[Bioc-devel] NEWS.md

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Wed Sep 26 13:22:21 CEST 2018 

As mentioned by Henrik,  The code referenced seems only implemented in R-devel currently.   Bioconductor will look at updating the code we use on our systems to match when our Bioconductor version is being built against R-devel  (after the October release) .


Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Henrik Bengtsson <henrik.bengtsson using gmail.com>
Sent: Tuesday, September 25, 2018 7:01:36 PM
To: lg390 using cam.ac.uk
Cc: Shepherd, Lori; lluis.revilla using gmail.com; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] NEWS.md

Forgot to mention that here's how news() select which file to parse if
there are several:

## Look for new-style inst/NEWS.Rd installed as NEWS.Rd
## If not found, look for NEWS.md.
## If not found, look at old-style
## NEWS inst/NEWS
## installed as NEWS (and ignore ChangeLog files).

Source: https://github.com/wch/r-source/blob/d20943d71407f9209cb6c7581ac0fce3b3517419/src/library/tools/R/news.R#L62-L66

/Henrik
On Tue, Sep 25, 2018 at 3:58 PM Henrik Bengtsson
<henrik.bengtsson using gmail.com> wrote:
>
> Note that in R-devel, we have that
> (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html):
>
> * news() gains support for �NEWS.md� files.
>
> That is, news(package = pkg) not only finds NEWS.md (as before) but
> also parses it (into sections etc.) analogously to how it parses
> NEWS.Rd and NEWS.
>
> Because of this, I'd say a package should use only one of the NEWS,
> NEWS.Rd, and NEWS.md files.
>
> Also, I believe CRAN has parsed NEWS.md files for quite a while now
> and rendered them as HTML.  I think Bioconductor should do the same
> thing (sounds like this is what Llu�s argued for), especially with the
> new NEWS.md support by news().
>
> /Henrik
> On Tue, Sep 25, 2018 at 2:08 PM Laurent Gatto <lg390 using cam.ac.uk> wrote:
> >
> >
> > Dear all,
> >
> > My experience (and things may have changed since I set this up) is that
> > NEWS and NEWS.md serve different purposes despite a very similar
> > syntax. The former is used by news() and displayed on the Bioconductor
> > page (would NEWS.md be used if NEWS was absent?), while the one with the
> > md extension displays nicely (including links) on github and in pkgdown
> > sites.
> >
> > My solution is a Makefile recipe [1] (contributed by Sebastian Gibb)
> > that converts NEWS.md into NEWS while updating the syntax and removing
> > markdown links (typically to github issues, that are automatically
> > expanded from #123 to a full URL via a github hook).
> >
> > NEWS: #' create plain text NEWS from NEWS.md if available
> >         test -f ${PKGDIR}/NEWS.md && sed '/^# .*$$/d; /^## .*$$/{s/^## //g; p; s/./-/g}; /^###\+/{s/./\u&/g}; s/^##\+ //g; 1,2{/^[[:space:]]*$$/d}; s/\[\(#[0-9]\+\)\]([^)]\+)/\1/g' ${PKGDIR}/NEWS.md > ${PKGDIR}/NEWS
> >
> > (where ${PKGDIR} is the package directory)
> >
> > Unsure whether this helps or adds further to the confusion.
> >
> > Best wishes,
> >
> > Laurent
> >
> > [1] https://github.com/ComputationalProteomicsUnit/maker
> >
> >
> > On 25 September 2018 13:55, Shepherd, Lori wrote:
> >
> > > It can be used currently.  If you remove the .md extension but keep the format in should be recognized.  As described in the ?news help page
> > >
> > >
> > >
> > >      If 'package' is '"R"' (default), a news db is built with the news
> > >      since the 3.0.0 release of R (corresponding to R's top-level
> > >      'NEWS' file).  Otherwise, if the given add-on package can be found
> > >      in the given libraries, it is attempted to read its news in
> > >      structured form from files 'inst/NEWS.Rd', 'NEWS' or 'inst/NEWS'
> > >      (in that order).
> > >
> > >
> > >
> > > Please also note your news file is formatted incorrectly.  from the ?news
> > >
> > >
> > >      The plain text 'NEWS' files in add-on packages use a variety of
> > >      different formats; the default news reader should be capable to
> > >      extract individual news entries from a majority of packages from
> > >      the standard repositories, which use (slight variations of) the
> > >      following format:
> > >
> > >         � Entries are grouped according to version, with version header
> > >           "Changes in version" at the beginning of a line, followed by
> > >           a version number, optionally followed by an ISO 8601 format
> > >           date, possibly parenthesized.
> > >
> > >         � Entries may be grouped according to category, with a category
> > >           header (different from a version header) starting at the
> > >           beginning of a line.
> > >
> > >         � Entries are written as itemize-type lists, using one of 'o',
> > >           '*', '-' or '+' as item tag.  Entries must be indented, and
> > >           ideally use a common indentation for the item texts.
> > >
> > >
> > >
> > >
> > > Please remove the pound sign (# ) from the header entry -  and use "Changes in version"  not "BioCor"
> > >
> > >
> > > so for example:
> > >
> > >
> > >
> > > # BioCor 0.99.25
> > >
> > > * Update Vignette to just output html
> > >
> > > # BioCor 0.99.24
> > >
> > > * Submit the package to the Bioconductor project
> > >
> > > # BioCor 0.99.23
> > >
> > > * Add the Bioconductor webhook
> > >
> > >
> > > Would become
> > >
> > >
> > > Changes in version 0.99.25
> > >
> > > * Update Vignette to just output html
> > >
> > > Changes in version 0.99.24
> > >
> > > * Submit the package to the Bioconductor project
> > >
> > > Changes in version 0.99.23
> > >
> > > * Add the Bioconductor webhook
> > >
> > >
> > >
> > >
> > > Lori Shepherd
> > >
> > > Bioconductor Core Team
> > >
> > > Roswell Park Cancer Institute
> > >
> > > Department of Biostatistics & Bioinformatics
> > >
> > > Elm & Carlton Streets
> > >
> > > Buffalo, New York 14263
> > >
> > > ________________________________
> > > From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Llu�s Revilla <lluis.revilla using gmail.com>
> > > Sent: Tuesday, September 25, 2018 3:20:39 AM
> > > To: bioc-devel
> > > Subject: [Bioc-devel] NEWS.md
> > >
> > > Dear Bioconductor team,
> > >
> > > I found that the new R version 3.5.1, to be used with the new release of
> > > Bioconductor, supports the �NEWS.md' files.
> > >
> > > I updated my package (BioCor) to use `NEWS.md`. However, on the devel
> > > landing page of the package stills shows the old file NEWS file. This is
> > > consistent with the developer page (
> > > https://www.bioconductor.org/developers/package-guidelines/#news).
> > >
> > > Will this be a requirement or can I keep the NEWS.md file?
> > >
> > > Many thanks,
> > >
> > > Llu�s
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >
> > >
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> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> > --
> > Laurent Gatto | @lgatt0
> > http://lgatto.github.io/
> >
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel


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