Merge branch 'ja_knitr_sweave_updates'

This merges updates from Koji Yokota, and adapts the ctests
accordingly.

development/autotests/ignoredTests

@@ -54,6 +54,11 @@ export/.*/zh_CN/.*texF
 # see also INVERTED.TODO_export/export/latex/ja_wrong_auto_encoding_(dvi|pdf(|3)).*
 # For a discussion of alternatives for Japanese with LaTeX , see also
 # http://www.preining.info/blog/2014/12/writing-japanese-in-latex-part-1-introduction/
+# 
+# Exception: ja knitr.lyx and sweave.lyx support only XeLaTeX with system fonts
+# because they use the "bxjsarticle" class
+!export/.*/ja/(knitr|sweave).*_(lyx.*|xhtml|pdf4_systemF)
+export/.*/ja/(knitr|sweave).*
 export/.*/ja/.*_(pdf[245]|dvi3).*
 
 # These files are not expected to compile, they use math-macros

lib/examples/ja/knitr.lyx

@@ -4,7 +4,7 @@
 \begin_header
 \save_transient_properties true
 \origin /systemlyxdir/examples/ja/
-\textclass article
+\textclass bxjsarticle
 \use_default_options true
 \begin_modules
 knitr
@@ -12,14 +12,14 @@ knitr
 \maintain_unincluded_children false
 \language japanese
 \language_package default
-\inputencoding auto
+\inputencoding utf8-platex
 \fontencoding global
 \font_roman "palatino" "default"
 \font_sans "lmss" "default"
 \font_typewriter "lmtt" "default"
 \font_math "auto" "auto"
 \font_default_family default
-\use_non_tex_fonts false
+\use_non_tex_fonts true
 \font_sc false
 \font_osf false
 \font_sf_scale 100 100
@@ -210,6 +210,25 @@ knitr
 ソース文書へのリンクがあります。
 \end_layout
 
+\begin_layout Standard
+\SpecialChar LyX
+ 2.3以降、
+\series bold
+knitr
+\series default
+を使ってコンパイルするためには
+\family sans
+設定\SpecialChar menuseparator
+ファイル処理\SpecialChar menuseparator
+変換子
+\family default
+で
+\emph on
+needauth
+\emph default
+変換子の使用を可能にする必要があります。
+\end_layout
+
 \begin_layout Standard
 
 \series bold
@@ -220,12 +239,22 @@ knitr
 \end_layout
 
 \begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<show-off>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+show-off
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -243,11 +272,6 @@ df=data.frame(y=rnorm(100), x=1:100)
 summary(lm(y~x, data=df))
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 

lib/examples/ja/sweave.lyx

@@ -4,7 +4,7 @@
 \begin_header
 \save_transient_properties true
 \origin /systemlyxdir/examples/ja/
-\textclass jarticle
+\textclass bxjsarticle
 \begin_preamble
 %% maxwidth is the original width if it's less than linewidth
 %% otherwise use linewidth (to make sure the graphics do not exceed the margin)
@@ -31,7 +31,7 @@ sweave
 \font_typewriter "lmtt" "default"
 \font_math "auto" "auto"
 \font_default_family default
-\use_non_tex_fonts false
+\use_non_tex_fonts true
 \font_sc false
 \font_osf false
 \font_sf_scale 100 100
@@ -303,12 +303,22 @@ bin
 \end_layout
 
 \begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<where-is-R-bin,eval=FALSE>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+where-is-R-bin,eval=FALSE
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -316,11 +326,6 @@ status open
 R.home('bin')
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -355,12 +360,22 @@ Sweave.sty
 \end_layout
 
 \begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<sweave-sty,eval=FALSE>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+sweave-sty,eval=FALSE
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -368,11 +383,6 @@ status open
 file.path(R.home('share'), 'texmf', 'tex', 'latex')
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -463,12 +473,22 @@ useFancyQuotes
 \end_layout
 
 \begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<setup, keep.source=TRUE>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+setup, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -481,14 +501,28 @@ status open
 options(width = 70, useFancyQuotes = FALSE, digits = 4)
 \end_layout
 
-\begin_layout Plain Layout
+\end_inset
+
 
-@
 \end_layout
 
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
 \begin_layout Plain Layout
 
-<<sweave-manual, eval=FALSE, keep.source=TRUE>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+sweave-manual, eval=FALSE, keep.source=TRUE
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -501,9 +535,23 @@ options(width = 70, useFancyQuotes = FALSE, digits = 4)
 vignette("Sweave", package = "utils")
 \end_layout
 
+\end_inset
+
+下記は、どのSエンジンでも動作する単純な例です。
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
 \begin_layout Plain Layout
 
-@
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+print-integers, keep.source=TRUE
 \end_layout
 
 \end_inset
@@ -511,19 +559,6 @@ vignette("Sweave", package = "utils")
 
 \end_layout
 
-\begin_layout Standard
-下記は、どのSエンジンでも動作する単純な例です。
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status open
-
-\begin_layout Plain Layout
-
-<<print-integers, keep.source=TRUE>>=
-\end_layout
-
 \begin_layout Plain Layout
 
 ## 1から10までの整数は
@@ -534,14 +569,28 @@ status open
 1:10
 \end_layout
 
-\begin_layout Plain Layout
+\end_inset
+
 
-@
 \end_layout
 
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
 \begin_layout Plain Layout
 
-<<hide-results, results=hide>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+hide-results, results=hide
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -554,9 +603,23 @@ status open
 print(1:20)
 \end_layout
 
+\end_inset
+
+単純な計算機をエミュレートすることもできます。
+\end_layout
+
+\begin_layout Standard
+\begin_inset Flex Chunk
+status open
+
 \begin_layout Plain Layout
 
-@
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+calculator
 \end_layout
 
 \end_inset
@@ -564,19 +627,6 @@ print(1:20)
 
 \end_layout
 
-\begin_layout Standard
-単純な計算機をエミュレートすることもできます。
-\end_layout
-
-\begin_layout Standard
-\begin_inset ERT
-status open
-
-\begin_layout Plain Layout
-
-<<calculator>>=
-\end_layout
-
 \begin_layout Plain Layout
 
 1 + pi
@@ -587,11 +637,6 @@ status open
 sin(pi/6)
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -602,12 +647,22 @@ sin(pi/6)
 \end_layout
 
 \begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<rnorm>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+rnorm
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -630,11 +685,6 @@ print(x)
 t1 <- t.test(x)
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -728,12 +778,22 @@ iris
 \end_layout
 
 \begin_layout Standard
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<iris-summary>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+iris-summary
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -741,11 +801,6 @@ status open
 summary(iris[,-5])
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -782,16 +837,22 @@ name "tab:xtable-demo"
 
 \begin_layout Plain Layout
 \align center
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-\end_layout
+\begin_inset Argument 1
+status open
 
 \begin_layout Plain Layout
 
-<<xtable-demo,results=tex,echo=FALSE>>=
+xtable-demo,results=tex,echo=FALSE
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -810,11 +871,6 @@ print(xtable(sapply(iris[,-5], quantile)), floating=FALSE)
 )')
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -889,12 +945,22 @@ epsとpdfの両方をtrueにして、latexとpdflatexの両方を動作するよ
 \end_inset
 
 
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+iris-pairs,fig=TRUE,width=4.5,height=4.5,eps=TRUE,pdf=TRUE
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -902,11 +968,6 @@ status open
 pairs(iris, col = iris$Species)
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -948,12 +1009,22 @@ status open
 
 \begin_layout Plain Layout
 \align center
-\begin_inset ERT
+\begin_inset Flex Chunk
 status open
 
 \begin_layout Plain Layout
 
-<<iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T>>=
+\begin_inset Argument 1
+status open
+
+\begin_layout Plain Layout
+
+iris-boxplots,fig=TRUE,width=7,height=2,keep.source=F,eps=T,pdf=T
+\end_layout
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout Plain Layout
@@ -966,11 +1037,6 @@ par(mar=c(4,5,.1,.3), las=1)
 boxplot(Sepal.Length~Species,data=iris,horizontal=TRUE,xlab='Sepal.Length')
 \end_layout
 
-\begin_layout Plain Layout
-
-@
-\end_layout
-
 \end_inset
 
 
@@ -1409,7 +1475,7 @@ reference "tab:xtable-demo"
 \end_layout
 
 \begin_layout Standard
-The user manual of Sweave is at 
+Sweaveの利用者の手引きは
 \begin_inset Flex URL
 status collapsed
 
@@ -1420,8 +1486,7 @@ https://stat.ethz.ch/R-manual/R-devel/library/utils/doc/Sweave.pdf
 
 \end_inset
 
-にあります。 The CRAN task view on 「Reproducible Research」にあるCRANタスクビューには、便利と思われるSweav
+にあります。「Reproducible Research」にあるCRANタスクビューには、便利と思われるSweave関連パッケージの一覧があります。
-e関連パッケージの一覧があります。
 \begin_inset Flex URL
 status collapsed