[R-pkg-devel] R-package-devel Digest, Vol 80, Issue 7
Duncan Murdoch
murdoch@dunc@n @end|ng |rom gm@||@com
Fri Dec 10 16:25:13 CET 2021
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>>
> To: 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>>
> 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>>.
> 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>>.
> 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>>,
> 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>>
> Cc: 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>> 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>>.
> > 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>>.
> > 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>>,
> > 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> mailing list
> > 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>>
> To: Eric Weine <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>
> 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>>
> 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>> 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>>.
> >> 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>>.
> >> 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>>,
> >> 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> mailing list
> >> 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> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
>
>
>
> **********************************************
>
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