[Sciviews-commits] r262 - komodo/SciViews-K/content/js komodo/SciViews-K/defaults pkg/SciViews/inst/doc pkg/svMisc
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat May 1 23:02:06 CEST 2010
Author: phgrosjean
Date: 2010-05-01 23:02:05 +0200 (Sat, 01 May 2010)
New Revision: 262
Added:
komodo/SciViews-K/defaults/R reference (0.9.15).kpz
komodo/SciViews-K/defaults/SciViews-K (0.9.15).kpz
komodo/SciViews-K/defaults/svGUI_0.9-47.tar.gz
komodo/SciViews-K/defaults/svGUI_0.9-47.zip
komodo/SciViews-K/defaults/svMisc_0.9-57.tar.gz
komodo/SciViews-K/defaults/svMisc_0.9-57.zip
pkg/SciViews/inst/doc/WhySciViews.lyx
Removed:
komodo/SciViews-K/defaults/R reference (0.9.12).kpz
komodo/SciViews-K/defaults/SciViews-K (0.9.12).kpz
komodo/SciViews-K/defaults/svGUI_0.9-46.tar.gz
komodo/SciViews-K/defaults/svGUI_0.9-46.zip
komodo/SciViews-K/defaults/svMisc_0.9-56.tar.gz
komodo/SciViews-K/defaults/svMisc_0.9-56.zip
Modified:
komodo/SciViews-K/content/js/commands.js
komodo/SciViews-K/content/js/pref-R.js
komodo/SciViews-K/content/js/sciviews.js
komodo/SciViews-K/defaults/SciViews_0.9-1.tar.gz
komodo/SciViews-K/defaults/SciViews_0.9-1.zip
komodo/SciViews-K/defaults/svSocket_0.9-48.tar.gz
komodo/SciViews-K/defaults/svSocket_0.9-48.zip
komodo/SciViews-K/defaults/svStart.R
pkg/svMisc/NEWS
Log:
Remove 00LOCK file on Komodo startup + install new R packages for version 0.9-15.
Note: changes recently made on R Interpreter selection and startup have broken everything and I cannot start R any more from SciViews-K/Komodo on my Mac (neither R terminal, nor R/R64.app)!!! Cannot solve this today, but must be solved URGENTLY!
Modified: komodo/SciViews-K/content/js/commands.js
===================================================================
--- komodo/SciViews-K/content/js/commands.js 2010-05-01 15:04:33 UTC (rev 261)
+++ komodo/SciViews-K/content/js/commands.js 2010-05-01 21:02:05 UTC (rev 262)
@@ -108,9 +108,11 @@
// trim just in case
var path = sv.tools.strings.trim(sv.prefs.getString("svRDefaultInterpreter"));
- if (!path || (sv.tools.file.exists(path) != sv.tools.file.TYPE_FILE)) {
+ // PhG: on Mac OS X, R.app is not a file, but a dir!!!
+ //if (!path || (sv.tools.file.exists(path) != sv.tools.file.TYPE_FILE)) {
+ if (!path || (sv.tools.file.exists(path) < 1)) {
if(ko.dialogs.okCancel(
- sv.translate("Default R interpreter is not set in " +
+ sv.translate("Default R interpreter is not (correctly) set in " +
"Preferences. Do you want to do it now?"),
"OK", null, "SciViews-K") == "OK") {
prefs_doGlobalPrefs("svPrefRItem", true);
Modified: komodo/SciViews-K/content/js/pref-R.js
===================================================================
--- komodo/SciViews-K/content/js/pref-R.js 2010-05-01 15:04:33 UTC (rev 261)
+++ komodo/SciViews-K/content/js/pref-R.js 2010-05-01 21:02:05 UTC (rev 262)
@@ -117,12 +117,12 @@
function OnPreferencePageOK(prefset) {
prefset = parent.hPrefWindow.prefset;
- //prefset.setStringPref("svRDefaultInterpreter",
- // document.getElementById("svRDefaultInterpreter")
- // .value);
- //prefset.setStringPref("svRApplication",
- // document.getElementById('svRApplication')
- // .selectedItem.getAttribute("data"));
+ prefset.setStringPref("svRDefaultInterpreter",
+ document.getElementById("svRDefaultInterpreter")
+ .value);
+ prefset.setStringPref("svRApplication",
+ document.getElementById('svRApplication')
+ .selectedItem.getAttribute("data"));
prefset.setStringPref("svRApplicationId",
document.getElementById('svRApplication')
.selectedItem.id);
Modified: komodo/SciViews-K/content/js/sciviews.js
===================================================================
--- komodo/SciViews-K/content/js/sciviews.js 2010-05-01 15:04:33 UTC (rev 261)
+++ komodo/SciViews-K/content/js/sciviews.js 2010-05-01 21:02:05 UTC (rev 262)
@@ -794,7 +794,7 @@
// Message prompting for removing old or duplicated toolboxes
sv.alert(sv.translate("Toolboxes %S have been added. " +
- "To avoid conflicts, you should remove any previous versions." +
+ "To avoid conflicts, you should remove any previous or duplicated versions." +
" To update the toolbars, restart Komodo.", "\"" +
tbxs.join("\" and \"") + "\""));
@@ -854,3 +854,22 @@
// Ensure we check the toolbox is installed once the extension is loaded
//addEventListener("load", function() {setTimeout (sv.checkToolbox, 5000) }, false);
//addEventListener("load", sv.checkToolbox, false);
+
+// PhG: there is a bug in the way R starts: at the begining, a dummy '00LOCK'
+// file is created that prevents to config another R process as SciViews socket
+// server. Everytime svStart.R is run, it looks if this '00LOCK' file exists,
+// and if it finds it, it refuses to configure R as a socket server.
+// OK, but what happens if the config of the SciViews R server fails in the
+// middle of the process? Well, '00LOCK' is not removed, and it is not possible
+// any more to configre R (automatically) as a SciViews socket server.
+// To cope with this problem, I make sure '00LOCK' is deleted everytime the
+// SciViews-K plugin is loaded in Komodo Edit. That way, restarting Komodo
+// solves the problem of the remaining '00LOCK' file, in case R failed...
+var lockfilepath = sv.tools.file.path("ProfD", "extensions",
+"sciviewsk at sciviews.org", "defaults", "00LOCK");
+var file = Components.classes["@mozilla.org/file/local;1"].
+ createInstance(Components.interfaces.nsILocalFile);
+try {
+ file.initWithPath(lockfilepath);
+ file.remove(true);
+} catch(e) { }
\ No newline at end of file
Deleted: komodo/SciViews-K/defaults/R reference (0.9.12).kpz
===================================================================
(Binary files differ)
Added: komodo/SciViews-K/defaults/R reference (0.9.15).kpz
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/R reference (0.9.15).kpz
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Deleted: komodo/SciViews-K/defaults/SciViews-K (0.9.12).kpz
===================================================================
(Binary files differ)
Added: komodo/SciViews-K/defaults/SciViews-K (0.9.15).kpz
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/SciViews-K (0.9.15).kpz
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: komodo/SciViews-K/defaults/SciViews_0.9-1.tar.gz
===================================================================
(Binary files differ)
Modified: komodo/SciViews-K/defaults/SciViews_0.9-1.zip
===================================================================
(Binary files differ)
Deleted: komodo/SciViews-K/defaults/svGUI_0.9-46.tar.gz
===================================================================
(Binary files differ)
Deleted: komodo/SciViews-K/defaults/svGUI_0.9-46.zip
===================================================================
(Binary files differ)
Added: komodo/SciViews-K/defaults/svGUI_0.9-47.tar.gz
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/svGUI_0.9-47.tar.gz
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: komodo/SciViews-K/defaults/svGUI_0.9-47.zip
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/svGUI_0.9-47.zip
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Deleted: komodo/SciViews-K/defaults/svMisc_0.9-56.tar.gz
===================================================================
(Binary files differ)
Deleted: komodo/SciViews-K/defaults/svMisc_0.9-56.zip
===================================================================
(Binary files differ)
Added: komodo/SciViews-K/defaults/svMisc_0.9-57.tar.gz
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/svMisc_0.9-57.tar.gz
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: komodo/SciViews-K/defaults/svMisc_0.9-57.zip
===================================================================
(Binary files differ)
Property changes on: komodo/SciViews-K/defaults/svMisc_0.9-57.zip
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Modified: komodo/SciViews-K/defaults/svSocket_0.9-48.tar.gz
===================================================================
(Binary files differ)
Modified: komodo/SciViews-K/defaults/svSocket_0.9-48.zip
===================================================================
(Binary files differ)
Modified: komodo/SciViews-K/defaults/svStart.R
===================================================================
--- komodo/SciViews-K/defaults/svStart.R 2010-05-01 15:04:33 UTC (rev 261)
+++ komodo/SciViews-K/defaults/svStart.R 2010-05-01 21:02:05 UTC (rev 262)
@@ -6,8 +6,8 @@
# TODO: also use value in koDebug to debug server from within R!
"svStart" <-
-function (minVersion = c(R = "2.6.0", svMisc = "0.9-56",
-svSocket = "0.9-48", svGUI = "0.9-46", ellipse = "0.3-5", SciViews = "0.9-1"),
+function (minVersion = c(R = "2.6.0", svMisc = "0.9-57",
+svSocket = "0.9-48", svGUI = "0.9-47", ellipse = "0.3-5", SciViews = "0.9-1"),
# NOTE: minVersion is now also used as a list of required packages
remote.repos = "http://R-Forge.R-project.org",
pkg.dir = ".",
Added: pkg/SciViews/inst/doc/WhySciViews.lyx
===================================================================
--- pkg/SciViews/inst/doc/WhySciViews.lyx (rev 0)
+++ pkg/SciViews/inst/doc/WhySciViews.lyx 2010-05-01 21:02:05 UTC (rev 262)
@@ -0,0 +1,320 @@
+#LyX 1.6.5 created this file. For more info see http://www.lyx.org/
+\lyxformat 345
+\begin_document
+\begin_header
+\textclass article
+\begin_preamble
+% \VignetteIndexEntry{Correlation tutorial}
+%\VignettePackage{SciViews}
+
+% provides caption formatting
+\usepackage[labelfont=bf, tableposition=top]{caption}
+\pdfimageresolution 96
+\end_preamble
+\use_default_options false
+\begin_modules
+sweave
+\end_modules
+\language english
+\inputencoding auto
+\font_roman palatino
+\font_sans berasans
+\font_typewriter beramono
+\font_default_family default
+\font_sc true
+\font_osf false
+\font_sf_scale 100
+\font_tt_scale 100
+
+\graphics default
+\float_placement tbh
+\paperfontsize default
+\spacing single
+\use_hyperref true
+\pdf_title "SciViews - Why SciViews?"
+\pdf_author "Philippe Grosjean"
+\pdf_subject "Rationates for the SciViews scientific suite"
+\pdf_keywords "Data analysis, Statistics, Reporting, Word processing, Slideshow"
+\pdf_bookmarks true
+\pdf_bookmarksnumbered false
+\pdf_bookmarksopen false
+\pdf_bookmarksopenlevel 1
+\pdf_breaklinks true
+\pdf_pdfborder false
+\pdf_colorlinks true
+\pdf_backref false
+\pdf_pdfusetitle true
+\pdf_quoted_options "linkcolor=blue, urlcolor=blue, citecolor=blue, pagecolor=blue"
+\papersize a4paper
+\use_geometry false
+\use_amsmath 0
+\use_esint 0
+\cite_engine natbib_authoryear
+\use_bibtopic false
+\paperorientation portrait
+\secnumdepth 3
+\tocdepth 3
+\paragraph_separation indent
+\defskip medskip
+\quotes_language english
+\papercolumns 1
+\papersides 2
+\paperpagestyle default
+\bullet 0 0 17 -1
+\bullet 1 0 15 -1
+\bullet 2 0 8 -1
+\bullet 3 0 9 -1
+\tracking_changes false
+\output_changes false
+\author ""
+\author ""
+\end_header
+
+\begin_body
+
+\begin_layout Title
+Why SciViews?
+\end_layout
+
+\begin_layout Author
+Ph.
+ Grosjean <phgrosjean at sciviews.org>
+\end_layout
+
+\begin_layout Part
+Introduction
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+setkeys{Gin}{width=1.00
+\backslash
+textwidth}
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout R-Opts
+keep.source = TRUE, pdf = TRUE, eps = FALSE
+\end_layout
+
+\begin_layout Standard
+There are several office suites, including (at least) a word processor,
+ a spreadsheet, a sildeshow presentation program, and tools to draw pictures
+ and write mathematic equations.
+ Microsoft Office and OpenOffice seem to fulfill the needs of most users.
+ Son why should a
+\emph on
+scientific
+\emph default
+ user need a different suite for his work? Well, we believe that those general
+ purpose office suites are not well adapted for scientists.
+ They need something radically different.
+ The
+\begin_inset Flex SciViews
+status collapsed
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+ Scientific Suite aims to provide those tools to them.
+ In short:
+\end_layout
+
+\begin_layout Itemize
+The spreadsheet paradigm is very popular to do calculations and graphs on
+ tabulated data.
+ However, there are many reasons why this paradigm is not efficient, error-prone
+ and barely fits the needs for more serious data analysis, as most scientists
+ need.
+ We believe that
+\begin_inset Flex R
+status collapsed
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+, together with a carefully ciseled GUI is a much more adequate general
+ purpose calculation and plotting engine.
+ That is why the
+\begin_inset Flex SciViews
+status collapsed
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+ Scientific Suite is build around
+\begin_inset Flex R
+status collapsed
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+, and reserves so little space to a spreadsheet program.
+\end_layout
+
+\begin_layout Itemize
+The Word Processor and its WYSIWYG
+\begin_inset Foot
+status open
+
+\begin_layout Plain Layout
+WYSIWYG = What You See Is What You Get.
+\end_layout
+
+\end_inset
+
+ paradigm makes a poor document preparation environment for scientific litteratu
+re like papers and books.
+ Scientific litterature is highly structured text and it does not fit well
+ with the loose presentation of text elements in a WYSIWYG program.
+ Also, Word Processors tend to be relatively poor and inefficient in mathematic
+ formula typesetting and in bibliographic references formatting.
+ LaTeX text processing system is much, much more adequate, but it requires
+ to
+\begin_inset Quotes eld
+\end_inset
+
+program
+\begin_inset Quotes erd
+\end_inset
+
+ your text, and not all scientists are ready to take thay way.
+ A good alternative is the WYSIWIM paradigm of LyX.
+ WYSIWIM stands for
+\begin_inset Quotes eld
+\end_inset
+
+What You See Is What You Mean
+\begin_inset Quotes erd
+\end_inset
+
+.
+ Here, you don't see the code hidden in you rich text formatted document,
+ but you don't see the final result either.
+ You see, instead, a very suggestive representation of the
+\emph on
+structure
+\emph default
+ of your text (titles, paragraphs, equations, etc.).
+ You can then concentrate on both the content and the structure, and deleguate
+ to the very capable LaTeX system that LyX uses to typeset its documents
+ on the background to produce the final result.
+ Thzt WYSIWIM approach, together with the possibility to include results,
+ tables and graphs from
+\begin_inset Flex R
+status collapsed
+
+\begin_layout Plain Layout
+
+\end_layout
+
+\end_inset
+
+ computations directly in the LyX document using the
+\series bold
+Sweave
+\series default
+ mechanism makes is a very suitable alternative to more traditional Word
+ Processing programs for scientists.
+\end_layout
+
+\begin_layout Itemize
+The WYSIWYG slideshow programs, like PowerPoint, are not well suitable for
+ scientists for the same reasons (mainly, a lack of correct formula typesetting
+ and the inhability to include code to produce calculation results, tables
+ or graphs directly in the presentation).
+ Here, we go back to LyX and Sweave again, but together with the excellent
+
+\series bold
+Beamer
+\series default
+ LaTeX package.
+\end_layout
+
+\begin_layout Standard
+...
+\end_layout
+
+\begin_layout Section
+Processing data, analysing data
+\end_layout
+
+\begin_layout Standard
+Scientist study facts, and they mostly convert these facts into numbers
+ by mean of measurements in a given context (observation or experiment).
+ They, then, manipulate these numbers in different ways...
+\end_layout
+
+\begin_layout R-Chunk
+\begin_inset listings
+inline false
+status open
+
+\begin_layout Plain Layout
+
+<<eval = FALSE>>=
+\end_layout
+
+\begin_layout Plain Layout
+
+options(para.port = 1) # If your card is connected to LPT1
+\end_layout
+
+\begin_layout Plain Layout
+
+para(c(T,F,F,T,F,F,F,T)) # Channels 1, 4, 8 ON, the others OFF
+\end_layout
+
+\begin_layout Plain Layout
+
+para(change = FALSE) # Read current state
+\end_layout
+
+\begin_layout Plain Layout
+
+para(c(F,F,F,F,F,F,F,F)) # All channels OFF
+\end_layout
+
+\begin_layout Plain Layout
+
+para(change = FALSE) # Make sure current state is changed
+\end_layout
+
+\begin_layout Plain Layout
+
+@
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Chapter
+xxx
+\end_layout
+
+\end_body
+\end_document
Property changes on: pkg/SciViews/inst/doc/WhySciViews.lyx
___________________________________________________________________
Added: svn:executable
+ *
Modified: pkg/svMisc/NEWS
===================================================================
--- pkg/svMisc/NEWS 2010-05-01 15:04:33 UTC (rev 261)
+++ pkg/svMisc/NEWS 2010-05-01 21:02:05 UTC (rev 262)
@@ -2,6 +2,8 @@
== Changes in svMisc 0.9-57
+* Small changes to objList() (now look at objects in their correct environment).
+
* A bug in descArgs() with R >= 2.10 did not allowed to gest arguments
description for functions using the '...' argument. Thanks to Diego Zardetto
for pointing this bug.
More information about the Sciviews-commits
mailing list