2010)
New Revision: 17
Added:
pkg/.gitignore
pkg/README.md
Removed:
pkg/README
Modified:
pkg/ChangeLog
pkg/DESCRIPTION
pkg/NEWS
pkg/R/pgfSweaveDriver.R
pkg/inst/doc/figs/fig-normalSweave.pdf
pkg/inst/doc/figs/fig-pgfSweave-hist.pdf
pkg/inst/doc/figs/fig-pgfSweave-tikz-hist.pdf
pkg/inst/doc/pgfSweave-example.pdf
pkg/inst/doc/pgfSweave.pdf
Log:
Version 1.0.6
Merge branch 'master' into r-forge-local
Conflicts:
ChangeLog
inst/doc/figs/fig-normalSweave.pdf
inst/doc/figs/fig-pgfSweave-hist.pdf
inst/doc/figs/fig-pgfSweave-tikz-hist.pdf
inst/doc/pgfSweave-example.pdf
inst/doc/pgfSweave.pdf
Added: pkg/.gitignore
===================================================================
--- pkg/.gitignore (rev 0)
+++ pkg/.gitignore 2010-08-06 16:45:11 UTC (rev 17)
@@ -0,0 +1 @@
+.DS_Store
Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog 2010-04-08 19:09:45 UTC (rev 16)
+++ pkg/ChangeLog 2010-08-06 16:45:11 UTC (rev 17)
@@ -1,7 +1,23 @@
-commit 64c157148d2582140afaddc553fa2da931eb6c03
+commit 7a8a931fc425c3816a2c48146432b21445e382d0
+Author: cameronbracken <cameronbracken at edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
+Date: Thu Apr 8 19:09:45 2010 +0000
+
+ Merge master branch
+
+ git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/pgfsweave/pkg@16 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
+
+ ChangeLog | 93 ++++++++++++++++++++++++++---
+ inst/doc/figs/fig-normalSweave.pdf | Bin 5510 -> 3083 bytes
+ inst/doc/figs/fig-pgfSweave-hist.pdf | Bin 17643 -> 17539 bytes
+ inst/doc/figs/fig-pgfSweave-tikz-hist.pdf | Bin 28962 -> 29032 bytes
+ inst/doc/pgfSweave-example.pdf | Bin 88108 -> 88361 bytes
+ inst/doc/pgfSweave.pdf | Bin 294220 -> 294023 bytes
+ 6 files changed, 84 insertions(+), 9 deletions(-)
+
+commit ba711ef7b690c45161572e5d413c78f39913d239
Merge: 9e9787a d8ec864
-Author: cameronbracken <cameron.bracken at gmail.com>
-Date: Thu Apr 8 13:05:15 2010 -0600
+Author: cameronbracken <cameronbracken at edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
+Date: Thu Apr 8 19:09:40 2010 +0000
Merge branch 'master' into r-forge-local
@@ -10,6 +26,8 @@
inst/doc/figs/fig-normalSweave.pdf
inst/doc/pgfSweave-example.pdf
inst/doc/pgfSweave.pdf
+
+ git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/pgfsweave/pkg@15 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
commit d8ec8642a7296225877f14a40098fdb43cf92cb8
Author: cameronbracken <cameron.bracken at gmail.com>
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2010-04-08 19:09:45 UTC (rev 16)
+++ pkg/DESCRIPTION 2010-08-06 16:45:11 UTC (rev 17)
@@ -1,8 +1,8 @@
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 at gmail.com> and Charlie Sharpsteen <source at sharpsteen.net>
Maintainer: Cameron Bracken <cameron.bracken at gmail.com>
Depends: stashR, filehash, tikzDevice, cacheSweave, getopt
Modified: pkg/NEWS
===================================================================
--- pkg/NEWS 2010-04-08 19:09:45 UTC (rev 16)
+++ pkg/NEWS 2010-08-06 16:45:11 UTC (rev 17)
@@ -1,6 +1,12 @@
-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
--------------------------
* Unlabeled code chunks are now allowed
Modified: pkg/R/pgfSweaveDriver.R
===================================================================
--- pkg/R/pgfSweaveDriver.R 2010-04-08 19:09:45 UTC (rev 16)
+++ pkg/R/pgfSweaveDriver.R 2010-08-06 16:45:11 UTC (rev 17)
@@ -163,8 +163,82 @@
shellfile
}
+## preserve comments in the R code and at the same time make them 'well-formatted'
+tidy.source = function(source = "clipboard", keep.comment = TRUE,
+ keep.blank.line = TRUE, begin.comment, end.comment, output = TRUE,
+ width.cutoff = 60L, ...) {
+ if (source == "clipboard" && Sys.info()["sysname"] == "Darwin") {
+ source = pipe("pbpaste")
+ }
+ tidy.block = function(block.text) {
+ exprs = base::parse(text = block.text)
+ n = length(exprs)
+ res = character(n)
+ for (i in 1:n) {
+ dep = paste(base::deparse(exprs[i], width.cutoff),
+ collapse = "\n")
+ res[i] = substring(dep, 12, nchar(dep) - 1)
+ }
+ return(res)
+ }
+ text.lines = readLines(source, warn = FALSE)
+ if (keep.comment) {
+ identifier = function() paste(sample(LETTERS), collapse = "")
+ if (missing(begin.comment))
+ begin.comment = identifier()
+ if (missing(end.comment))
+ end.comment = identifier()
+ text.lines = gsub("^[[:space:]]+|[[:space:]]+$", "",
+ text.lines)
+ while (length(grep(sprintf("%s|%s", begin.comment, end.comment),
+ text.lines))) {
+ begin.comment = identifier()
+ end.comment = identifier()
+ }
+ head.comment = substring(text.lines, 1, 1) == "#"
+ if (any(head.comment)) {
+ text.lines[head.comment] = gsub("\"", "'", text.lines[head.comment])
+ text.lines[head.comment] = sprintf("%s=\"%s%s\"",
+ begin.comment, text.lines[head.comment], end.comment)
+ }
+ blank.line = text.lines == ""
+ if (any(blank.line) & keep.blank.line)
+ text.lines[blank.line] = sprintf("%s=\"%s\"", begin.comment,
+ end.comment)
+ text.mask = tidy.block(text.lines)
+ text.tidy = gsub(sprintf("%s = \"|%s\"", begin.comment,
+ end.comment), "", text.mask)
+ }
+ else {
+ text.tidy = text.mask = tidy.block(text.lines)
+ begin.comment = end.comment = ""
+ }
+ if (output)
+ cat(paste(text.tidy, collapse = "\n"), "\n", ...)
+ invisible(list(text.tidy = text.tidy, text.mask = text.mask,
+ begin.comment = begin.comment, end.comment = end.comment))
+}
+## to replace the default parse()
+parse2 = function(text, ...) {
+ zz = tempfile()
+ enc = options(encoding = "native.enc")
+ writeLines(text, zz)
+ tidy.res = tidy.source(zz, out = FALSE, keep.blank.line = FALSE)
+ options(enc)
+ unlink(zz)
+ options(begin.comment = tidy.res$begin.comment, end.comment = tidy.res$end.comment)
+ base::parse(text = tidy.res$text.mask)
+}
+## to replace the default deparse()
+deparse2 = function(expr, ...) {
+ gsub(sprintf("%s = \"|%s\"", getOption("begin.comment"),
+ getOption("end.comment")), "", base::deparse(expr, ...))
+}
+
+
+
## This function is essentially unchanged from the original Sweave
## version, except I compute the digest of the entire chunk, write out
## information to the map file, and use 'cacheSweaveEvalWithOpt'
@@ -217,7 +291,7 @@
SweaveHooks(options, run=TRUE)
## parse entire chunk block
- chunkexps <- try(parse(text=chunk), silent=TRUE)
+ chunkexps <- try(parse2(text=chunk), silent=TRUE)
RweaveTryStop(chunkexps, options)
## [CWB] Create a DB entry which is simply the digest of the text of
@@ -278,7 +352,7 @@
leading <- leading - 1
}
} else {
- dce <- deparse(ce, width.cutoff = 0.75*getOption("width"))
+ dce <- deparse2(ce, width.cutoff = 0.75*getOption("width"))
leading <- 1
}
if(object$debug)
Deleted: pkg/README
===================================================================
--- pkg/README 2010-04-08 19:09:45 UTC (rev 16)
+++ pkg/README 2010-08-06 16:45:11 UTC (rev 17)
@@ -1,126 +0,0 @@
-$Id$
-
-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]
Added: pkg/README.md
===================================================================
--- pkg/README.md (rev 0)
+++ pkg/README.md 2010-08-06 16:45:11 UTC (rev 17)
@@ -0,0 +1,128 @@
+#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]
Modified: pkg/inst/doc/figs/fig-normalSweave.pdf
===================================================================
--- pkg/inst/doc/figs/fig-normalSweave.pdf 2010-04-08 19:09:45 UTC (rev 16)
+++ pkg/inst/doc/figs/fig-normalSweave.pdf 2010-08-06 16:45:11 UTC (rev 17)
@@ -2,10 +2,10 @@
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===================================================================
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Modified: pkg/inst/doc/figs/fig-pgfSweave-tikz-hist.pdf
===================================================================
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pgfsweave -r 17
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