[R-pkg-devel] R-package-devel Digest, Vol 80, Issue 7
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Fri Dec 10 17:56:03 CET 2021
On 10/12/2021 11:08 a.m., Eric Weine wrote:
> That does not solve the issue.
>
> First, the html file that's already there is what is desired. But I
> believe that regardless R CMD will rebuild the package vignettes from
> scratch. I tried removing the html and recreating the package but I end
> up with the same result in the .tar.gz file. The central question is why
> this difference exists between R CMD and building vignettes otherwise.
I suspect you still have a copy of the old .html file, maybe in inst/doc
if you've removed it from vignettes. If all your inst/doc files are
produced from vignettes (which is the recommended way to do things, but
isn't required) then you shouldn't have inst/doc in the source at all.
R CMD build will create it when it builds the tarball.
Duncan Murdoch
>
> Eric.
>
> On Fri, Dec 10, 2021 at 10:25 AM Duncan Murdoch
> <murdoch.duncan using gmail.com <mailto:murdoch.duncan using gmail.com>> wrote:
>
> Just delete the .html output from earlier runs before you run R CMD
> build, and it will have no choice but to rebuild them.
>
> Duncan Murdoch
>
> On 10/12/2021 9:29 a.m., Eric Weine wrote:
> > Hello,
> >
> > Sorry yes, I think that my initial post on stack overflow is a bit
> > misleading. I have checked the file that is built when I run "R CMD
> > build ...", and it looks like what is on CRAN. The question is
> why is
> > that different from when I run "devtools::build_vignette" or when
> I just
> > knit the vignette in RStudio. I know that "R CMD build" creates the
> > vignette each time from scratch. Should I update my R version or
> > something? I'm just trying to isolate the difference between R
> CMD build
> > and the other tools I have to knit vignette so I can ensure they are
> > consistent.
> >
> > Thanks for the help,
> >
> > Eric.
> >
> > Date: Thu, 9 Dec 2021 16:52:09 -0500
> > From: Eric Weine <ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com> <mailto:ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com>>>
> > To: r-package-devel using r-project.org
> <mailto:r-package-devel using r-project.org>
> <mailto:r-package-devel using r-project.org
> <mailto:r-package-devel using r-project.org>>
> > Subject: [R-pkg-devel] R Vignette Knitting Issues in CRAN Release
> > Message-ID:
> >
> >
> <CAO=DOOayQEiiunh=0HrzaYiDHJjgaLQ2EkRFnatsbBL0+YUKYA using mail.gmail.com <mailto:0HrzaYiDHJjgaLQ2EkRFnatsbBL0%2BYUKYA using mail.gmail.com>
> > <mailto:0HrzaYiDHJjgaLQ2EkRFnatsbBL0%2BYUKYA using mail.gmail.com
> <mailto:0HrzaYiDHJjgaLQ2EkRFnatsbBL0%252BYUKYA using mail.gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hello,
> >
> > I'm having an issue where my vignette created using R CMD
> build does not
> > match the vignette created using devtools::build_vignettes or
> when I
> > knit
> > with RStudio. I posted about this issue on stack overflow here
> >
> <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623 <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623>
> >
> <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623 <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623>>>.
> > Originally I thought that this might be related to an
> omission in the
> > DESCRIPTION file, but this no longer seems to be the case.
> Here is a
> > repost
> > of my initial stack overflow post:
> >
> > I recently released a vignette with version 1.1 of my R
> package. The Rmd
> > for the vignette can be found here
> >
> <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd>
> >
> <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd>>>.
> > When I create the vignette locally, I see author information
> and the
> > table
> > of contents at the top of the vignette, as expected. However,
> when I
> > submitted this package to CRAN and the vignette was created there
> >
> <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html>
> >
> <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html>>>,
> > I no longer see the table of contents or author information.
> Does anyone
> > know why this may be happening?
> >
> > Thanks,
> >
> > Eric.
> >
> > [[alternative HTML version deleted]]
> >
> >
> >
> >
> > ------------------------------
> >
> > Date: Fri, 10 Dec 2021 11:41:31 +1300
> > From: Simon Urbanek <simon.urbanek using R-project.org>
> > To: Eric Weine <ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com> <mailto:ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com>>>
> > Cc: r-package-devel using r-project.org
> <mailto:r-package-devel using r-project.org>
> <mailto:r-package-devel using r-project.org
> <mailto:r-package-devel using r-project.org>>
> > Subject: Re: [R-pkg-devel] R Vignette Knitting Issues in CRAN
> Release
> > Message-ID: <52EC72DC-B583-4D1B-97C3-979EC96FF9C2 using R-project.org>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Eric,
> >
> > did you check the contents of the package file you submitted? The
> > session info in the vignette is quite old, and the build has been
> > packaged by you so I don't think it has anything to do with CRAN,
> > but to make sure, check the file you submitted.
> >
> > Cheers,
> > Simon
> >
> >
> > > On Dec 10, 2021, at 10:52 AM, Eric Weine
> <ericweine15 using gmail.com <mailto:ericweine15 using gmail.com>
> > <mailto:ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com>>> wrote:
> > >
> > > Hello,
> > >
> > > I'm having an issue where my vignette created using R CMD
> build
> > does not
> > > match the vignette created using devtools::build_vignettes or
> > when I knit
> > > with RStudio. I posted about this issue on stack overflow here
> > >
> >
> <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623 <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623>
> >
> <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623 <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623>>>.
> > > Originally I thought that this might be related to an
> omission in the
> > > DESCRIPTION file, but this no longer seems to be the case.
> Here
> > is a repost
> > > of my initial stack overflow post:
> > >
> > > I recently released a vignette with version 1.1 of my R
> package.
> > The Rmd
> > > for the vignette can be found here
> > >
> >
> <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd>
> >
> <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd>>>.
> > > When I create the vignette locally, I see author
> information and
> > the table
> > > of contents at the top of the vignette, as expected.
> However, when I
> > > submitted this package to CRAN and the vignette was
> created there
> > >
> >
> <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html>
> >
> <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html>>>,
> > > I no longer see the table of contents or author
> information. Does
> > anyone
> > > know why this may be happening?
> > >
> > > Thanks,
> > >
> > > Eric.
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org>
> > <mailto:R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org>> mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> > <https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>>
> > >
> >
> >
> >
> >
> > ------------------------------
> >
> > Date: Fri, 10 Dec 2021 05:38:15 -0500
> > From: Duncan Murdoch <murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>
> > <mailto:murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>>>
> > To: Eric Weine <ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com> <mailto:ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com>>>
> > Cc: r-package-devel using r-project.org
> <mailto:r-package-devel using r-project.org>
> <mailto:r-package-devel using r-project.org
> <mailto:r-package-devel using r-project.org>>
> > Subject: Re: [R-pkg-devel] R Vignette Knitting Issues in CRAN
> Release
> > Message-ID: <02621081-6881-de33-2d8f-a5bcdcc3c70c using gmail.com
> <mailto:02621081-6881-de33-2d8f-a5bcdcc3c70c using gmail.com>
> > <mailto:02621081-6881-de33-2d8f-a5bcdcc3c70c using gmail.com
> <mailto:02621081-6881-de33-2d8f-a5bcdcc3c70c using gmail.com>>>
> > Content-Type: text/plain; charset="utf-8"; Format="flowed"
> >
> > On 09/12/2021 5:41 p.m., Simon Urbanek wrote:
> > > Eric,
> > >
> > > did you check the contents of the package file you
> submitted? The
> > session info in the vignette is quite old, and the build has been
> > packaged by you so I don't think it has anything to do with CRAN,
> > but to make sure, check the file you submitted.
> >
> > Yes, I think the tarball contained an old version of the
> .html file.
> > The timestamp on it is the same as on many other items in the
> tarball,
> > and that likely means it was put into inst/doc by the build
> process.
> >
> > Eric, on Github I notice you have a committed copy of the
> HTML file in
> > the vignettes directory. This could be the cause of your
> problem.
> > Normally you should only have the vignette source in the
> vignettes
> > directory. I wouldn't be surprised if git the build process
> thinks the
> > .html file is newer than the .Rmd and doesn't rebuild it,
> putting a
> > stale copy into the tarball.
> >
> > Duncan Murdoch
> >
> > >
> > > Cheers,
> > > Simon
> > >
> > >
> > >> On Dec 10, 2021, at 10:52 AM, Eric Weine
> <ericweine15 using gmail.com <mailto:ericweine15 using gmail.com>
> > <mailto:ericweine15 using gmail.com
> <mailto:ericweine15 using gmail.com>>> wrote:
> > >>
> > >> Hello,
> > >>
> > >> I'm having an issue where my vignette created using R CMD
> build
> > does not
> > >> match the vignette created using devtools::build_vignettes or
> > when I knit
> > >> with RStudio. I posted about this issue on stack overflow
> here
> > >>
> >
> <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623 <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623>
> >
> <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623 <https://stackoverflow.com/questions/70204611/vignette-table-of-contents-missing-when-package-published-to-cran/70205623?noredirect=1#comment124116982_70205623>>>.
> > >> Originally I thought that this might be related to an
> omission
> > in the
> > >> DESCRIPTION file, but this no longer seems to be the
> case. Here
> > is a repost
> > >> of my initial stack overflow post:
> > >>
> > >> I recently released a vignette with version 1.1 of my R
> package.
> > The Rmd
> > >> for the vignette can be found here
> > >>
> >
> <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd>
> >
> <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd <https://github.com/eweine/qqconf/blob/master/qqconf/vignettes/qqconf_introduction.Rmd>>>.
> > >> When I create the vignette locally, I see author
> information and
> > the table
> > >> of contents at the top of the vignette, as expected.
> However, when I
> > >> submitted this package to CRAN and the vignette was
> created there
> > >>
> >
> <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html>
> >
> <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html <https://cloud.r-project.org/web/packages/qqconf/vignettes/qqconf_introduction.html>>>,
> > >> I no longer see the table of contents or author information.
> > Does anyone
> > >> know why this may be happening?
> > >>
> > >> Thanks,
> > >>
> > >> Eric.
> > >>
> > >> [[alternative HTML version deleted]]
> > >>
> > >> ______________________________________________
> > >> R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org>
> > <mailto:R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org>> mailing list
> > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> > <https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>>
> > >>
> > >
> > > ______________________________________________
> > > R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org>
> > <mailto:R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org>> mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> > <https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>>
> >
> >
> >
> > **********************************************
> >
>
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