[R-pkg-devel] R Vignette Knitting Issues in CRAN Release

2021-12-09 Thread Eric Weine 
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
.
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
.
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
,
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]]

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R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2021-12-10 Thread Eric Weine 
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 
> To: r-package-devel@r-project.org
> Subject: [R-pkg-devel] R Vignette Knitting Issues in CRAN Release
> Message-ID:
>  0hrzayidhjjgalq2ekrfnatsbbl0+yu...@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
> >.
> 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
> >.
> 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
> >,
> 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 
> To: Eric Weine 
> Cc: 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  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
> >.
> > 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
> >.
> > 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
> >,
> > 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 mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
>
>
>
> --
>
> Date: Fri, 10 Dec 2021 05:38:15 -0500
>

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

2021-12-10 Thread Eric Weine 
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.

Eric.

On Fri, Dec 10, 2021 at 10:25 AM Duncan Murdoch 
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>>
> > To: r-package-devel@r-project.org  r-package-devel@r-project.org>
> > Subject: [R-pkg-devel] R Vignette Knitting Issues in CRAN Release
> > Message-ID:
> >
> >  > <mailto:0hrzayidhjjgalq2ekrfnatsbbl0%2byu...@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 
> > To: Eric Weine mailto:ericwein...@gmail.com
> >>
> > Cc: r-package-devel@r-project.org  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,
> > Sim

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

2021-12-10 Thread Eric Weine 
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 
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
> > 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  > <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:
> >  >
> >  >
> >0hrzayidhjjgalq2ekrfnatsbbl0+yu...@mail.gmail.com  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
&g