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.dun...@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.dun...@gmail.com <mailto:murdoch.dun...@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 <ericwein...@gmail.com > > <mailto:ericwein...@gmail.com> <mailto:ericwein...@gmail.com > > <mailto:ericwein...@gmail.com>>> > > > To: r-package-devel@r-project.org > > <mailto:r-package-devel@r-project.org> > > <mailto:r-package-devel@r-project.org > > <mailto:r-package-devel@r-project.org>> > > > Subject: [R-pkg-devel] R Vignette Knitting Issues in CRAN > Release > > > Message-ID: > > > > > > > > <CAO=DOOayQEiiunh= > 0hrzayidhjjgalq2ekrfnatsbbl0+yu...@mail.gmail.com <mailto: > 0hrzayidhjjgalq2ekrfnatsbbl0%2byu...@mail.gmail.com> > > > <mailto:0hrzayidhjjgalq2ekrfnatsbbl0%2byu...@mail.gmail.com > > <mailto:0hrzayidhjjgalq2ekrfnatsbbl0%252byu...@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.urba...@r-project.org> > > > To: Eric Weine <ericwein...@gmail.com > > <mailto:ericwein...@gmail.com> <mailto:ericwein...@gmail.com > > <mailto:ericwein...@gmail.com>>> > > > Cc: r-package-devel@r-project.org > > <mailto:r-package-devel@r-project.org> > > <mailto:r-package-devel@r-project.org > > <mailto:r-package-devel@r-project.org>> > > > Subject: Re: [R-pkg-devel] R Vignette Knitting Issues in CRAN > > Release > > > Message-ID: > <52ec72dc-b583-4d1b-97c3-979ec96ff...@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 > > <ericwein...@gmail.com <mailto:ericwein...@gmail.com> > > > <mailto:ericwein...@gmail.com > > <mailto:ericwein...@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@r-project.org > > <mailto:R-package-devel@r-project.org> > > > <mailto:R-package-devel@r-project.org > > <mailto:R-package-devel@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.dun...@gmail.com > > <mailto:murdoch.dun...@gmail.com> > > > <mailto:murdoch.dun...@gmail.com > > <mailto:murdoch.dun...@gmail.com>>> > > > To: Eric Weine <ericwein...@gmail.com > > <mailto:ericwein...@gmail.com> <mailto:ericwein...@gmail.com > > <mailto:ericwein...@gmail.com>>> > > > Cc: r-package-devel@r-project.org > > <mailto:r-package-devel@r-project.org> > > <mailto:r-package-devel@r-project.org > > <mailto:r-package-devel@r-project.org>> > > > Subject: Re: [R-pkg-devel] R Vignette Knitting Issues in CRAN > > Release > > > Message-ID: <02621081-6881-de33-2d8f-a5bcdcc3c...@gmail.com > > <mailto:02621081-6881-de33-2d8f-a5bcdcc3c...@gmail.com> > > > <mailto:02621081-6881-de33-2d8f-a5bcdcc3c...@gmail.com > > <mailto:02621081-6881-de33-2d8f-a5bcdcc3c...@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 > > <ericwein...@gmail.com <mailto:ericwein...@gmail.com> > > > <mailto:ericwein...@gmail.com > > <mailto:ericwein...@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@r-project.org > > <mailto:R-package-devel@r-project.org> > > > <mailto:R-package-devel@r-project.org > > <mailto:R-package-devel@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@r-project.org > > <mailto:R-package-devel@r-project.org> > > > <mailto:R-package-devel@r-project.org > > <mailto:R-package-devel@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>> > > > > > > > > > > > > ********************************************** > > > > > > > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
