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
[Bioc-devel] NEWS.md
7 messages · Laurent Gatto, Henrik Bengtsson, Shepherd, Lori +1 more
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 at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at gmail.com>
Sent: Tuesday, September 25, 2018 3:20:39 AM
To: bioc-devel
Subject: [Bioc-devel] NEWS.md
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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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 at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Laurent Gatto | @lgatt0 http://lgatto.github.io/
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 at 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 at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Laurent Gatto | @lgatt0 http://lgatto.github.io/
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 at 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 at 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 at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Laurent Gatto | @lgatt0 http://lgatto.github.io/
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 at gmail.com>
Sent: Tuesday, September 25, 2018 7:01:36 PM
To: lg390 at cam.ac.uk
Cc: Shepherd, Lori; lluis.revilla at gmail.com; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] NEWS.md
Sent: Tuesday, September 25, 2018 7:01:36 PM
To: lg390 at cam.ac.uk
Cc: Shepherd, Lori; lluis.revilla at gmail.com; bioc-devel at 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 at 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 at 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 at r-project.org> on behalf of Llu?s Revilla <lluis.revilla at 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 at r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > > > > This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioc-devel at r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > > > -- > > Laurent Gatto | @lgatt0 > > http://lgatto.github.io/ > > > > _______________________________________________ > > Bioc-devel at r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
Yes I was arguing if NEWS.md could be used. Only after Lori reply I realized the changes don't apply for the next release of Bioconductor. Anyway, thanks Laurent for the command, and the team for considering it in its due time. Llu?s On Wed, 26 Sep 2018 at 13:22, Shepherd, Lori <Lori.Shepherd at roswellpark.org> wrote:
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 at gmail.com> *Sent:* Tuesday, September 25, 2018 7:01:36 PM *To:* lg390 at cam.ac.uk *Cc:* Shepherd, Lori; lluis.revilla at gmail.com; bioc-devel at 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 at 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 at 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 at r-project.org> on behalf of
Llu?s Revilla <lluis.revilla at 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 at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or
confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
-- Laurent Gatto | @lgatt0 http://lgatto.github.io/
_______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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