[R-pkg-devel] R-package-devel Digest, Vol 80, Issue 7

Eric Weine er|cwe|ne15 @end|ng |rom gm@||@com
Fri Dec 10 18:52:04 CET 2021


I don't think that is related. I just updated to the newest version of R
(4.1.2) and that resolved the issue.

Thank you for your time!

Eric.

On Fri, Dec 10, 2021 at 11:56 AM Duncan Murdoch <murdoch.duncan using gmail.com>
wrote:

> 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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