Re: [Rd] string concatenation operator (revisited)

[Grant McDermott]

Sorry I haven't had a chance to reply to anyone. I feel like I dropped a 
grenade in a room and promptly bolted...

Just to say, then, that I really appreciate everyone's comments and 
suggestions. While I'm tempted to push back on some points, I don't think it's 
worth on balance, or will add much beyond what's already been said.

It's interesting to see that there appears to be at least some appetite for 
additional (f)string operators in base R... notwithstanding the valid 
objections and the difficulties raised in this thread.

Cheers,
Grant

Get Outlook for Android

From: Grant McDermott
Sent: Saturday, December 4, 2021 12:36:44 PM
To: r-devel@r-project.org 
Subject: string concatenation operator (revisited)

Hi all,

I wonder if the R Core team might reconsider an old feature request, as 
detailed in this 2005 thread: 
https://stat.ethz.ch/pipermail/r-help/2005-February/thread.html#66698

The TL;DR version is base R support for a `+.character` method. This would 
essentially provide a shortcut to `paste​0`, in much the same way that `\(x)` 
now provides a shortcut to `function(x)`.

> a = "hello "; b = "world"
> a + b
> [1] "hello world"

I appreciate some of the original concerns raised against a native "string1 + 
string2" implementation. The above thread also provides several 
use-at-your-own-risk workarounds. But sixteen years is a long time in software 
development and R now stands as something of an exception on this score. 
Python, Julia, Stata, and SQL (among various others) all support native string 
concatenation/interpolation using binary/arithmetic operators. It's been a 
surprising source of frustration for students in some of the classes I teach, 
particularly those coming from another language.

Many thanks for considering.

PS. I hope I didn't miss any additional discussion of this issue beyond the 
original 2005 thread. My search efforts didn't turn anything else up, except 
this popular Stackoverflow question: 
https://stackoverflow.com/questions/4730551/making-a-string-concatenation-operator-in-r

Grant McDermott
Assistant Professor
Department of Economics
University of Oregon
www.grantmcdermott.com


[[alternative HTML version deleted]]

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Re: [Bioc-devel] Git recognizes me but denies access

[Vincent Carey]

How are we doing with this?  Can destiny be maintained?  Do we need more
git assistance?
I am told the package is not passing check in 3.14.

On Thu, Nov 18, 2021 at 4:24 AM Philipp A.  wrote:

> My addresses are phil.ange...@gmail.com (not philipp) and
> flying-sh...@web.de.
>
> I’ll add a key as soon as I’m able to log in.
>
> Am Mo., 15. Nov. 2021 um 15:56 Uhr schrieb Nitesh Turaga <
> nturaga.b...@gmail.com>:
>
> > You have to activate the account at
> > https://git.bioconductor.org/BiocCredentials/account_activation. Set a
> > password and add Ssh keys.
> >
> > Once again, the email you are trying to activate is '
> > philipp.ange...@gmail.com’.
> >
> > The problem seems to be non-matching key pairs. Add new SSH keys.
> >
> > Best,
> >
> > Nitesh
> >
> >
> > Nitesh Turaga
> > Scientist II, Department of Data Science,
> > Bioconductor Core Team Member
> > Dana Farber Cancer Institute
> >
> > > On Nov 15, 2021, at 9:54 AM, Nitesh Turaga 
> > wrote:
> > >
> > > Hi Philipp,
> > >
> > > The email address that is registered to BiocCredentials right now is '
> > philipp.ange...@gmail.com'. It doesn’t look like an institutional email
> > address.
> > >
> > > Could you please confirm the email change to flying-sh...@web.de ??
> > >
> > > Best,
> > >
> > > Nitesh
> > >
> > > Nitesh Turaga
> > > Scientist II, Department of Data Science,
> > > Bioconductor Core Team Member
> > > Dana Farber Cancer Institute
> > >
> > >> On Nov 15, 2021, at 2:36 AM, Carsten Marr <
> > carsten.m...@helmholtz-muenchen.de> wrote:
> > >>
> > >> confirmed!
> > >>
> > >>
> > >> best,
> > >> c
> > >>
> > >>
> > >>
> > >>> Am 13.11.2021 um 15:56 schrieb Philipp A. :
> > >>>
> > >>> I no longer have control of this email address.
> > >>>
> > >>> Please add the one I’m writing from to the account.
> > >>>
> > >>> My supervisor (CC) from when I was at the institution can confirm
> that
> > I’m the same person.
> > >>>
> > >>> Best, Phil
> > >>>
> > >>> Am Di., 9. Nov. 2021 um 16:24 Uhr schrieb Nitesh Turaga <
> > nturaga.b...@gmail.com>:
> > >>> Dear Phil,
> > >>>
> > >>> Please activate your account at
> > https://git.bioconductor.org/BiocCredentials/account_activation. Add new
> > SSH keys, because it’s possible you are not using the correct key-pairs.
> > >>>
> > >>> Nothing on our end seems out of place.
> > >>>
> > >>> The FAQ section from #13 onwards has other debugging options as well,
> > https://bioconductor.org/developers/how-to/git/faq/.
> > >>>
> > >>> Best,
> > >>>
> > >>> Nitesh
> > >>>
> > >>>
> > >>> Nitesh Turaga
> > >>> Scientist II, Department of Data Science,
> > >>> Bioconductor Core Team Member
> > >>> Dana Farber Cancer Institute
> > >>>
> >  On Nov 8, 2021, at 12:23 PM, Philipp A. 
> wrote:
> > 
> >  Hi,
> > 
> >  My package (destiny) has been deprecated because Bioconductor’s
> LaTeX
> >  environment keeps changing and breaking my docs.
> > 
> >  I‘m trying to fix it once again, but I get:
> > 
> >  $ git push upstream masterFATAL: W any packages/destiny p.angerer
> >  DENIED by fallthru
> > 
> >  *Please note that this isn’t covered in the FAQ*:
> > 
> >  “p.angerer” indicates that it recognizes me, but still doesn’t allow
> > me to
> >  push commits.
> > 
> >  Best, Phil
> > 
> >   [[alternative HTML version deleted]]
> > 
> >  ___
> >  Bioc-devel@r-project.org mailing list
> >  https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>>
> > >>
> > >> ---
> > >> Carsten Marr
> > >> +49 89 3187 2158
> > >> AIH Institute of AI for Health
> > >> Helmholtz Zentrum München
> > >> www.helmholtz-muenchen.de/aih/index.html
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> Helmholtz Zentrum München
> > >> Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)
> > >> Ingolstädter Landstr. 1
> > >> 85764 Neuherberg
> > >> www.helmholtz-muenchen.de
> > >> Aufsichtsratsvorsitzende: MinDir.in Prof. Dr. Veronika von Messling
> > >> Geschäftsführung: Prof. Dr. med. Dr. h.c. Matthias Tschöp, Kerstin
> > Günther
> > >> Registergericht: Amtsgericht München HRB 6466
> > >> USt-IdNr: DE 129521671
> > >>
> > >
> >
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

-- 
The information in this e-mail is intended only for the ...{{dropped:18}}

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

[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  >   > >>
> >  > 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  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
> >
> >  >
> >   <
> 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
> >  

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

[Duncan Murdoch]

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> >>
 >     To: 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
 >   
  
 >   
  >>.

 >     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 

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

[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:
> >
> >  > >
> > 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,
> > 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
> > <
> 

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

[Duncan Murdoch]

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>>
To: r-package-devel@r-project.org 
Subject: [R-pkg-devel] R Vignette Knitting Issues in CRAN Release
Message-ID:


>
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

>.
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]]




--

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 
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 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
 >

>.
 > 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 

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

[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
> From: Duncan Murdoch 
> To: Eric Weine 
> Cc: 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>
> 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 

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

[Duncan Murdoch]

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  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
.
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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