[Pgfsweave-commits] r30 - in pkg: . R inst/doc inst/doc/figs inst/example inst/misc/vignette-src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 6 00:51:52 CEST 2011
Author: cameronbracken
Date: 2011-04-06 00:51:50 +0200 (Wed, 06 Apr 2011)
New Revision: 30
Added:
pkg/inst/doc/figs/fig-pgfSweave-tikz-hist.tikz
pkg/inst/example/pgfSweave-xelatex-example.Rnw
Modified:
pkg/ChangeLog
pkg/DESCRIPTION
pkg/NEWS
pkg/R/pgfSweave.R
pkg/R/pgfSweaveDriver.R
pkg/R/utilities.R
pkg/R/zzz.R
pkg/inst/doc/figs/fig-normalSweave.pdf
pkg/inst/doc/figs/fig-pgfSweave-hist.pgf
pkg/inst/doc/figs/fig-pgfSweave-tikz-hist.pdf
pkg/inst/doc/pgfSweave-example.pdf
pkg/inst/doc/pgfSweave.Rnw
pkg/inst/doc/pgfSweave.pdf
pkg/inst/doc/pgfSweave_hans.pdf
pkg/inst/misc/vignette-src/Makefile
pkg/inst/misc/vignette-src/pgfSweave-vignette-source.Rnw
Log:
Version 1.2.1
Modified: pkg/ChangeLog
===================================================================
--- pkg/ChangeLog 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/ChangeLog 2011-04-05 22:51:50 UTC (rev 30)
@@ -1,3 +1,162 @@
+commit e1b1d11fee5419f1747636461a5af7f46248826f
+Merge: 629df4f 5536f8f
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 16:26:46 2011 -0600
+
+ Merge branch 'rel-patch2'
+
+commit 629df4f8c9925ccf1a970d10552153ff26123ced
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 16:26:06 2011 -0600
+
+ Only try to call make if the makefile exists
+
+ R/pgfSweave.R | 12 ++++++------
+ 1 files changed, 6 insertions(+), 6 deletions(-)
+
+commit 5536f8f46e781bb2e8193dcbcbf2265b20612e34
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 16:15:56 2011 -0600
+
+ Apply rel2.patch
+
+ R/pgfSweaveDriver.R | 23 +++++++++++++++++++++--
+ 1 files changed, 21 insertions(+), 2 deletions(-)
+
+commit d6159fa723942cc7ad361290114e555404430d2f
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 16:05:14 2011 -0600
+
+ Slightly change message for re-run external chunks
+
+ R/pgfSweaveDriver.R | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+commit edc5f628bb174fe19ae84884194863d7a1a41557
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 15:50:57 2011 -0600
+
+ Update NEWS
+
+ NEWS | 5 +++--
+ 1 files changed, 3 insertions(+), 2 deletions(-)
+
+commit ff49d90675be7118283af2120c93499cf9c164cf
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 15:48:58 2011 -0600
+
+ XeLaTeX example, see the warning in the file for directions on how to get around the bug in pgf
+
+ inst/example/pgfSweave-xelatex-example.Rnw | 72 ++++++++++++++++++++++++++++
+ 1 files changed, 72 insertions(+), 0 deletions(-)
+
+commit 2d57ccae18b14134aead7851da22cf8fade8d34a
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 14:55:03 2011 -0600
+
+ Fix the internal caching layer so that external graphics are now properly recreated only when the chunk has changed; also fixes the external library dependency feature
+
+ R/pgfSweaveDriver.R | 21 +++++++++++----------
+ R/utilities.R | 2 +-
+ 2 files changed, 12 insertions(+), 11 deletions(-)
+
+commit 5fc6321fe08d009b07dc89314ab1f8dda0cb7d6f
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Tue Apr 5 13:24:53 2011 -0600
+
+ Add chunk options 'width' and 'height' to the chunk digest; when chages are made to these options but not the chunk code itself, still regenerate the graphic
+
+ R/utilities.R | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+commit 7aa7eb28373f601b1d65d09e7b1c2b543c1d3a5a
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Mon Apr 4 14:45:24 2011 -0600
+
+ Add encoding to vignette for R 2.13
+
+ ChangeLog | 52 ++++++
+ inst/doc/figs/fig-normalSweave.pdf | Bin 12749 -> 12524 bytes
+ inst/doc/figs/fig-pgfSweave-hist.pgf | 186 +++++++++++---------
+ inst/doc/figs/fig-pgfSweave-tikz-hist.pdf | Bin 28614 -> 28559 bytes
+ inst/doc/figs/fig-pgfSweave-tikz-hist.tikz | 70 ++++----
+ inst/doc/pgfSweave-example-tex.in | 10 +-
+ inst/doc/pgfSweave-example.pdf | Bin 78284 -> 76347 bytes
+ inst/doc/pgfSweave.Rnw | 2 +
+ inst/doc/pgfSweave.pdf | Bin 327561 -> 288573 bytes
+ .../vignette-src/pgfSweave-vignette-source.Rnw | 2 +
+ 10 files changed, 190 insertions(+), 132 deletions(-)
+
+commit 354e7f790cbf28be8fee88dbc4ee61a349770182
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Mon Apr 4 14:44:32 2011 -0600
+
+ Update News
+
+ NEWS | 10 ++++++++++
+ 1 files changed, 10 insertions(+), 0 deletions(-)
+
+commit 69700eb5e3bfbef6d743d1d719a5b663c799bc00
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Sun Apr 3 21:02:43 2011 -0600
+
+ Remove null device code since it can cause problems with grid graphics
+
+ R/pgfSweaveDriver.R | 5 -----
+ 1 files changed, 0 insertions(+), 5 deletions(-)
+
+commit 1db2157b7f913a011f23c9ac8912b7b265ce983c
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Sun Apr 3 17:21:07 2011 -0600
+
+ Bump version number, recompile vignette to only depend on PGF 2.00
+
+ ChangeLog | 51 ++++++
+ DESCRIPTION | 2 +-
+ inst/doc/figs/fig-normalSweave.pdf | Bin 2960 -> 12749 bytes
+ inst/doc/figs/fig-pgfSweave-hist.pgf | 188 +++++++++-----------
+ inst/doc/figs/fig-pgfSweave-tikz-hist.pdf | Bin 28559 -> 28614 bytes
+ inst/doc/figs/fig-pgfSweave-tikz-hist.tikz | 74 ++++----
+ inst/doc/pgfSweave-example-tex.in | 2 -
+ inst/doc/pgfSweave-example.pdf | Bin 78061 -> 78284 bytes
+ inst/doc/pgfSweave.Rnw | 21 +--
+ inst/doc/pgfSweave.pdf | Bin 281287 -> 327561 bytes
+ inst/misc/vignette-src/Makefile | 5 +-
+ .../vignette-src/pgfSweave-vignette-source.Rnw | 10 +-
+ 12 files changed, 191 insertions(+), 162 deletions(-)
+
+commit 21154a3acba563ecd2cb2586bb02dfad7acf0acb
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Sun Apr 3 17:20:13 2011 -0600
+
+ Allow package to be installed if PGF 2.10 is not available but issue
+ message at startup.
+
+ R/zzz.R | 9 ++++++---
+ 1 files changed, 6 insertions(+), 3 deletions(-)
+
+commit 1443cf949766b3dcd598a6d94ef799e1abc74c6d
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Sun Apr 3 17:17:55 2011 -0600
+
+ Dont include \tikzexternalfiledependsonfile command because it caused
+ figures to get recompiled every time. Only put in list and make command
+ the first time.
+
+ R/pgfSweaveDriver.R | 23 ++++++++++++++---------
+ 1 files changed, 14 insertions(+), 9 deletions(-)
+
+commit 103005f9ced1a9e07599f5625a1bd6456441473c
+Author: cameronbracken <cameron.bracken at gmail.com>
+Date: Sun Apr 3 17:16:20 2011 -0600
+
+ Do not run (pdf)latex initially when makefile exists
+
+ R/pgfSweave.R | 22 ++-
+ inst/doc/figs/fig-pgfSweave-hist.pgf | 255 ++++++++++++++++++++++++++++
+ inst/doc/figs/fig-pgfSweave-tikz-hist.tikz | 110 ++++++++++++
+ 3 files changed, 381 insertions(+), 6 deletions(-)
+
commit 224c98c100ecaeb90085b30e5978e3736f97e6f1
Author: cameronbracken <cameron.bracken at gmail.com>
Date: Wed Mar 23 17:32:21 2011 -0600
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/DESCRIPTION 2011-04-05 22:51:50 UTC (rev 30)
@@ -1,8 +1,8 @@
Package: pgfSweave
Type: Package
Title: Quality speedy graphics compilation and caching with Sweave
-Version: 1.2.0
-Date: 2011-01-16
+Version: 1.2.1
+Date: 2011-05-05
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, highlight, optparse, formatR
Modified: pkg/NEWS
===================================================================
--- pkg/NEWS 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/NEWS 2011-04-05 22:51:50 UTC (rev 30)
@@ -1,6 +1,20 @@
Please see the README.md file for development info
--------------------------
+Version 1.2.1 - 2011-04-03
+--------------------------
+* [NEW] If PGF 2.10 is not available, issue a startup message but still load
+ the package (So the package can go on CRAN). PGF 2.10 is still
+ required to compile .tex file produced with pgfSweave
+* [NEW] Remove null device code which could cause problems with grid graphics
+* [NEW] Example using xelatex for external graphics
+* [NEW] Chunk options `relwidth' and `relheight' for scaling figures relative
+ to the `width' and `height' options (thanks to Fabrice Rossi for the
+ patch)
+* [CHANGED] Fix the internal caching of external graphics, it now works as
+ expected and can save significant time
+
+--------------------------
Version 1.2.0 - 2011-02-21
--------------------------
* [NEW] Use the tikz externalization library instead of the pgf backend. This
Modified: pkg/R/pgfSweave.R
===================================================================
--- pkg/R/pgfSweave.R 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/R/pgfSweave.R 2011-04-05 22:51:50 UTC (rev 30)
@@ -7,27 +7,37 @@
#if available compile pgf graphics
if(compile.tex){
+ changefile <- '.FigureChunkChanged'
+
#Strip the extension
fn <- tools::file_path_sans_ext(file)
+ makefile <- paste(fn,".makefile",sep='')
# set initial calls to latex or pdflatex to generate makefile and
# dependency lists
cmd <-
- if(is.null(match.call()$pdf))
+ if(pdf)
+ Sys.getenv("PDFLATEX","pdflatex")
+ else
Sys.getenv("LATEX","latex")
- else
- Sys.getenv("PDFLATEX","pdflatex")
# Initial call to pdflatex or latex
- system(paste(cmd,fn))
-
+ if(!file.exists(makefile)){
+ message(paste('Not regenerating makefile for externalization,',
+ 'if your figures have changed, remove',makefile,
+ 'and recompile.'))
+ system(paste(cmd,fn))
+ }
+
# call make to externalize graphics
make <- Sys.which('make')
- if(file.access(make, 1) == 0)
- system(paste(make," -j ",np," -f ",fn,".makefile",sep=""))
- else
- warning('`make` is not available, graphics will not be externalized.')
-
+ if(file.access(make, 1) == 0){
+ if(file.exists(makefile))
+ system(paste(make," -j ",np," -f ",makefile,sep=""))
+ }else{
+ warning('`make` is not available, graphics will not be externalized.')
+ }
+
if(!graphics.only){
#run texi2dvi on the tex file
tools::texi2dvi(paste(fn,'tex',sep='.'), pdf = pdf, ...)
Modified: pkg/R/pgfSweaveDriver.R
===================================================================
--- pkg/R/pgfSweaveDriver.R 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/R/pgfSweaveDriver.R 2011-04-05 22:51:50 UTC (rev 30)
@@ -28,7 +28,7 @@
runcode = pgfSweaveRuncode,
writedoc = pgfSweaveWritedoc,
finish = utils::RweaveLatexFinish,
- checkopts = utils::RweaveLatexOptions
+ checkopts = pgfSweaveOptions
)
}
@@ -61,6 +61,8 @@
out$options[["sanitize"]] <- sanitize
out$options[["highlight"]] <- ifelse(echo,highlight,FALSE)
out$options[["tidy"]] <- tidy
+ out$options[["relwidth"]] <- 1
+ out$options[["relheight"]] <- 1
out[["haveHighlightSyntaxDef"]] <- FALSE
out[["haveRealjobname"]] <- FALSE
## end [CWB]
@@ -74,15 +76,27 @@
out[["srcfileName"]] <-paste(tools::file_path_sans_ext(file), "tex", sep='')
out[["jobname"]] <- basename(tools::file_path_sans_ext(file))
######################################################################
-
- # Avoids creation of Rplots.pdf
- options(device = function(...) {
- .Call("R_GD_nullDevice", PACKAGE = "grDevices")
- })
-
+
out
}
+ # This function checks the options. Most of the checks is delegated to
+ # utils::RweaveLatexOptions, expect for the rel* options
+pgfSweaveOptions <- function(options)
+{
+ options.norel <- options
+ options.norel[c("relwidth","relheight")] <- NULL
+ options.norel <- utils::RweaveLatexOptions(options.norel)
+ for(opt in c("relwidth","relheight")) {
+ if(!is.null(options[[opt]])) {
+ options.norel[opt] <- as.numeric(options[[opt]])
+ }
+ }
+ options.norel$width <- options.norel$width * options.norel$relwidth
+ options.norel$height <- options.norel$height * options.norel$relheight
+ options.norel
+}
+
# This function checks for the \usepackage{Sweave} line and the
# \tikzexternalize line
pgfSweaveWritedoc <- function(object, chunk)
@@ -91,12 +105,15 @@
if(length(grep("\\usepackage[^\\}]*Sweave.*\\}", chunk)))
object$havesty <- TRUE
+
+ if(is.null(object$havetikzexternalize)){
+ object$havetikzexternalize <-
+ if(length(grep("\\tikzexternalize.*^", chunk)))
+ TRUE
+ else
+ FALSE
+ }
- havetikzexternalize <- FALSE
- if(length(grep("\\tikzexternalize.*^", chunk)))
- havetikzexternalize <- TRUE
-
-
if(!object$havesty){
begindoc <- "^[[:space:]]*\\\\begin\\{document\\}"
which <- grep(begindoc, chunk)
@@ -110,7 +127,7 @@
}
# add tikzexternalize if it doesnt exist
- if(!havetikzexternalize){
+ if(!object$havetikzexternalize){
# add the lines after the \usepackage{tikz} statement
which <- grep("^[[:space:]]*\\\\usepackage\\{.*tikz.*\\}", chunk)
if(length(which)){
@@ -170,7 +187,7 @@
opts <- sub(paste(".*", object$syntax$docopt, ".*", sep=""),
"\\1", chunk[pos[1L]])
object$options <- utils:::SweaveParseOptions(opts, object$options,
- utils:::RweaveLatexOptions)
+ pgfSweaveOptions)
if (isTRUE(object$options$concordance)
&& !object$haveconcordance) {
savelabel <- object$options$label
@@ -498,13 +515,14 @@
thisline <- thisline + 1
}
- chunkChanged <-
- if( options$cache )
- hasChunkChanged(chunk,chunkprefix,options)
- else
- TRUE
-
if(options$fig && options$eval){
+
+ chunkChanged <-
+ if( options$external )
+ hasChunkChanged(chunk,chunkprefix,options)
+ else
+ TRUE
+ if(chunkChanged & options$external) cat('(Re)Running External Chunk:',options$label,'\n')
if(options$eps & !options$pgf & !options$tikz){
# Still apply graphics caching to postscript device
@@ -606,6 +624,7 @@
})
grDevices::dev.off()
if(inherits(err, "try-error")) stop(err)
+
}
}
@@ -619,6 +638,7 @@
linesout[thisline + 1] <- srcline
thisline <- thisline + 1
+
}
# Write the includegraphics command for eps or pdf
Modified: pkg/R/utilities.R
===================================================================
--- pkg/R/utilities.R 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/R/utilities.R 2011-04-05 22:51:50 UTC (rev 30)
@@ -28,7 +28,7 @@
# caching may not be used but use the caching directory anyway
cachedir <- getCacheDir()
- chunkDigest <- digest(chunk)
+ chunkDigest <- digest(list(chunk[1:length(chunk)],options$width,options$height))
dbName <- makeChunkDatabaseName(cachedir, options, chunkDigest)
# Create 'stashR' database if it does not exist
Modified: pkg/R/zzz.R
===================================================================
--- pkg/R/zzz.R 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/R/zzz.R 2011-04-05 22:51:50 UTC (rev 30)
@@ -9,7 +9,7 @@
stop(gettextf("'%s' package required", pkg))
}
- requirePGFVersionOrDie("2.10")
+ requirePGFVersion("2.10")
}
.onAttach <- function(lib, pkg) {
@@ -17,7 +17,7 @@
stop("'utils' package required to use 'Sweave'")
}
-requirePGFVersionOrDie <- function(req.version="2.10"){
+requirePGFVersion <- function(req.version="2.10"){
texDir <- tempdir()
cwd <- getwd()
@@ -60,7 +60,10 @@
setwd(cwd)
if(compareVersion(version,req.version) < 0)
- stop(paste("PGF >=",req.version,"is required to use pgfSweave, you are using version",match))
+ packageStartupMessage(paste("PGF >=",req.version,
+ "is required to use pgfSweave, you are using version",match,
+ "\n\tYou can use pgfSweave but you may not be able to compile",
+ "\n\tdocuments produced by pgfSweave, please update if possible."))
else
packageStartupMessage(paste('pgfSweave: Using PGF Version',match))
Modified: pkg/inst/doc/figs/fig-normalSweave.pdf
===================================================================
--- pkg/inst/doc/figs/fig-normalSweave.pdf 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/inst/doc/figs/fig-normalSweave.pdf 2011-04-05 22:51:50 UTC (rev 30)
@@ -2,10 +2,10 @@
%âãÏÓ\r
1 0 obj
<<
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-/ModDate (D:20110323174358)
+/CreationDate (D:20110405163136)
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/Title (R Graphics Output)
-/Producer (R 2.12.1)
+/Producer (R 2.12.2)
/Creator (R)
>>
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@@ -47,43 +47,35 @@
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BT
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-/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 102.91 Tm (1000) Tj
+/F2 1 Tf 0.00 12.00 -12.00 0.00 41.76 103.57 Tm (1000) Tj
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@@ -91,28 +83,26 @@
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@@ -159,14 +149,14 @@
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trailer
<<
/Size 11
@@ -174,5 +164,5 @@
/Root 2 0 R
>>
startxref
-2785
+2541
%%EOF
Modified: pkg/inst/doc/figs/fig-pgfSweave-hist.pgf
===================================================================
--- pkg/inst/doc/figs/fig-pgfSweave-hist.pgf 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/inst/doc/figs/fig-pgfSweave-hist.pgf 2011-04-05 22:51:50 UTC (rev 30)
@@ -1,4 +1,4 @@
-% Created by Eps2pgf 0.7.0 (build on 2008-08-24) on Wed Mar 23 17:43:59 MDT 2011
+% Created by Eps2pgf 0.7.0 (build on 2008-08-24) on Tue Apr 05 16:31:37 MDT 2011
\begin{pgfpicture}
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@@ -41,78 +41,71 @@
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@@ -127,119 +120,112 @@
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\pgfpathclose
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Modified: pkg/inst/doc/figs/fig-pgfSweave-tikz-hist.pdf
===================================================================
--- pkg/inst/doc/figs/fig-pgfSweave-tikz-hist.pdf 2011-03-23 23:50:37 UTC (rev 29)
+++ pkg/inst/doc/figs/fig-pgfSweave-tikz-hist.pdf 2011-04-05 22:51:50 UTC (rev 30)
@@ -1,21 +1,24 @@
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[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pgfsweave -r 30
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