[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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