Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Dear Shu Fai,
This approach is certainly relevant, and I think it is slightly better
than using R.rsp. My preference is still to include the original .Rmd
file along with a note to CRAN about the long-running vignette.
Thank you,
John
On 2023-10-17 9:25 p.m., Shu Fai Cheung wrote:
Caution: External email.
Please pardon me if I suggest something unrelated below. Many experts
have made suggestions that I would also like to consider because I
also have a similar issue with some packages.
This is an approach I found, for Rmarkdown vignettes:
https://www.kloppenborg.ca/2021/06/long-running-vignettes/
This is similar to some of the suggestions. The vignette is rendered
locally. It uses the trick that, If we render the vignette by calling
knitr::knit() directly, the extension of the source file does not
matter. The output, although with the extension ".Rmd", actually
contains the results of the code, in chunks starting with "```r", not
"```{r}".
When this pre-buiult .Rmd file is built again, it will just convert
the file to an HTML file, with no need to rerun the code.
The method uses an extension for the source Rmd file (".orig" in the
post) to make sure the "real" source files are ignored when building
the vignettes.
Perhaps this is also a feasible solution for long running vignettes?
Regards,
Shu Fai
On Wed, Oct 18, 2023 at 6:51 AM John Fox wrote:
Dear John,
Unless I'm mistaken, the *installation* time of the package isn't really
at issue. If a user installs a package from a tarball provided by CRAN,
the vignettes aren't normally rebuilt.
Best,
John
On 2023-10-17 6:30 p.m., John Harrold wrote:
Caution: External email.
I ask myself the question: Who is the vignette for? It does server two
purposes. One is testing but primarily it's for the users to learn how to
use a package. I think the testing is secondary, and if it slows down
installation or general usability I'd sacrifice the testing. If it's that
important, then the tests can be added explicitly in tests/.
On Tue, Oct 17, 2023 at 3:04 PM Dirk Eddelbuettel wrote:
On 18 October 2023 at 08:51, Simon Urbanek wrote:
| John,
|
| the short answer is it won't work (it defeats the purpose of vignettes).
Not exactly. Everything is under our (i.e. package author) control, and
when
we want to replace 'computed' values with cached values we can.
All this is somewhat of a charade. "Of course" we want vignettes to run
tests. But then we don't want to fall over random missing .sty files or
fonts
(macOS machines have been less forgiving than others), not to mention
compile
time.
So for simplicity I often pre-make pdf vignettes that get included in other
latex code as source. Works great, never fails, CRAN never complained --
which is somewhat contrary to your statement.
It is effectively the same with tests. We all want maximum test surfaces.
But
when tests fail, or when they run too long, or [insert many other reasons
here] so many packages run tests conditionally. Such is life.
Dirk
| However, this sounds like a purely hypothetical question - CRAN policies
allow long-running vignettes if they declared.
|
| Cheers,
| Simon
|
|
| > On 18/10/2023, at 3:02 AM, John Fox wrote:
| >
| > Hello Dirk,
| >
| > Thank you (and Kevin and John) for addressing my questions.
| >
| > No one directly answered my first question, however, which was whether
the approach that I suggested would work. I guess that the implication is
that it won't, but it would be nice to confirm that before I try something
else, specifically using R.rsp.
| >
| > Best,
| > John
| >
| > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote:
| >> Caution: External email.
| >> On 16 October 2023 at 10:42, Kevin R Coombes wrote:
| >> | Produce a PDF file yourself, then use the "as.is" feature of the
R.rsp
| >> | package.
| >> For completeness, that approach also works directly with Sweave.
Described in
| >> a blog post by Mark van der Loo in 2019, and used in a number of
packages
| >> including a few of mine.
| >> That said, I also used the approach described by John Harrold and
cached
| >> results myself.
| >> Dirk
| >> --
| >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| >> __
| >> R-package-devel@r-project.org mailing list
| >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
| >
| > __
| > R-package-devel@r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-package-devel
| >
|
| __
| R-package-devel@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[[alternative HTML version deleted]]
__
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Please pardon me if I suggest something unrelated below. Many experts
have made suggestions that I would also like to consider because I
also have a similar issue with some packages.
This is an approach I found, for Rmarkdown vignettes:
https://www.kloppenborg.ca/2021/06/long-running-vignettes/
This is similar to some of the suggestions. The vignette is rendered
locally. It uses the trick that, If we render the vignette by calling
knitr::knit() directly, the extension of the source file does not
matter. The output, although with the extension ".Rmd", actually
contains the results of the code, in chunks starting with "```r", not
"```{r}".
When this pre-buiult .Rmd file is built again, it will just convert
the file to an HTML file, with no need to rerun the code.
The method uses an extension for the source Rmd file (".orig" in the
post) to make sure the "real" source files are ignored when building
the vignettes.
Perhaps this is also a feasible solution for long running vignettes?
Regards,
Shu Fai
On Wed, Oct 18, 2023 at 6:51 AM John Fox wrote:
>
> Dear John,
>
> Unless I'm mistaken, the *installation* time of the package isn't really
> at issue. If a user installs a package from a tarball provided by CRAN,
> the vignettes aren't normally rebuilt.
>
> Best,
> John
>
> On 2023-10-17 6:30 p.m., John Harrold wrote:
> > Caution: External email.
> >
> >
> > I ask myself the question: Who is the vignette for? It does server two
> > purposes. One is testing but primarily it's for the users to learn how to
> > use a package. I think the testing is secondary, and if it slows down
> > installation or general usability I'd sacrifice the testing. If it's that
> > important, then the tests can be added explicitly in tests/.
> >
> > On Tue, Oct 17, 2023 at 3:04 PM Dirk Eddelbuettel wrote:
> >
> >>
> >> On 18 October 2023 at 08:51, Simon Urbanek wrote:
> >> | John,
> >> |
> >> | the short answer is it won't work (it defeats the purpose of vignettes).
> >>
> >> Not exactly. Everything is under our (i.e. package author) control, and
> >> when
> >> we want to replace 'computed' values with cached values we can.
> >>
> >> All this is somewhat of a charade. "Of course" we want vignettes to run
> >> tests. But then we don't want to fall over random missing .sty files or
> >> fonts
> >> (macOS machines have been less forgiving than others), not to mention
> >> compile
> >> time.
> >>
> >> So for simplicity I often pre-make pdf vignettes that get included in other
> >> latex code as source. Works great, never fails, CRAN never complained --
> >> which is somewhat contrary to your statement.
> >>
> >> It is effectively the same with tests. We all want maximum test surfaces.
> >> But
> >> when tests fail, or when they run too long, or [insert many other reasons
> >> here] so many packages run tests conditionally. Such is life.
> >>
> >> Dirk
> >>
> >>
> >> | However, this sounds like a purely hypothetical question - CRAN policies
> >> allow long-running vignettes if they declared.
> >> |
> >> | Cheers,
> >> | Simon
> >> |
> >> |
> >> | > On 18/10/2023, at 3:02 AM, John Fox wrote:
> >> | >
> >> | > Hello Dirk,
> >> | >
> >> | > Thank you (and Kevin and John) for addressing my questions.
> >> | >
> >> | > No one directly answered my first question, however, which was whether
> >> the approach that I suggested would work. I guess that the implication is
> >> that it won't, but it would be nice to confirm that before I try something
> >> else, specifically using R.rsp.
> >> | >
> >> | > Best,
> >> | > John
> >> | >
> >> | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote:
> >> | >> Caution: External email.
> >> | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote:
> >> | >> | Produce a PDF file yourself, then use the "as.is" feature of the
> >> R.rsp
> >> | >> | package.
> >> | >> For completeness, that approach also works directly with Sweave.
> >> Described in
> >> | >> a blog post by Mark van der Loo in 2019, and used in a number of
> >> packages
> >> | >> including a few of mine.
> >> | >> That said, I also used the approach described by John Harrold and
> >> cached
> >> | >> results myself.
> >> | >> Dirk
> >> | >> --
> >> | >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> >> | >> __
> >> | >> R-package-devel@r-project.org mailing list
> >> | >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> | >
> >> | > __
> >> | > R-package-devel@r-project.org mailing list
> >> | > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> | >
> >> |
> >> | __
> >> | R-package-devel@r-project.org mailing list
> >> | https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >> --
> >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> >>
> >> __
> >> R-package-devel@r-project.org mailing list
> >>
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Dear John, Unless I'm mistaken, the *installation* time of the package isn't really at issue. If a user installs a package from a tarball provided by CRAN, the vignettes aren't normally rebuilt. Best, John On 2023-10-17 6:30 p.m., John Harrold wrote: Caution: External email. I ask myself the question: Who is the vignette for? It does server two purposes. One is testing but primarily it's for the users to learn how to use a package. I think the testing is secondary, and if it slows down installation or general usability I'd sacrifice the testing. If it's that important, then the tests can be added explicitly in tests/. On Tue, Oct 17, 2023 at 3:04 PM Dirk Eddelbuettel wrote: On 18 October 2023 at 08:51, Simon Urbanek wrote: | John, | | the short answer is it won't work (it defeats the purpose of vignettes). Not exactly. Everything is under our (i.e. package author) control, and when we want to replace 'computed' values with cached values we can. All this is somewhat of a charade. "Of course" we want vignettes to run tests. But then we don't want to fall over random missing .sty files or fonts (macOS machines have been less forgiving than others), not to mention compile time. So for simplicity I often pre-make pdf vignettes that get included in other latex code as source. Works great, never fails, CRAN never complained -- which is somewhat contrary to your statement. It is effectively the same with tests. We all want maximum test surfaces. But when tests fail, or when they run too long, or [insert many other reasons here] so many packages run tests conditionally. Such is life. Dirk | However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. | | Cheers, | Simon | | | > On 18/10/2023, at 3:02 AM, John Fox wrote: | > | > Hello Dirk, | > | > Thank you (and Kevin and John) for addressing my questions. | > | > No one directly answered my first question, however, which was whether the approach that I suggested would work. I guess that the implication is that it won't, but it would be nice to confirm that before I try something else, specifically using R.rsp. | > | > Best, | > John | > | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: | >> Caution: External email. | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: | >> | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | >> | package. | >> For completeness, that approach also works directly with Sweave. Described in | >> a blog post by Mark van der Loo in 2019, and used in a number of packages | >> including a few of mine. | >> That said, I also used the approach described by John Harrold and cached | >> results myself. | >> Dirk | >> -- | >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | >> __ | >> R-package-devel@r-project.org mailing list | >> https://stat.ethz.ch/mailman/listinfo/r-package-devel | > | > __ | > R-package-devel@r-project.org mailing list | > https://stat.ethz.ch/mailman/listinfo/r-package-devel | > | | __ | R-package-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-package-devel -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list 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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
And if the vignette claims to help the users, but contains errors? Then it's not very helpful at all. That's what the testing is there to detect. Duncan Murdoch On 17/10/2023 6:30 p.m., John Harrold wrote: I ask myself the question: Who is the vignette for? It does server two purposes. One is testing but primarily it's for the users to learn how to use a package. I think the testing is secondary, and if it slows down installation or general usability I'd sacrifice the testing. If it's that important, then the tests can be added explicitly in tests/. On Tue, Oct 17, 2023 at 3:04 PM Dirk Eddelbuettel wrote: On 18 October 2023 at 08:51, Simon Urbanek wrote: | John, | | the short answer is it won't work (it defeats the purpose of vignettes). Not exactly. Everything is under our (i.e. package author) control, and when we want to replace 'computed' values with cached values we can. All this is somewhat of a charade. "Of course" we want vignettes to run tests. But then we don't want to fall over random missing .sty files or fonts (macOS machines have been less forgiving than others), not to mention compile time. So for simplicity I often pre-make pdf vignettes that get included in other latex code as source. Works great, never fails, CRAN never complained -- which is somewhat contrary to your statement. It is effectively the same with tests. We all want maximum test surfaces. But when tests fail, or when they run too long, or [insert many other reasons here] so many packages run tests conditionally. Such is life. Dirk | However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. | | Cheers, | Simon | | | > On 18/10/2023, at 3:02 AM, John Fox wrote: | > | > Hello Dirk, | > | > Thank you (and Kevin and John) for addressing my questions. | > | > No one directly answered my first question, however, which was whether the approach that I suggested would work. I guess that the implication is that it won't, but it would be nice to confirm that before I try something else, specifically using R.rsp. | > | > Best, | > John | > | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: | >> Caution: External email. | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: | >> | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | >> | package. | >> For completeness, that approach also works directly with Sweave. Described in | >> a blog post by Mark van der Loo in 2019, and used in a number of packages | >> including a few of mine. | >> That said, I also used the approach described by John Harrold and cached | >> results myself. | >> Dirk | >> -- | >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | >> __ | >> R-package-devel@r-project.org mailing list | >> https://stat.ethz.ch/mailman/listinfo/r-package-devel | > | > __ | > R-package-devel@r-project.org mailing list | > https://stat.ethz.ch/mailman/listinfo/r-package-devel | > | | __ | R-package-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-package-devel -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list 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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
I ask myself the question: Who is the vignette for? It does server two purposes. One is testing but primarily it's for the users to learn how to use a package. I think the testing is secondary, and if it slows down installation or general usability I'd sacrifice the testing. If it's that important, then the tests can be added explicitly in tests/. On Tue, Oct 17, 2023 at 3:04 PM Dirk Eddelbuettel wrote: > > On 18 October 2023 at 08:51, Simon Urbanek wrote: > | John, > | > | the short answer is it won't work (it defeats the purpose of vignettes). > > Not exactly. Everything is under our (i.e. package author) control, and > when > we want to replace 'computed' values with cached values we can. > > All this is somewhat of a charade. "Of course" we want vignettes to run > tests. But then we don't want to fall over random missing .sty files or > fonts > (macOS machines have been less forgiving than others), not to mention > compile > time. > > So for simplicity I often pre-make pdf vignettes that get included in other > latex code as source. Works great, never fails, CRAN never complained -- > which is somewhat contrary to your statement. > > It is effectively the same with tests. We all want maximum test surfaces. > But > when tests fail, or when they run too long, or [insert many other reasons > here] so many packages run tests conditionally. Such is life. > > Dirk > > > | However, this sounds like a purely hypothetical question - CRAN policies > allow long-running vignettes if they declared. > | > | Cheers, > | Simon > | > | > | > On 18/10/2023, at 3:02 AM, John Fox wrote: > | > > | > Hello Dirk, > | > > | > Thank you (and Kevin and John) for addressing my questions. > | > > | > No one directly answered my first question, however, which was whether > the approach that I suggested would work. I guess that the implication is > that it won't, but it would be nice to confirm that before I try something > else, specifically using R.rsp. > | > > | > Best, > | > John > | > > | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: > | >> Caution: External email. > | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: > | >> | Produce a PDF file yourself, then use the "as.is" feature of the > R.rsp > | >> | package. > | >> For completeness, that approach also works directly with Sweave. > Described in > | >> a blog post by Mark van der Loo in 2019, and used in a number of > packages > | >> including a few of mine. > | >> That said, I also used the approach described by John Harrold and > cached > | >> results myself. > | >> Dirk > | >> -- > | >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > | >> __ > | >> R-package-devel@r-project.org mailing list > | >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > | > > | > __ > | > R-package-devel@r-project.org mailing list > | > https://stat.ethz.ch/mailman/listinfo/r-package-devel > | > > | > | __ > | R-package-devel@r-project.org mailing list > | https://stat.ethz.ch/mailman/listinfo/r-package-devel > > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > > __ > R-package-devel@r-project.org mailing list > 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
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Dirk, I think you misread the email - John was was asking specifically about his approach to use REBUILD_CV_VIGNETTES without any caching since that was the original question which no one answered in the thread - and that was what I was answering. The alternative approaches were already discussed to death so I didn't comment on those. Cheers, Simon > On 18/10/2023, at 11:03 AM, Dirk Eddelbuettel wrote: > > > On 18 October 2023 at 08:51, Simon Urbanek wrote: > | John, > | > | the short answer is it won't work (it defeats the purpose of vignettes). > > Not exactly. Everything is under our (i.e. package author) control, and when > we want to replace 'computed' values with cached values we can. > > All this is somewhat of a charade. "Of course" we want vignettes to run > tests. But then we don't want to fall over random missing .sty files or fonts > (macOS machines have been less forgiving than others), not to mention compile > time. > > So for simplicity I often pre-make pdf vignettes that get included in other > latex code as source. Works great, never fails, CRAN never complained -- > which is somewhat contrary to your statement. > > It is effectively the same with tests. We all want maximum test surfaces. But > when tests fail, or when they run too long, or [insert many other reasons > here] so many packages run tests conditionally. Such is life. > > Dirk > > > | However, this sounds like a purely hypothetical question - CRAN policies > allow long-running vignettes if they declared. > | > | Cheers, > | Simon > | > | > | > On 18/10/2023, at 3:02 AM, John Fox wrote: > | > > | > Hello Dirk, > | > > | > Thank you (and Kevin and John) for addressing my questions. > | > > | > No one directly answered my first question, however, which was whether > the approach that I suggested would work. I guess that the implication is > that it won't, but it would be nice to confirm that before I try something > else, specifically using R.rsp. > | > > | > Best, > | > John > | > > | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: > | >> Caution: External email. > | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: > | >> | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp > | >> | package. > | >> For completeness, that approach also works directly with Sweave. > Described in > | >> a blog post by Mark van der Loo in 2019, and used in a number of packages > | >> including a few of mine. > | >> That said, I also used the approach described by John Harrold and cached > | >> results myself. > | >> Dirk > | >> -- > | >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > | >> __ > | >> R-package-devel@r-project.org mailing list > | >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > | > > | > __ > | > R-package-devel@r-project.org mailing list > | > https://stat.ethz.ch/mailman/listinfo/r-package-devel > | > > | > | __ > | R-package-devel@r-project.org mailing list > | https://stat.ethz.ch/mailman/listinfo/r-package-devel > > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
On 18 October 2023 at 08:51, Simon Urbanek wrote: | John, | | the short answer is it won't work (it defeats the purpose of vignettes). Not exactly. Everything is under our (i.e. package author) control, and when we want to replace 'computed' values with cached values we can. All this is somewhat of a charade. "Of course" we want vignettes to run tests. But then we don't want to fall over random missing .sty files or fonts (macOS machines have been less forgiving than others), not to mention compile time. So for simplicity I often pre-make pdf vignettes that get included in other latex code as source. Works great, never fails, CRAN never complained -- which is somewhat contrary to your statement. It is effectively the same with tests. We all want maximum test surfaces. But when tests fail, or when they run too long, or [insert many other reasons here] so many packages run tests conditionally. Such is life. Dirk | However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. | | Cheers, | Simon | | | > On 18/10/2023, at 3:02 AM, John Fox wrote: | > | > Hello Dirk, | > | > Thank you (and Kevin and John) for addressing my questions. | > | > No one directly answered my first question, however, which was whether the approach that I suggested would work. I guess that the implication is that it won't, but it would be nice to confirm that before I try something else, specifically using R.rsp. | > | > Best, | > John | > | > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: | >> Caution: External email. | >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: | >> | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | >> | package. | >> For completeness, that approach also works directly with Sweave. Described in | >> a blog post by Mark van der Loo in 2019, and used in a number of packages | >> including a few of mine. | >> That said, I also used the approach described by John Harrold and cached | >> results myself. | >> Dirk | >> -- | >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org | >> __ | >> R-package-devel@r-project.org mailing list | >> https://stat.ethz.ch/mailman/listinfo/r-package-devel | > | > __ | > R-package-devel@r-project.org mailing list | > https://stat.ethz.ch/mailman/listinfo/r-package-devel | > | | __ | R-package-devel@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-package-devel -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Hello Duncan, On 2023-10-17 4:43 p.m., Duncan Murdoch wrote: Caution: External email. On 17/10/2023 4:21 p.m., John Fox wrote: Hello Simon, On 2023-10-17 3:51 p.m., Simon Urbanek wrote: Caution: External email. John, the short answer is it won't work (it defeats the purpose of vignettes). Thank you for confirming that. However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. I assume that we'd declare the long-running vignette in our submission note to CRAN. Maybe that's better than pre-building the HTML vignettes in the package. There's also the "BuildVignettes: false" field in DESCRIPTION, but its use is discouraged, and I don't think it allows you to ask CRAN to build some vignettes but not all. Thanks, I wasn't aware of that. There are two vignettes, one of which is slow to build. Given Simon's suggestion, we'll likely submit the package with a note about the long-running vignette, and if that proves problematic, we can use R.asp to pre-build the HTML vignettes. Best, John Duncan Murdoch Best, John Cheers, Simon On 18/10/2023, at 3:02 AM, John Fox wrote: Hello Dirk, Thank you (and Kevin and John) for addressing my questions. No one directly answered my first question, however, which was whether the approach that I suggested would work. I guess that the implication is that it won't, but it would be nice to confirm that before I try something else, specifically using R.rsp. Best, John On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: Caution: External email. On 16 October 2023 at 10:42, Kevin R Coombes wrote: | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | package. For completeness, that approach also works directly with Sweave. Described in a blog post by Mark van der Loo in 2019, and used in a number of packages including a few of mine. That said, I also used the approach described by John Harrold and cached results myself. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
On 17/10/2023 4:21 p.m., John Fox wrote: Hello Simon, On 2023-10-17 3:51 p.m., Simon Urbanek wrote: Caution: External email. John, the short answer is it won't work (it defeats the purpose of vignettes). Thank you for confirming that. However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. I assume that we'd declare the long-running vignette in our submission note to CRAN. Maybe that's better than pre-building the HTML vignettes in the package. There's also the "BuildVignettes: false" field in DESCRIPTION, but its use is discouraged, and I don't think it allows you to ask CRAN to build some vignettes but not all. Duncan Murdoch Best, John Cheers, Simon On 18/10/2023, at 3:02 AM, John Fox wrote: Hello Dirk, Thank you (and Kevin and John) for addressing my questions. No one directly answered my first question, however, which was whether the approach that I suggested would work. I guess that the implication is that it won't, but it would be nice to confirm that before I try something else, specifically using R.rsp. Best, John On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: Caution: External email. On 16 October 2023 at 10:42, Kevin R Coombes wrote: | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | package. For completeness, that approach also works directly with Sweave. Described in a blog post by Mark van der Loo in 2019, and used in a number of packages including a few of mine. That said, I also used the approach described by John Harrold and cached results myself. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Hello Simon, On 2023-10-17 3:51 p.m., Simon Urbanek wrote: Caution: External email. John, the short answer is it won't work (it defeats the purpose of vignettes). Thank you for confirming that. However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. I assume that we'd declare the long-running vignette in our submission note to CRAN. Maybe that's better than pre-building the HTML vignettes in the package. Best, John Cheers, Simon On 18/10/2023, at 3:02 AM, John Fox wrote: Hello Dirk, Thank you (and Kevin and John) for addressing my questions. No one directly answered my first question, however, which was whether the approach that I suggested would work. I guess that the implication is that it won't, but it would be nice to confirm that before I try something else, specifically using R.rsp. Best, John On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: Caution: External email. On 16 October 2023 at 10:42, Kevin R Coombes wrote: | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | package. For completeness, that approach also works directly with Sweave. Described in a blog post by Mark van der Loo in 2019, and used in a number of packages including a few of mine. That said, I also used the approach described by John Harrold and cached results myself. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Dear Henrik,
I'd already read the R.rsp vignette to which you refer, and, as I said,
confirmed that I can use R.rsp to implement static HTML vignettes for
our package.
Thank you for the confirmation,
John
On 2023-10-17 3:50 p.m., Henrik Bengtsson wrote:
Caution: External email.
On Tue, Oct 17, 2023 at 12:45 PM John Fox wrote:
Hello Dirk,
Thank you for the additional information.
As you suggest, what you did to distribute pre-built PDF vignettes is
quite similar to what R.rsp does, except that the latter also supports
pre-built HTML vignettes, which is what I'd prefer to distribute. Since
Author of R.rsp here: It supports both static PDFs and static HTMLs, cf.
https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf
/Henrik
I apparently have that working now, we'll probably go with it unless we
hit snags when the package is sent to CRAN.
While I appreciate the offer, it's probably not necessary for you to
spend more time on this now.
Thanks again,
John
On 2023-10-17 3:19 p.m., Dirk Eddelbuettel wrote:
Caution: External email.
John,
On 17 October 2023 at 10:02, John Fox wrote:
| Hello Dirk,
|
| Thank you (and Kevin and John) for addressing my questions.
|
| No one directly answered my first question, however, which was whether
| the approach that I suggested would work. I guess that the implication
| is that it won't, but it would be nice to confirm that before I try
| something else, specifically using R.rsp.
I am a little remote here, both mentally and physically. What I might do here
in the case of your long-running vignette, and have done in about half a
dozen packages where I wanted 'certainty' and no surprises, is to render the
pdf vignette I want as I want them locally, ship them in the package as an
included file (sometimes from a subdirectory) and have a five-or-so line
Sweave .Rnw file include it. That works without hassles. Here is the Rnw I
use for package anytime
-
\documentclass{article}
\usepackage{pdfpages}
%\VignetteIndexEntry{Introduction to anytime}
%\VignetteKeywords{anytime, date, datetime, conversion}
%\VignettePackage{anytime}
%\VignetteEncoding{UTF-8}
\begin{document}
\includepdf[pages=-, fitpaper=true]{anytime-intro.pdf}
\end{document}
-
That is five lines of LaTeX code slurping in the pdf (per the blog post by
Mark). As I understand it R.rsp does something similar at the marginal cost
of an added dependency.
Now, as mentioned, you can also 'conditionally' conpute in a vignette and
choose if and when to use a data cache. I think that we show most of that in
the package described in the RJournal piece by Brooke and myself on drat for
data repositories. (We may be skipping the compute when the data is not
accessible. Loading a precomputed set is similar. I may be doing that in the
much older never quite finished gcbd package and its vignette.
Hope this helps, maybe more once I am back home.
Cheers, Dirk
| Best,
| John
|
| On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote:
| > Caution: External email.
| >
| >
| > On 16 October 2023 at 10:42, Kevin R Coombes wrote:
| > | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp
| > | package.
| >
| > For completeness, that approach also works directly with Sweave. Described
in
| > a blog post by Mark van der Loo in 2019, and used in a number of packages
| > including a few of mine.
| >
| > That said, I also used the approach described by John Harrold and cached
| > results myself.
| >
| > Dirk
| >
| > --
| > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| >
| > __
| > R-package-devel@r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-package-devel
|
--
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__
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Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
John, the short answer is it won't work (it defeats the purpose of vignettes). However, this sounds like a purely hypothetical question - CRAN policies allow long-running vignettes if they declared. Cheers, Simon > On 18/10/2023, at 3:02 AM, John Fox wrote: > > Hello Dirk, > > Thank you (and Kevin and John) for addressing my questions. > > No one directly answered my first question, however, which was whether the > approach that I suggested would work. I guess that the implication is that it > won't, but it would be nice to confirm that before I try something else, > specifically using R.rsp. > > Best, > John > > On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: >> Caution: External email. >> On 16 October 2023 at 10:42, Kevin R Coombes wrote: >> | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp >> | package. >> For completeness, that approach also works directly with Sweave. Described in >> a blog post by Mark van der Loo in 2019, and used in a number of packages >> including a few of mine. >> That said, I also used the approach described by John Harrold and cached >> results myself. >> Dirk >> -- >> dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >> __ >> R-package-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
On Tue, Oct 17, 2023 at 12:45 PM John Fox wrote:
>
> Hello Dirk,
>
> Thank you for the additional information.
>
> As you suggest, what you did to distribute pre-built PDF vignettes is
> quite similar to what R.rsp does, except that the latter also supports
> pre-built HTML vignettes, which is what I'd prefer to distribute. Since
Author of R.rsp here: It supports both static PDFs and static HTMLs, cf.
https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf
/Henrik
> I apparently have that working now, we'll probably go with it unless we
> hit snags when the package is sent to CRAN.
>
> While I appreciate the offer, it's probably not necessary for you to
> spend more time on this now.
>
> Thanks again,
> John
>
> On 2023-10-17 3:19 p.m., Dirk Eddelbuettel wrote:
> > Caution: External email.
> >
> >
> > John,
> >
> > On 17 October 2023 at 10:02, John Fox wrote:
> > | Hello Dirk,
> > |
> > | Thank you (and Kevin and John) for addressing my questions.
> > |
> > | No one directly answered my first question, however, which was whether
> > | the approach that I suggested would work. I guess that the implication
> > | is that it won't, but it would be nice to confirm that before I try
> > | something else, specifically using R.rsp.
> >
> > I am a little remote here, both mentally and physically. What I might do
> > here
> > in the case of your long-running vignette, and have done in about half a
> > dozen packages where I wanted 'certainty' and no surprises, is to render the
> > pdf vignette I want as I want them locally, ship them in the package as an
> > included file (sometimes from a subdirectory) and have a five-or-so line
> > Sweave .Rnw file include it. That works without hassles. Here is the Rnw I
> > use for package anytime
> >
> > -
> > \documentclass{article}
> > \usepackage{pdfpages}
> > %\VignetteIndexEntry{Introduction to anytime}
> > %\VignetteKeywords{anytime, date, datetime, conversion}
> > %\VignettePackage{anytime}
> > %\VignetteEncoding{UTF-8}
> >
> > \begin{document}
> > \includepdf[pages=-, fitpaper=true]{anytime-intro.pdf}
> > \end{document}
> > -
> >
> > That is five lines of LaTeX code slurping in the pdf (per the blog post by
> > Mark). As I understand it R.rsp does something similar at the marginal cost
> > of an added dependency.
> >
> > Now, as mentioned, you can also 'conditionally' conpute in a vignette and
> > choose if and when to use a data cache. I think that we show most of that in
> > the package described in the RJournal piece by Brooke and myself on drat for
> > data repositories. (We may be skipping the compute when the data is not
> > accessible. Loading a precomputed set is similar. I may be doing that in the
> > much older never quite finished gcbd package and its vignette.
> >
> > Hope this helps, maybe more once I am back home.
> >
> > Cheers, Dirk
> >
> > | Best,
> > | John
> > |
> > | On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote:
> > | > Caution: External email.
> > | >
> > | >
> > | > On 16 October 2023 at 10:42, Kevin R Coombes wrote:
> > | > | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp
> > | > | package.
> > | >
> > | > For completeness, that approach also works directly with Sweave.
> > Described in
> > | > a blog post by Mark van der Loo in 2019, and used in a number of
> > packages
> > | > including a few of mine.
> > | >
> > | > That said, I also used the approach described by John Harrold and cached
> > | > results myself.
> > | >
> > | > Dirk
> > | >
> > | > --
> > | > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
> > | >
> > | > __
> > | > R-package-devel@r-project.org mailing list
> > | > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > |
> >
> > --
> > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Hello Dirk,
Thank you for the additional information.
As you suggest, what you did to distribute pre-built PDF vignettes is
quite similar to what R.rsp does, except that the latter also supports
pre-built HTML vignettes, which is what I'd prefer to distribute. Since
I apparently have that working now, we'll probably go with it unless we
hit snags when the package is sent to CRAN.
While I appreciate the offer, it's probably not necessary for you to
spend more time on this now.
Thanks again,
John
On 2023-10-17 3:19 p.m., Dirk Eddelbuettel wrote:
Caution: External email.
John,
On 17 October 2023 at 10:02, John Fox wrote:
| Hello Dirk,
|
| Thank you (and Kevin and John) for addressing my questions.
|
| No one directly answered my first question, however, which was whether
| the approach that I suggested would work. I guess that the implication
| is that it won't, but it would be nice to confirm that before I try
| something else, specifically using R.rsp.
I am a little remote here, both mentally and physically. What I might do here
in the case of your long-running vignette, and have done in about half a
dozen packages where I wanted 'certainty' and no surprises, is to render the
pdf vignette I want as I want them locally, ship them in the package as an
included file (sometimes from a subdirectory) and have a five-or-so line
Sweave .Rnw file include it. That works without hassles. Here is the Rnw I
use for package anytime
-
\documentclass{article}
\usepackage{pdfpages}
%\VignetteIndexEntry{Introduction to anytime}
%\VignetteKeywords{anytime, date, datetime, conversion}
%\VignettePackage{anytime}
%\VignetteEncoding{UTF-8}
\begin{document}
\includepdf[pages=-, fitpaper=true]{anytime-intro.pdf}
\end{document}
-
That is five lines of LaTeX code slurping in the pdf (per the blog post by
Mark). As I understand it R.rsp does something similar at the marginal cost
of an added dependency.
Now, as mentioned, you can also 'conditionally' conpute in a vignette and
choose if and when to use a data cache. I think that we show most of that in
the package described in the RJournal piece by Brooke and myself on drat for
data repositories. (We may be skipping the compute when the data is not
accessible. Loading a precomputed set is similar. I may be doing that in the
much older never quite finished gcbd package and its vignette.
Hope this helps, maybe more once I am back home.
Cheers, Dirk
| Best,
| John
|
| On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote:
| > Caution: External email.
| >
| >
| > On 16 October 2023 at 10:42, Kevin R Coombes wrote:
| > | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp
| > | package.
| >
| > For completeness, that approach also works directly with Sweave. Described
in
| > a blog post by Mark van der Loo in 2019, and used in a number of packages
| > including a few of mine.
| >
| > That said, I also used the approach described by John Harrold and cached
| > results myself.
| >
| > Dirk
| >
| > --
| > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| >
| > __
| > R-package-devel@r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-package-devel
|
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
__
R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
John,
On 17 October 2023 at 10:02, John Fox wrote:
| Hello Dirk,
|
| Thank you (and Kevin and John) for addressing my questions.
|
| No one directly answered my first question, however, which was whether
| the approach that I suggested would work. I guess that the implication
| is that it won't, but it would be nice to confirm that before I try
| something else, specifically using R.rsp.
I am a little remote here, both mentally and physically. What I might do here
in the case of your long-running vignette, and have done in about half a
dozen packages where I wanted 'certainty' and no surprises, is to render the
pdf vignette I want as I want them locally, ship them in the package as an
included file (sometimes from a subdirectory) and have a five-or-so line
Sweave .Rnw file include it. That works without hassles. Here is the Rnw I
use for package anytime
-
\documentclass{article}
\usepackage{pdfpages}
%\VignetteIndexEntry{Introduction to anytime}
%\VignetteKeywords{anytime, date, datetime, conversion}
%\VignettePackage{anytime}
%\VignetteEncoding{UTF-8}
\begin{document}
\includepdf[pages=-, fitpaper=true]{anytime-intro.pdf}
\end{document}
-
That is five lines of LaTeX code slurping in the pdf (per the blog post by
Mark). As I understand it R.rsp does something similar at the marginal cost
of an added dependency.
Now, as mentioned, you can also 'conditionally' conpute in a vignette and
choose if and when to use a data cache. I think that we show most of that in
the package described in the RJournal piece by Brooke and myself on drat for
data repositories. (We may be skipping the compute when the data is not
accessible. Loading a precomputed set is similar. I may be doing that in the
much older never quite finished gcbd package and its vignette.
Hope this helps, maybe more once I am back home.
Cheers, Dirk
| Best,
| John
|
| On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote:
| > Caution: External email.
| >
| >
| > On 16 October 2023 at 10:42, Kevin R Coombes wrote:
| > | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp
| > | package.
| >
| > For completeness, that approach also works directly with Sweave. Described
in
| > a blog post by Mark van der Loo in 2019, and used in a number of packages
| > including a few of mine.
| >
| > That said, I also used the approach described by John Harrold and cached
| > results myself.
| >
| > Dirk
| >
| > --
| > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
| >
| > __
| > R-package-devel@r-project.org mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-package-devel
|
--
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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] Suppressing long-running vignette code in CRAN submission
Hello Dirk, Thank you (and Kevin and John) for addressing my questions. No one directly answered my first question, however, which was whether the approach that I suggested would work. I guess that the implication is that it won't, but it would be nice to confirm that before I try something else, specifically using R.rsp. Best, John On 2023-10-17 4:02 a.m., Dirk Eddelbuettel wrote: Caution: External email. On 16 October 2023 at 10:42, Kevin R Coombes wrote: | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | package. For completeness, that approach also works directly with Sweave. Described in a blog post by Mark van der Loo in 2019, and used in a number of packages including a few of mine. That said, I also used the approach described by John Harrold and cached results myself. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Dear Sylvain, В Tue, 17 Oct 2023 09:45:25 + (UTC) "cartograf...@gmail.com" пишет: > I've uploaded cartogRaflow version 1.0.4 with sf package. > I've submitted yesterday the version 1.0.4 in CRAN and received 2 two > error message because cartogRaflow is archived and use rgeos maptools > in version 1.0.3 Could you please show us the full R CMD check report e-mailed to you in response to the CRAN submission? A NOTE saying that the previous version had been archived is to be expected. If it's all your package got, it will be manually reviewed later and published. -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
On 16 October 2023 at 10:42, Kevin R Coombes wrote: | Produce a PDF file yourself, then use the "as.is" feature of the R.rsp | package. For completeness, that approach also works directly with Sweave. Described in a blog post by Mark van der Loo in 2019, and used in a number of packages including a few of mine. That said, I also used the approach described by John Harrold and cached results myself. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission
Produce a PDF file yourself, then use the "as.is" feature of the R.rsp
package.
Specifically, include this line in your DESCRIPTION file:
VignetteBuilder: R.rsp
Let's say the pdf file is called "myfile.pdf". Create a file called
"myfile.pdf.asis" that contains the vignette instructions. Put it in the
vignette directory along with the PDF file. Mine looks like:
%\VignetteIndexEntry{PUT VIGNETTE TITLE HERE}
%\VignetteKeywords{PUT KEYWORDS HERE}
%\VignetteDepends{PACKAGE_NAME}
%\VignettePackage{PACKAGE_NAME}
%\VignetteEngine{R.rsp::asis}
I am not certain if this works for an HTML vignette, but I see no reason
why it shouldn't.
Best,
Kevin
On 10/16/2023 10:14 AM, John Fox wrote:
Dear list members,
I believe that this issue has been discussed previously, but I'm not
sure that I have the solution right.
Georges Monette and I have developed a package that we intend to
submit soon to CRAN which has a vignette including code that takes a
long time to run. The sources for the package are available at
.
We figure that we have to suppress running the code the vignette when
CRAN checks the package or the check time will be excessive.
The vignette is written as a .Rmd file to be compiled by knitr,
producing an HTML vignette. The top of the .Rmd file looks like this:
--- snip ---
---
title: "Cross-validation of regression models"
author: "John Fox and Georges Monette"
date: "`r Sys.Date()`"
package: cv
output:
rmarkdown::html_vignette:
fig_caption: yes
bibliography: ["cv.bib"]
csl: apa.csl
vignette: >
%\VignetteIndexEntry{Cross-validation of regression models}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r setup, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
message = TRUE,
warning = TRUE,
fig.align = "center",
fig.height = 6,
fig.width = 7,
fig.path = "fig/",
dev = "png",
comment = "#>",
eval = nzchar(Sys.getenv("REBUILD_CV_VIGNETTES"))
)
### other irrelevant setup code not shown ###
```
--- snip ---
So (near the bottom), if the environment variable REBUILD_CV_VIGNETTES
isn't empty, the code blocks in the vignette are evaluated, otherwise
not. To build the tarball for the package to be submitted to CRAN, we
will set REBUILD_CV_VIGNETTES to "true". That works as intended.
If we submit the tarball to CRAN, I believe that the package as
distributed by CRAN will include the HTML vignette from our tarball,
showing the evaluated code blocks, but when CRAN checks the package,
these long-running code blocks will not be executed (because
REBUILD_CV_VIGNETTES will not exist on the CRAN check machines).
My questions:
Is that correct?
If not, how can we ensure that the complete vignette is distributed by
CRAN without causing an overly long CRAN check time?
In particular, we don't want CRAN to rebuild and distribute the
vignette, because the resulting HTML file won't show the evaluated code.
Any assistance would be appreciated.
Thank you,
John
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