CVS commit: pkgsrc/print/R-knitr

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Apr 23 02:07:00 UTC 2022

Modified Files:
        pkgsrc/print/R-knitr: Makefile distinfo

Log Message:
(print/R-knitr) Updated 1.34 to 1.38

knitr 1.38
-------------------------------------------------------
NEW FEATURES

  * The chunk option file can take a vector of file paths now, i.e., this
    option can be used to read more than one file (e.g., file = c("foo.R",
    "bar.R").

  * Added a new engine named exec (#2073) to execute an arbitrary command on
    the code chunk, e.g.,

    ```{exec, command='Rscript'}
    1 + 1
    ```

    The above code chunk executes the Rscript command with the chunk body as
    its input (which basically means executing the R code in a new R session).
    See the example #124 in the repo https://github.com/yihui/knitr-examples
    for more info.

    There exists several command-based engines in knitr, such as awk, bash,
    perl, go, and dot, etc. This new exec engine provides a general mechanism
    to execute any command that users provide. For example, the code chunk

    ```{bash}
    echo 'Hello world!'
    ```

    is equivalent to the chunk using the exec engine and the bash command:

    ```{exec, command='bash'}
    echo 'Hello world!'
    ```

    With this new engine, we no longer need to provide or maintain other simple
    command-based engines. For example, to support TypeScript (#1833), we only
    need to specify command = 'ts-node' with the exec engine.

    If the command has significant side-effects (e.g., compile source code to
    an executable and run the executable, or generate plots to be included in
    the output), it is also possible to create a new engine based on the exec
    engine. The example #124 in the knitr-examples repo has provided a gcc
    example.

    We'd like to thank @TianyiShi2001 for the inspiration (#1829 #1823 #1833).

  * Added a new engine ditaa based on the exec engine to convert ASCII art
    diagrams to bitmaps via the ditaa command (thanks, @kondziu, #2092).

  * Added two new chunk options, class.chunk and attr.chunk, for R Markdown
    output. These options can enclose the whole chunk output (source and
    results) in a fenced Div. Their syntax follows other chunk options with the
    similar names class.* and attr.* (e.g., class.source and attr.source). For
    example, class.chunk = "foo" would wrap the chunk output inside ::: {.foo}
    and ::: (thanks, @atusy, #2099).

  * Added a new chunk option lang to set the language name of a code chunk. By
    default, the language name is the engine name. This is primarily useful for
    syntax highlighting the source chunks in Markdown-based output. Previously
    the lang option was only available to a few engines such as verbatim and
    embed. Now it is available to all engines.

  * Added a new wrapper function rnw2pdf(). It allows users to specify an
    arbitrary output file path, clean the intermediate files, and stop when any
    error occurs in knitting (thanks, @shrektan, #2113).

  * New calling.handlers option for opts_chunk$set() to register calling
    handlers within chunks. See ?evaluate::new_output_handler for details.

MAJOR CHANGES

  * The minimal required version of R was bumped from 3.2.3 to 3.3.0 (thanks,
    @essemenoff, #2100).

  * The working directory under which chunk options are evaluated has been
    changed to the directory of the source document by default. If the package
    option root.dir is set to a different directory, that directory will be
    used as the working directory (#2081).

  * include_graphics() will expand ~ in the image paths now and also warn
    against absolute paths (thanks, @kcarnold, #2063).

  * opts_chunk$set() returns values of old chunk options after setting new
    chunk options now, instead of returning NULL, which can make it a little
    simpler to reset chunk options, e.g., you can temporarily change a few
    chunk options and save them with old = opts_chunk$set(error = FALSE,
    fig.height = 3), and reset them later with opts_chunk$set(old). This works
    for any other objects in knitr that have the $set() methods, such as
    opts_knit, opts_hooks, knit_hooks, knit_engines, and so on.

MINOR CHANGES

  * The chunk option fig.scap has been added to eval.after in opts_knit
    (thanks, @knokknok, #2061).

BUG FIXES

  * Chunk options defined in the #| style are not recognized when the code
    chunk is indented or quoted (thanks, @mine-cetinkaya-rundel, #2086).

  * Fixed a bug in Sweave2knitr() #2097 (thanks, @chroetz).

knitr 1.37
----------------------------------------------------------------
NEW FEATURES

  * Added a new chunk option named file so that the chunk content can be read
    from an external file. Setting the chunk option file = "test.R" is
    equivalent to using the chunk option code = xfun::read_utf8("test.R").

  * For R Markdown documents, code chunks can be embedded in a parent code
    chunk with more backticks now. For example, a code chunk with four
    backticks can contain code chunks with three backticks. One application is
    to conditionally include some verbatim content that contains code chunks
    via the asis engine, e.g.,

    ````{asis, echo=format(Sys.Date(), "%w") == 1}
    Some conditional content only included when report is built on a Monday

    ```{r}
    1 + 1
    ```

    On another day, this content won't be included.
    ````

    Note that the embedded child code chunks (e.g., in the asis chunk above)
    are not parsed or evaluated by knitr, and only the top-level code chunk is
    parsed and evaluated.

  * Added a new engine named comment to comment out content, e.g.,

    ````{comment}
    Arbitrary content to be commented out.

    ```{r}
    1 + 1
    ```

    The above code chunk will not be executed.
    Inline code like `r pi * 5^2` will be ignored, too.
    ````

    Note that if any line of the content to be commented out contains N
    backticks, you will have to use at least N + 1 backticks in the chunk
    header and footer of the comment chunk.

  * Added a new engine named verbatim mainly for R Markdown documents to output
    verbatim content that contains code chunks and/or inline expressions, e.g.,

    ````{verbatim}
    We can output arbitrary content verbatim.

    ```{r}
    1 + 1
    ```

    The content can contain inline code like
    `r pi * 5^2`, too.
    ````

    By default, the verbatim content is placed in a fenced default code block:

    ````default
    We can output arbitrary content verbatim.

    ```{r}
    1 + 1
    ```

    The content can contain inline code like
    `r pi * 5^2`, too.
    ````

    You can change the default language name of the block via the chunk option
    lang, e.g., lang = 'markdown' will output a code block like this:

    ````markdown
    We can output arbitrary content verbatim.

    ```{r}
    1 + 1
    ```

    The content can contain inline code like
    `r pi * 5^2`, too.
    ````

    To disable the language name on the block, use an empty string lang = ''.

    The difference between the verbatim and asis engine is that the former will
    put the content in a fenced code block, and the latter just output the
    content as-is.

    You can also display a file verbatim by using the chunk option file, e.g.,

    ```{verbatim, file="test.Rmd"}
    ```

    This engine also works for other types of documents (e.g., Rnw) but it will
    not allow for nested code chunks within the verbatim code chunk.

  * Added a new engine named embed to embed external plain-text files. It is
    essentially a simple wrapper based on the verbatim engine, with the chunk
    content read from an external file and default language guessed from file
    extension. That is,

    ```{embed, file="foo.R"}
    ```

    is equivalent to

    ```{verbatim, file="foo.R", lang="r"}
    ```

    If you provide the chunk option file to the embed engine, it will read the
    file and show its content verbatim in the output document. Alternatively,
    you can specify the file path in the chunk body, e.g.,

    ```{embed}
    "foo.txt"
    ```

    The quotes are optional but can be helpful for editors (e.g., RStudio IDE)
    to autocomplete the file paths.

    The syntax highlighting language name is from the filename extension by
    default, and you can override it with the chunk option lang (e.g., file =
    "foo.sh", lang = "bash") which is then identical to the verbatim engine.

BUG FIXES

  * The chunk option child also respects the package option root.dir now
    (thanks, @salim-b, https://community.rstudio.com/t/117563).

  * Fixed a LaTeX error "Package xcolor Error: Undefined color `fgcolor'" with
    .Rnw documents (thanks, Kurt Hornik).

MINOR CHANGES

  * Improved the (warning) message when unbalanced chunk delimiters are
    detected in R Markdown documents, to make it easier for users to fix the
    problem. The message now contains the line numbers of the opening fence and
    closing fence, as well as the opening and closing backticks. For example,
    the opening fence may be "````{r}" (four backticks) but the closing fence
    is "```" (three backticks---should also be four to match the opening
    fence), or the opening fence is indented " ```{r}" but the closing fence is
    not "```". Note that this warning message may become an error in the
    future, i.e., unbalanced chunk delimiters will no longer be allowed.

knitr 1.36
-----------------------------------------------
MAJOR CHANGES

  * In knitr 1.35, if the indentation of the closing backticks does not match
    the indentation of the chunk header in an Rmd document, the closing
    backticks would not be treated as closing fence of a code chunk. This
    behavior has been reverted because we have discovered several cases in
    which the indentation was accidental. A warning message will be issued
    instead, and you are still recommended to fix the improper indentation if
    discovered.

BUG FIXES

  * Fixed a regression in knitr 1.31 that caused package vignettes to generate
    (tangle) invalid R scripts (thanks, @t-kalinowski @halldc, #2052).

knitr 1.35
-------------------------------------------------
NEW FEATURES

  * Chunk options can also be written inside a code chunk now after the special
    comment #|, e.g.,

    ```{r}
    #| echo = FALSE, fig.width = 10,
    #| fig.cap = "This is a long caption."

    plot(cars)
    ```

    The main differences between this new syntax and traditional syntax (i.e.,
    chunk options in the chunk header) are: 1) the chunk options can be freely
    wrapped, i.e., you can write them on as many lines as you prefer; 2) you
    can also use the YAML syntax instead of the comma-separated syntax if you
    like, e.g.,

    ```{r}
    #| echo: false
    #| fig.width: 10
    ```

    Chunk options provided inside a code chunk will override options with the
    same names in the chunk header if chunk options are provided in both
    places, e.g.,

    ```{r, echo = TRUE}
    #| echo = FALSE, fig.width = 10
    ```

    The effective chunk options for the above chunk are echo = FALSE and
    fig.width = 10.

MAJOR CHANGES

  * For R Markdown documents, if the chunk header is indented, the closing
    backticks (usually ```) of the chunk must be indented with the same amount
    of spaces (thanks, @atusy, #2047). For example, the following is no longer
    a valid code chunk because the chunk header is indented but the closing
    backticks are not:

     ```{r}
    1 + 1
    ```

    If you see an error "attempt to use zero-length variable name" when
    knitting an Rmd document, it may be because of this change, and you may
    have indented the chunk header by accident. If that is the case, you need
    to remove the extra white spaces before the chunk header.

    The same problem applies to blockquotes, i.e., > before ```. If you quote
    the chunk header, you have to quote the footer as well, e.g.,

    > ```{r}
    1 + 1
    ```

    The above unbalanced code chunk needs to be corrected to:

    > ```{r}
    > 1 + 1
    > ```

    Quoting the chunk body is optional but recommended.

BUG FIXES

  * Fixed a regression in v1.34: now blank lines in code chunks are stripped
    only when collapse = FALSE but no longer stripped by default when collapse
    = TRUE. If you prefer blank lines to be always stripped, set strip.white =
    TRUE globally or on the per chunk basis (thanks, @IndrajeetPatil, rstudio/
    rmarkdown#2220, #2046).

  * In knitr::combine_words(), when words is length 2 and and = "", sep will
    now be used (thanks, @eitsupi, #2044).

  * For R Markdown documents, if the chunk output contains N backticks, the
    output hook will use N + 1 backticks to wrap the output, so that the N
    verbatim backticks can be correctly preserved (thanks, @atusy, #2047).


To generate a diff of this commit:
cvs rdiff -u -r1.11 -r1.12 pkgsrc/print/R-knitr/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/print/R-knitr/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/print/R-knitr/Makefile
diff -u pkgsrc/print/R-knitr/Makefile:1.11 pkgsrc/print/R-knitr/Makefile:1.12
--- pkgsrc/print/R-knitr/Makefile:1.11  Sat Sep 18 13:40:56 2021
+++ pkgsrc/print/R-knitr/Makefile       Sat Apr 23 02:07:00 2022
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.11 2021/09/18 13:40:56 mef Exp $
+# $NetBSD: Makefile,v 1.12 2022/04/23 02:07:00 mef Exp $
 
 R_PKGNAME=     knitr
-R_PKGVER=      1.34
+R_PKGVER=      1.38
 CATEGORIES=    print
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
@@ -9,7 +9,7 @@ COMMENT=        General-purpose package for dyn
 LICENSE=       gnu-gpl-v1 OR gnu-gpl-v2 OR gnu-gpl-v3
 
 DEPENDS+=      R-evaluate>=0.10:../../devel/R-evaluate
-DEPENDS+=      R-xfun>=0.21:../../devel/R-xfun
+DEPENDS+=      R-xfun>=0.29:../../devel/R-xfun
 DEPENDS+=      R-digest>=0.6.4:../../security/R-digest
 DEPENDS+=      R-formatR>=0.10:../../textproc/R-formatR
 DEPENDS+=      R-highr>=0.8:../../textproc/R-highr

Index: pkgsrc/print/R-knitr/distinfo
diff -u pkgsrc/print/R-knitr/distinfo:1.10 pkgsrc/print/R-knitr/distinfo:1.11
--- pkgsrc/print/R-knitr/distinfo:1.10  Tue Oct 26 11:12:02 2021
+++ pkgsrc/print/R-knitr/distinfo       Sat Apr 23 02:07:00 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.10 2021/10/26 11:12:02 nia Exp $
+$NetBSD: distinfo,v 1.11 2022/04/23 02:07:00 mef Exp $
 
-BLAKE2s (R/knitr_1.34.tar.gz) = 1dd0019542be5a2a8fb9badfc7f9fd838bf4cb1c07570c72160da1ccbfbd555f
-SHA512 (R/knitr_1.34.tar.gz) = c89b333fc901fe3ae48f9e2ab537b6fdd1dc822f9789ed19efb2f8f703965711bf2e75d3a96bdfa737e78326d622d43d6a4a554302d7005ddbd353715e529aec
-Size (R/knitr_1.34.tar.gz) = 895165 bytes
+BLAKE2s (R/knitr_1.38.tar.gz) = f3760985597717bd9f9f89d272c813f17c5f778006e319695685fb353c5df87b
+SHA512 (R/knitr_1.38.tar.gz) = 4ae22fa21d10d4251bfa75803b700f1cbd3fab0203e45b5e9e4243b837ece5d30b86f637fa99d0d95d56c2fb5728d1153ce82dac7cb90c5246a2ea670cf8efaa
+Size (R/knitr_1.38.tar.gz) = 898373 bytes