[Sciviews-commits] r505 - komodo/SciViews-K/udl komodo/SciViews-K-dev/.komodotools/Project pkg/svSweave/R pkg/svSweave/inst/asciidoc pkg/svSweave/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 2 19:54:24 CET 2013
Author: phgrosjean
Date: 2013-01-02 19:54:24 +0100 (Wed, 02 Jan 2013)
New Revision: 505
Removed:
komodo/SciViews-K-dev/.komodotools/Project/R_2-way_communication_test.komodotool
komodo/SciViews-K-dev/.komodotools/Project/R_test_for_connection_with_R.komodotool
komodo/SciViews-K-dev/.komodotools/Project/R_toggle_status.komodotool
komodo/SciViews-K-dev/.komodotools/Project/Restart_Komodo.komodotool
komodo/SciViews-K-dev/.komodotools/Project/Smart_highlight.komodotool
komodo/SciViews-K-dev/.komodotools/Project/Test_R_completion.komodotool
komodo/SciViews-K-dev/.komodotools/Project/restartSocketServer.komodotool
komodo/SciViews-K-dev/.komodotools/Project/startSocketServer.komodotool
komodo/SciViews-K-dev/.komodotools/Project/stopSocketServer.komodotool
Modified:
komodo/SciViews-K/udl/wiki2R.udl
komodo/SciViews-K/udl/wikilex.udl
pkg/svSweave/R/asciidoc.R
pkg/svSweave/inst/asciidoc/asciidoc.conf
pkg/svSweave/man/Rdoc.Rd
Log:
Further work on the Rdoc process in svSweave and on wiki chunks highlighters in SciViews-K
Modified: komodo/SciViews-K/udl/wiki2R.udl
===================================================================
--- komodo/SciViews-K/udl/wiki2R.udl 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K/udl/wiki2R.udl 2013-01-02 18:54:24 UTC (rev 505)
@@ -36,7 +36,7 @@
family markup
state in_wiki_default_start_of_line:
-/[!]<<.*>>="/ : paint(upto, M_CDATA), paint(include, M_TAGNAME), => IN_M_WIKI_STOP
+/<<.*>>="/ : paint(upto, M_CDATA), paint(include, M_TAGNAME), => IN_M_WIKI_STOP
state IN_M_WIKI_STOP:
/^/ : paint(upto, M_CDATA), => IN_SSL_DEFAULT
Modified: komodo/SciViews-K/udl/wikilex.udl
===================================================================
--- komodo/SciViews-K/udl/wikilex.udl 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K/udl/wikilex.udl 2013-01-02 18:54:24 UTC (rev 505)
@@ -42,7 +42,27 @@
state in_wiki_default_start_of_line:
#'{{{' : paint(upto, M_DEFAULT), paint(include, M_TAGNAME), => in_wiki_triple_brace_start
-'#': paint(upto, M_CDATA), paint(include, M_COMMENT), => in_wiki_have_comment
+'##': paint(upto, M_CDATA), paint(include, M_COMMENT), => in_wiki_have_comment
+
+# This is for the item list
+'* ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'** ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'*** ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'**** ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'***** ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+
+# This is for the numbered list
+'. ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'.. ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'... ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'.... ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'..... ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+/[1-9]\. /: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+/[a-z]\. /: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+/[A-Z]\. /: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+/[ivx]+\) /: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+/[IVX]+\) /: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+
'===== ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_finish_header
'==== ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_finish_header
'=== ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_finish_header
@@ -50,32 +70,40 @@
'= ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_finish_header
'.': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_finish_header
-# This is for the item list
-'* ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
-'** ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
-'*** ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
-'**** ': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+# This is for special paragraphs
+'NOTE:': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'IMPORTANT:': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'WARNING:': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'CAUTION:': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+'TIP:': paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_on_line
+# Everything between [] on the beginning of a line, or with name:: is tag
+/\[.*\]$/: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_start_of_line
+/[a-zA-Z][a-zA-Z _0-9]+::$/: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_start_of_line
+
/./: redo, => in_wiki_default_on_line
state in_wiki_finish_header:
/$/ : paint(upto, M_PI), paint(include, M_PI), => in_wiki_default_start_of_line
#/\s+/ : #stay
-'#': paint(upto, M_PI), paint(include, M_COMMENT), => in_wiki_have_comment
+'##': paint(upto, M_PI), paint(include, M_COMMENT), => in_wiki_have_comment
#/./: redo, => in_wiki_default_on_line
state in_wiki_default_on_line:
-'#': paint(upto, M_CDATA), paint(include, M_COMMENT), => in_wiki_have_comment
+'##': paint(upto, M_CDATA), paint(include, M_COMMENT), => in_wiki_have_comment
+# Line break with +
+/ \+$/: paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_default_start_of_line
/$/: => in_wiki_default_start_of_line
"//" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_italic
"**" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_bold
+"++" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_monospaced
"'''''" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_q5
"'''" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_q3
"''" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_q2
"~~" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_tilde2
-"^" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_caret
+"^^" : paint(upto, M_CDATA), paint(include, M_TAGNAME), => in_wiki_caret
'{{{' : paint(upto, M_CDATA), => in_wiki_brace_3
/!'+/: #stay
@@ -134,6 +162,10 @@
/!\*+/: #stay
"**" : paint(upto, M_TAGNAME), paint(include, M_TAGNAME), => in_wiki_default_on_line
+state in_wiki_monospaced:
+/!\++/: #stay
+"++" : paint(upto, CSL_STRING), paint(include, M_TAGNAME), => in_wiki_default_on_line
+
state in_wiki_q5:
/!'+/: #stay
"'''''" : paint(upto, M_STRING), paint(include, M_TAGNAME), => in_wiki_default_on_line
@@ -148,8 +180,8 @@
/!~+/: #stay
"~~" : paint(upto, M_STRING), paint(include, M_TAGNAME), => in_wiki_default_on_line
state in_wiki_caret:
-/!^/: #stay
-"^" : paint(upto, M_STRING), paint(include, M_TAGNAME), => in_wiki_default_on_line
+/!^+/: #stay
+"^^" : paint(upto, M_STRING), paint(include, M_TAGNAME), => in_wiki_default_on_line
#}}}
################ End of State Handling ################
Deleted: komodo/SciViews-K-dev/.komodotools/Project/R_2-way_communication_test.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/R_2-way_communication_test.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/R_2-way_communication_test.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,19 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "R: 2-way communication test",
- "language": "JavaScript",
- "trigger_enabled": false,
- "value": [
- "sv.cmdout.clear();",
- "sv.cmdout.append(sv.rconn.evalAtOnce(\"cat('R<-Komodo : OK', '\\n')\").trim());",
- "sv.rconn.eval(\"cat(koCmd('\\\"R->Komodo : OK\\\"', type='j'))\", function(res) {",
- "\tsv.cmdout.append(res.trim());",
- "}, \"h\");"
- ],
- "trigger": "trigger_postopen",
- "rank": 100,
- "version": "1.0.7",
- "async": false,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/disconnect.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/R_test_for_connection_with_R.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/R_test_for_connection_with_R.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/R_test_for_connection_with_R.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,22 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "R: test for connection with R",
- "language": "JavaScript",
- "trigger_enabled": false,
- "value": [
- "var RConnectionSuccess = sv.rconn.testRAvailability();",
- "sv.command.updateRStatus(RConnectionSuccess);",
- "",
- "var ltb = document.getElementById(\"leftTabBox\");",
- "var rotp = document.getElementById(\"sciviews_robjects_tabpanel\");",
- "var rot = document.getElementById(\"sciviews_robjects_tab\");",
- "rotp.disabled = rot.disabled = !RConnectionSuccess;",
- ""
- ],
- "trigger": "trigger_postopen",
- "rank": 100,
- "version": "1.0.7",
- "async": false,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/connect.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/R_toggle_status.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/R_toggle_status.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/R_toggle_status.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,15 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "R: toggle status",
- "language": "JavaScript",
- "trigger_enabled": 0,
- "rank": 100,
- "trigger": "trigger_postopen",
- "value": [
- "sv.command.updateRStatus()"
- ],
- "version": "1.0.7",
- "async": 0,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/bug_go.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/Restart_Komodo.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/Restart_Komodo.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/Restart_Komodo.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,35 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "Restart Komodo",
- "language": "JavaScript",
- "trigger_enabled": false,
- "value": [
- "const Cc = Components.classes;",
- "const Ci = Components.interfaces;",
- "",
- "function restartApp() {",
- " // Notify all windows that an application quit has been requested.",
- " var os = Cc[\"@mozilla.org/observer-service;1\"].",
- " getService(Ci.nsIObserverService);",
- " var cancelQuit = Cc[\"@mozilla.org/supports-PRBool;1\"].",
- " createInstance(Ci.nsISupportsPRBool);",
- " os.notifyObservers(cancelQuit, \"quit-application-requested\", null);",
- "",
- " // Something aborted the quit process.",
- " if (cancelQuit.data)",
- " return;",
- "",
- " var as = Cc[\"@mozilla.org/toolkit/app-startup;1\"].",
- " getService(Ci.nsIAppStartup);",
- " as.quit(Ci.nsIAppStartup.eRestart | Ci.nsIAppStartup.eAttemptQuit);",
- "}",
- "",
- "restartApp();"
- ],
- "trigger": "trigger_postopen",
- "rank": 100,
- "version": "1.0.7",
- "async": false,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/application_lightning.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/Smart_highlight.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/Smart_highlight.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/Smart_highlight.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,27 +0,0 @@
-{
- "keyboard_shortcut": "Ctrl+1",
- "name": "Smart highlight",
- "language": "JavaScript",
- "trigger_enabled": 0,
- "rank": 100,
- "trigger": "trigger_postopen",
- "value": [
- "var findSvc = Components.classes[\"@activestate.com/koFindService;1\"]",
- " .getService(Components.interfaces.koIFindService);",
- "",
- "findSvc.options.patternType = findSvc.options.FOT_SIMPLE;",
- "",
- "var context = Components.classes[\"@activestate.com/koFindContext;1\"]",
- " .createInstance(Components.interfaces.koIFindContext);",
- "context.type = context.FCT_CURRENT_DOC;",
- "",
- "findSvc.options.matchWord = true;",
- "findSvc.options.displayInFindResults2 = true;",
- "Find_FindAll(self, context, ko.interpolate.getWordUnderCursor(), null,",
- "\t\t\t function() {});"
- ],
- "version": "1.0.7",
- "async": 1,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/rainbow.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/Test_R_completion.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/Test_R_completion.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/Test_R_completion.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,20 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "Test: R completion",
- "language": "JavaScript",
- "trigger_enabled": false,
- "value": [
- "var svuSvc = Components.classes[\"@sciviews.org/svUtils;1\"].getService(Components.interfaces.svIUtils);",
- "try {",
- " svuSvc.complete(\"\")",
- "} catch(e) {",
- " sv.cmdout.append(e)",
- "}"
- ],
- "trigger": "trigger_postopen",
- "rank": 100,
- "version": "1.0.7",
- "async": false,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/bug.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/restartSocketServer.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/restartSocketServer.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/restartSocketServer.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,16 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "restartSocketServer",
- "language": "JavaScript",
- "trigger_enabled": false,
- "value": [
- "sv.rconn.restartSocketServer();",
- ""
- ],
- "trigger": "trigger_postopen",
- "rank": 100,
- "version": "1.0.7",
- "async": false,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/server_lightning.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/startSocketServer.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/startSocketServer.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/startSocketServer.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,16 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "startSocketServer",
- "language": "JavaScript",
- "trigger_enabled": false,
- "value": [
- "sv.cmdout.append(sv.rconn.startSocketServer());",
- ""
- ],
- "trigger": "trigger_postopen",
- "rank": 100,
- "version": "1.0.7",
- "async": false,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/server_go.png"
-}
\ No newline at end of file
Deleted: komodo/SciViews-K-dev/.komodotools/Project/stopSocketServer.komodotool
===================================================================
--- komodo/SciViews-K-dev/.komodotools/Project/stopSocketServer.komodotool 2013-01-02 11:34:43 UTC (rev 504)
+++ komodo/SciViews-K-dev/.komodotools/Project/stopSocketServer.komodotool 2013-01-02 18:54:24 UTC (rev 505)
@@ -1,15 +0,0 @@
-{
- "keyboard_shortcut": "",
- "name": "stopSocketServer",
- "language": "JavaScript",
- "trigger_enabled": false,
- "value": [
- "sv.rconn.stopSocketServer();"
- ],
- "trigger": "trigger_postopen",
- "rank": 100,
- "version": "1.0.7",
- "async": false,
- "type": "macro",
- "icon": "chrome://famfamfamsilk/skin/icons/server_delete.png"
-}
\ No newline at end of file
Modified: pkg/svSweave/R/asciidoc.R
===================================================================
--- pkg/svSweave/R/asciidoc.R 2013-01-02 11:34:43 UTC (rev 504)
+++ pkg/svSweave/R/asciidoc.R 2013-01-02 18:54:24 UTC (rev 505)
@@ -5,15 +5,14 @@
## in the initialisation block (second line) of the SciViews Rdoc!
Rdoc <- function (title, author, email, revnumber = NULL, revdate = NULL,
-revremark = NULL, copyright = "cc-by", encoding = "utf-8", lang = "en",
+revremark = NULL, copyright = "cc-by", encoding = "UTF-8", lang = "en",
pagetitle = NULL, description = "SciViews Rdoc", keywords = NULL,
-format = "html", theme = "SciViews", max.width = 720, width = "100%",
-toc = c("top", "side", "manual", "none"), toc.title = NULL, toclevels = 3,
+theme = "SciViews", max.width = 640, width = NULL,
+toc = c("top", "side", "manual", "none"), toc.title = NULL, toclevels = 2,
numbered = TRUE, data.uri = TRUE, frame = "topbot", grid = "rows",
align = "center", halign = "center", pygments = FALSE, slidefontsizeadjust = 0,
-SweaveOpts = list(prefix.string = "figures/fig", width = 7.2, height = 7.2, pdf = TRUE),
-SweaveInit = { options(width = 90); options(SweaveHooks = list(fig = function()
-par(col.lab = "#434366", col.main = "#434366")))}
+SweaveInit = { options(width = 80); options(SweaveHooks = list(fig = function()
+par(col.lab = "#434366", col.main = "#434366"))) }
)
{
## Format AsciiDocsciidoc attributes
@@ -28,7 +27,6 @@
stop("You must provide a title for your Rdoc")
## Idem for author, but allow several names
- ## TODO: Allows for first middle last and must replace space inside items by _
author <- paste(author, collapse = ", ")
if (!length(author))
stop("You must provide at least one author for your Rdoc")
@@ -40,14 +38,14 @@
## Compute revision field: [revnumber], [revdate]:\n[revremark]
if (length(revnumber))
- revfield <- paste0(revfield, ", ") else revfield <- ""
+ revfield <- paste0("v", revnumber, ", ") else revfield <- ""
if (!length(revdate)) revdate <- format(Sys.Date(), format = "%B %Y")
revfield <- paste0(revfield, revdate)
if (length(revremark))
revfield <- paste0(revfield, ":\n", paste(revremark, collapse = "\n"))
## Create the Asciidoc header
- header <- paste0("!\"\n",
+ header <- paste0(
"= ", title, "\n",
author, " <", email, ">\n",
revfield, "\n"
@@ -68,7 +66,6 @@
header <- asciiAttr(header, "title", pagetitle)
header <- asciiAttr(header, "description", description)
header <- asciiAttr(header, "keywords", keywords)
- header <- asciiAttr(header, "format", format)
header <- asciiAttr(header, "theme", theme)
header <- asciiAttr(header, "max-width", max.width)
header <- asciiAttr(header, "width", width)
@@ -91,31 +88,16 @@
header <- asciiAttr(header, "halign", halign)
if (isTRUE(pygments)) header <- paste0(header, ":pygments:\n")
header <- asciiAttr(header, "slidefontsizeadjust", slidefontsizeadjust)
+ header <- paste0(header, "\n") # End of header section
- ## Rework SweaveOpts
- if (length(SweaveOpts)) {
- if (!is.list(SweaveOpts))
- stop("'SweaveOpts' must be a named list or NULL")
- SweaveOpts <- paste(names(SweaveOpts), SweaveOpts, sep = " = ",
- collapse = ", ")
- header <- paste0(header,
- "\n//////////\n",
- "\\SweaveOpts{", SweaveOpts, "}\n",
- "//////////\n"
- )
- } else header <- paste0(header, "\n") # End of header section
-
- ## Add SweaveInit chunk here... or !<<>>="
- ## TODO: allow for either require(SciViews), or a def of `!`
- if (is.null(SweaveInit)) SweaveInit <- "" else
- SweaveInit <- paste(deparse(substitute(SweaveInit)), collapse = "\n")
- header <- paste0(header,
- "!<<init, echo = FALSE, results = hide>>=\"\n",
- "## SweaveInit code\n",
- SweaveInit,
- "\n## More initialization\n",
- "require(\"SciViews\")\n"
- )
+ ## Run SweaveInit now
+ SweaveInit
+ ## More initialization
+ req <- base::require
+ req("SciViews", quietly = TRUE, warn.conflicts = FALSE)
+
+ ## Print the header and return it invisibly
+ if (!interactive()) cat(header)
invisible(header)
}
@@ -163,11 +145,9 @@
## Check that the SciViews Rdoc file starts with #!
if (!grepl("^#!", Rscript[1]))
stop("Incorrect SciViews Rdoc (it must start with #!)")
+ ## Change this line into an init code chunk
+ Rscript[1] <- "<<init, echo=FALSE, results=ascii>>="
- ## TODO: change this into a header constructor from svSweave::Rdoc()
- ## Locate the header, which is one or several lines of initialization R code
- inHeader <- 2:(lstart[1] - 1)
-
## Doc chunks are lines where cstart > cend
inDoc <- cstart > cend
@@ -180,15 +160,14 @@
## Convert comments blocks using four or more #### by ////
Rscript[inDoc] <- gsub("^####+$", "////", Rscript[inDoc])
- ## Convert line comments using ## by //
- Rscript[inDoc] <- gsub("^##", "//", Rscript[inDoc])
+ ## Convert line comments using ## by __
+ Rscript[inDoc] <- gsub("^##", "__", Rscript[inDoc])
## Replace all doc chunk starters (!") by @
Rscript[start] <- "@"
- ## Replace all doc chunk ends (!<<.*>>=") by the same without leading !
- ## and trailing "
- Rscript[end] <- sub('!^(.*>>=)"[ \t]*$', "\\1", Rscript[end])
+ ## Replace all doc chunk ends (<<.*>>=") by the same without trailing "
+ Rscript[end] <- sub('^(.*>>=)"[ \t]*$', "\\1", Rscript[end])
## Polish the end of the document...
lastDoc <- lend[length(lend)]
@@ -202,16 +181,6 @@
Rscript <- c(Rscript, "@")
}
- ## Now, rework the header lines to be compatible with a .Rnw file
- ## Place initialization R code in a 'echo = FALSE' code chunk just before
- ## the first current code chunck
- firstChunk <- lend[1]
- header <- paste(Rscript[inHeader], collapse = "\n")
- Rscript[firstChunk] <- paste("<<echo = FALSE>>=\n", header,
- "\n@\n\n", Rscript[firstChunk], sep = "")
- ## Now eliminate the header from the script
- Rscript <- Rscript[-c(1, inHeader, max(inHeader) + 1)]
-
## Write result to the RnwFile
## TODO: check encoding of .Rnw file on all platforms
# utf8conv <- function(x) gsub("<U\\+([0-9A-F]{4})>","\\\\u\\1", x)
@@ -274,7 +243,7 @@
## Do we show the resulting Html file in the current browser at the end?
## By default YES, unless in non-interactive mode
- if (missing(show.it)) show.it <- getOption("Rdoc.showIt", interactive())
+ if (missing(show.it)) show.it <- getOption("Rdoc.show.it", interactive())
## Do we keep intermediary .Rnw and .txt files? Default to FALSE
if (missing(keep.RnwFile))
@@ -339,8 +308,10 @@
if (!isTRUE(keep.TxtFile)) unlink(TxtFile)
})
- ## Sweave this document...
- Asciidoc(RnwFile2, encoding = encoding) # This should create the TxtFile
+ ## Sweave this document... (creating the TxtFile)
+ ## Note: we change some default options here!
+ Asciidoc(RnwFile2, encoding = encoding, prefix.string = "figures/fig",
+ width = 7.2, height = 7.2, png = TRUE, jpeg = FALSE, format = "png")
if (!file.exists(TxtFile))
stop("Problems while creating the Asciidoc file (", TxtFile, ")")
@@ -380,6 +351,9 @@
## A function to run an a SciViews Rdoc file, and that looks at the #!
## line to determine what function to run for compiling the final document
+ ## If RdocFile is missing, try to get it from option or the command line
+ if (missing(RdocFile)) RdocFile <- .RdocFile()
+
## Check RdocFile
if (missing(RdocFile) || !length(RdocFile)) stop("No file provided")
if (!file.exists(RdocFile)) stop("RdocFile not found (", RdocFile, ")")
Modified: pkg/svSweave/inst/asciidoc/asciidoc.conf
===================================================================
--- pkg/svSweave/inst/asciidoc/asciidoc.conf 2013-01-02 11:34:43 UTC (rev 504)
+++ pkg/svSweave/inst/asciidoc/asciidoc.conf 2013-01-02 18:54:24 UTC (rev 505)
@@ -73,7 +73,7 @@
[quotes]
# The order is important, quotes are processed in conf file order.
**=#strong
-*=strong
+**=strong
``|''=doublequoted
'=emphasis
`|'=singlequoted
@@ -86,13 +86,13 @@
+++=#unquoted
$$=#unquoted
++=#monospaced
-+=monospaced
-__=#emphasis
-_=emphasis
+++=monospaced
+//=#emphasis
+//=emphasis
\##=#unquoted
\#=unquoted
-^=#superscript
-~=#subscript
+^^=#superscript
+~~=#subscript
[specialwords]
emphasizedwords=
@@ -276,7 +276,7 @@
endif::no-inline-literal[]
# Inline comment.
-(?mu)^[\\]?//(?P<passtext>[^/].*|)$=comment[specialcharacters]
+(?mu)^[\\]?__(?P<passtext>[^/].*|)$=comment[specialcharacters]
# Default (catchall) inline macro is not implemented so there is no ambiguity
# with previous definition that could result in double substitution of escaped
@@ -294,7 +294,7 @@
^'{3,}$=#ruler
^<{3,}$=#pagebreak
-^//(?P<passtext>[^/].*|)$=#comment[specialcharacters]
+^__(?P<passtext>[^/].*|)$=#comment[specialcharacters]
# Implemented in HTML backends.
[unfloat-blockmacro]
Modified: pkg/svSweave/man/Rdoc.Rd
===================================================================
--- pkg/svSweave/man/Rdoc.Rd 2013-01-02 11:34:43 UTC (rev 504)
+++ pkg/svSweave/man/Rdoc.Rd 2013-01-02 18:54:24 UTC (rev 505)
@@ -14,15 +14,14 @@
\usage{
Rdoc(title, author, email, revnumber = NULL, revdate = NULL,
-revremark = NULL, copyright = "cc-by", encoding = "utf-8", lang = "en",
-pagetitle = NULL, description = "SciViews Rdoc", keywords = NULL,
-format = "html", theme = "SciViews", max.width = 720, width = "100\%",
-toc = c("top", "side", "manual", "none"), toc.title = NULL, toclevels = 3,
-numbered = TRUE, data.uri = TRUE, frame = "topbot", grid = "rows",
-align = "center", halign = "center", pygments = FALSE, slidefontsizeadjust = 0,
-SweaveOpts = list(prefix.string = "figures/fig", width = 7.2, height = 7.2,
- pdf = TRUE), SweaveInit = { options(width = 90); options(SweaveHooks =
- list(fig = function() par(col.lab = "#434366", col.main = "#434366")))}
+ revremark = NULL, copyright = "cc-by", encoding = "UTF-8", lang = "en",
+ pagetitle = NULL, description = "SciViews Rdoc", keywords = NULL,
+ theme = "SciViews", max.width = 640, width = NULL,
+ toc = c("top", "side", "manual", "none"), toc.title = NULL, toclevels = 2,
+ numbered = TRUE, data.uri = TRUE, frame = "topbot", grid = "rows",
+ align = "center", halign = "center", pygments = FALSE, slidefontsizeadjust = 0,
+ SweaveInit = { options(width = 80); options(SweaveHooks = list(fig = function()
+ par(col.lab = "#434366", col.main = "#434366"))) }
)
}
@@ -44,7 +43,7 @@
cc-by, John Does, 2013, or just the first part (cc-by) and the author and
year will be appended automatically. If \code{NULL}, it is omitted. }
\item{encoding}{ a character string with the encoding of your SciViews Rdoc.
- It is not advised to change from the default, utf-8. Make sure you save
+ It is not advised to change from the default, UTF-8. Make sure you save
your document in UTF-8 encoding before you process it! }
\item{lang}{ the (main) language used in your SciViews Rdoc. By default, it is
English (en), but Asciidoc can also use de, el, es, fr, hu, it, nl, pt, ru
@@ -55,11 +54,7 @@
to use in the head section of the HTML document. If \code{NULL}, it is
omitted. }
\item{keywords}{ a character string with one or more keywords to use in the
- head section of the HTML document. If \code{NULL}, it is omitted. }
- \item{format}{ a character string with the format into which the Rdoc should
- be converted. By default (\code{"html"}), an HTML document is compiled. Valid
- formats are: html, html4, html5, slidy, slidy2, wordpress, docbook,
- docbook45 and latex (see the AsciiDoc man page). }
+ head section of the HTML document. If \code{NULL}, it is omitted. }
\item{theme}{ the theme to use with the Asciidoc HTML file. By default, it is
\code{"SciViews"}. }
\item{max.width}{ the maximum width of the page, in pixels or in percent.
@@ -76,7 +71,7 @@
default (Table of Contents, or its translation in the main language of the
SciViews Rdoc) is used. }
\item{toclevels}{ how deep in title levels should the table of contents be
- generated (1, 2, 3 or 4)? By default, it is 3. }
+ generated (1, 2, 3 or 4)? By default, it is 2. }
\item{numbered}{ should the titles be numbered (\code{TRUE}, by default), or
not (\code{FALSE})? }
\item{data.uri}{ should figures, scripts and styles be embedded in the main
@@ -93,8 +88,6 @@
\code{FALSE} by default. }
\item{slidefontsizeadjust}{ adjustment of font size in slidy and slidy2
documents. }
- \item{SweaveOpts}{ options for Sweave. A reasonable default is provided.
- See ?sweave. }
\item{SweaveInit}{ code to be run in the init code chunk, related to sweave.
Reasonable defaults are provided. See ?sweave. }
}
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