[R-pkg-devel] CRAN Windows failure due to old pandoc ?
I had a submission fail and bomb with this error on Windows: Flavor: r-devel-windows-ix86+x86_64 Check: re-building of vignette outputs, Result: WARNING Error(s) in re-building vignettes: --- re-building 'vignettefilename.Rmd' using rmarkdown pandoc.exe: unrecognized option `--lua-filter' unrecognized option `--lua-filter' unrecognized option `--lua-filter' Try pandoc.exe --help for more information. Error: processing vignette 'vignettefilename.Rmd' failed with diagnostics: pandoc document conversion failed with error 2 --- failed re-building 'vignettefilename.Rmd' SUMMARY: processing the following file failed: 'vignettefilename.Rmd' Error: Vignette re-building failed. Execution halted This looks like a host configuration problem: edd@rob:~$ pandoc --help | grep lua -L SCRIPTPATH --lua-filter=SCRIPTPATH edd@rob:~$ pandoc --version | head -1 pandoc 2.9.2.1 edd@rob:~$ Can we expect CRAN to update its pandoc binary? Or will we have to 'for now' rely on 'reply-all', explaining to CRAN that the failure is from their end? As they in the press, I had reached out to CRAN but they 'have not yet responded to requests for comments' as we know they're busy. Anybody seen this error though? Dirk -- https://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] CRAN Windows failure due to old pandoc ?
On 26/09/2020 9:14 a.m., Dirk Eddelbuettel wrote:
I had a submission fail and bomb with this error on Windows:
Flavor: r-devel-windows-ix86+x86_64
Check: re-building of vignette outputs, Result: WARNING
Error(s) in re-building vignettes:
--- re-building 'vignettefilename.Rmd' using rmarkdown
pandoc.exe: unrecognized option `--lua-filter'
unrecognized option `--lua-filter'
unrecognized option `--lua-filter'
Try pandoc.exe --help for more information.
Error: processing vignette 'vignettefilename.Rmd' failed with diagnostics:
pandoc document conversion failed with error 2
--- failed re-building 'vignettefilename.Rmd'
SUMMARY: processing the following file failed:
'vignettefilename.Rmd'
Error: Vignette re-building failed.
Execution halted
This looks like a host configuration problem:
edd@rob:~$ pandoc --help | grep lua
-L SCRIPTPATH --lua-filter=SCRIPTPATH
edd@rob:~$ pandoc --version | head -1
pandoc 2.9.2.1
edd@rob:~$
Can we expect CRAN to update its pandoc binary? Or will we have to 'for now'
rely on 'reply-all', explaining to CRAN that the failure is from their end?
As they in the press, I had reached out to CRAN but they 'have not yet
responded to requests for comments' as we know they're busy. Anybody seen
this error though?
I haven't seen that one, but I regularly get errors in rgl and tables
because of missing or insufficient pandoc on some systems. I added
lines like
SystemRequirements: pandoc (>= 1.12.3) for vignettes
to DESCRIPTION to state the Pandoc version, added rmarkdown to the
Suggests list, and added code like this to the start of HTML vignettes:
```{r echo = FALSE}
if (!requireNamespace("rmarkdown") ||
!rmarkdown::pandoc_available("1.12.3")) {
warning("This vignette requires pandoc version 1.12.3; code will not
run in older versions.")
knitr::opts_chunk$set(eval = FALSE)
}
```
This makes the test happy, though it also makes the vignette pretty
useless on systems that don't meet the stated requirements. Since
SystemRequirements is free-form, I can see why CRAN doesn't do automatic
interpretation of it, but it would be nice if they did.
Duncan Murdoch
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Re: [R-pkg-devel] CRAN Windows failure due to old pandoc ?
On 26 September 2020 at 11:50, Duncan Murdoch wrote:
| On 26/09/2020 9:14 a.m., Dirk Eddelbuettel wrote:
| >
| > I had a submission fail and bomb with this error on Windows:
| >
| >Flavor: r-devel-windows-ix86+x86_64
| >Check: re-building of vignette outputs, Result: WARNING
| > Error(s) in re-building vignettes:
| > --- re-building 'vignettefilename.Rmd' using rmarkdown
| > pandoc.exe: unrecognized option `--lua-filter'
| > unrecognized option `--lua-filter'
| > unrecognized option `--lua-filter'
| > Try pandoc.exe --help for more information.
| > Error: processing vignette 'vignettefilename.Rmd' failed with
diagnostics:
| > pandoc document conversion failed with error 2
| > --- failed re-building 'vignettefilename.Rmd'
| >
| > SUMMARY: processing the following file failed:
| >'vignettefilename.Rmd'
| >
| > Error: Vignette re-building failed.
| > Execution halted
| >
| > This looks like a host configuration problem:
| >
| >edd@rob:~$ pandoc --help | grep lua
| > -L SCRIPTPATH --lua-filter=SCRIPTPATH
| >edd@rob:~$ pandoc --version | head -1
| >pandoc 2.9.2.1
| >edd@rob:~$
| >
| > Can we expect CRAN to update its pandoc binary? Or will we have to 'for now'
| > rely on 'reply-all', explaining to CRAN that the failure is from their end?
| >
| > As they in the press, I had reached out to CRAN but they 'have not yet
| > responded to requests for comments' as we know they're busy. Anybody seen
| > this error though?
|
| I haven't seen that one, but I regularly get errors in rgl and tables
| because of missing or insufficient pandoc on some systems. I added
| lines like
|
|SystemRequirements: pandoc (>= 1.12.3) for vignettes
|
| to DESCRIPTION to state the Pandoc version, added rmarkdown to the
| Suggests list, and added code like this to the start of HTML vignettes:
|
| ```{r echo = FALSE}
| if (!requireNamespace("rmarkdown") ||
| !rmarkdown::pandoc_available("1.12.3")) {
|warning("This vignette requires pandoc version 1.12.3; code will not
| run in older versions.")
|knitr::opts_chunk$set(eval = FALSE)
| }
| ```
Good point! Brooke and I actually recommend exactly that---conditional
vignette builds---in our R Journal paper on drat for data repos (via Suggests).
But (because of the overall fragility of these pipelines as well as
preference for generally lighter setups) my vignettes actually tend to not
even run code. I mostly just use three backticks followed by the language
for which I desire highlighting from pandoc, i.e. ```r or ```c++.
Maybe we would need to pass the minimum version check into rmarkdown as an
option so that rmarkdown knows not to ask for `--lua-filter` on setups where
rmarkdown knows pandoc is too old? Or maybe make the vignette builder barf?
| This makes the test happy, though it also makes the vignette pretty
| useless on systems that don't meet the stated requirements. Since
| SystemRequirements is free-form, I can see why CRAN doesn't do automatic
| interpretation of it, but it would be nice if they did.
Alas, the free-form requirement has been a constraint for a long time indeed.
Dirk
--
https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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Re: [R-pkg-devel] CRAN Windows failure due to old pandoc ?
On 26/09/2020 12:54 p.m., Dirk Eddelbuettel wrote:
On 26 September 2020 at 11:50, Duncan Murdoch wrote:
| On 26/09/2020 9:14 a.m., Dirk Eddelbuettel wrote:
| >
| > I had a submission fail and bomb with this error on Windows:
| >
| >Flavor: r-devel-windows-ix86+x86_64
| >Check: re-building of vignette outputs, Result: WARNING
| > Error(s) in re-building vignettes:
| > --- re-building 'vignettefilename.Rmd' using rmarkdown
| > pandoc.exe: unrecognized option `--lua-filter'
| > unrecognized option `--lua-filter'
| > unrecognized option `--lua-filter'
| > Try pandoc.exe --help for more information.
| > Error: processing vignette 'vignettefilename.Rmd' failed with
diagnostics:
| > pandoc document conversion failed with error 2
| > --- failed re-building 'vignettefilename.Rmd'
| >
| > SUMMARY: processing the following file failed:
| >'vignettefilename.Rmd'
| >
| > Error: Vignette re-building failed.
| > Execution halted
| >
| > This looks like a host configuration problem:
| >
| >edd@rob:~$ pandoc --help | grep lua
| > -L SCRIPTPATH --lua-filter=SCRIPTPATH
| >edd@rob:~$ pandoc --version | head -1
| >pandoc 2.9.2.1
| >edd@rob:~$
| >
| > Can we expect CRAN to update its pandoc binary? Or will we have to 'for now'
| > rely on 'reply-all', explaining to CRAN that the failure is from their end?
| >
| > As they in the press, I had reached out to CRAN but they 'have not yet
| > responded to requests for comments' as we know they're busy. Anybody seen
| > this error though?
|
| I haven't seen that one, but I regularly get errors in rgl and tables
| because of missing or insufficient pandoc on some systems. I added
| lines like
|
|SystemRequirements: pandoc (>= 1.12.3) for vignettes
|
| to DESCRIPTION to state the Pandoc version, added rmarkdown to the
| Suggests list, and added code like this to the start of HTML vignettes:
|
| ```{r echo = FALSE}
| if (!requireNamespace("rmarkdown") ||
| !rmarkdown::pandoc_available("1.12.3")) {
|warning("This vignette requires pandoc version 1.12.3; code will not
| run in older versions.")
|knitr::opts_chunk$set(eval = FALSE)
| }
| ```
Good point! Brooke and I actually recommend exactly that---conditional
vignette builds---in our R Journal paper on drat for data repos (via Suggests).
But (because of the overall fragility of these pipelines as well as
preference for generally lighter setups) my vignettes actually tend to not
even run code. I mostly just use three backticks followed by the language
for which I desire highlighting from pandoc, i.e. ```r or ```c++.
Hmmm, that's strange. From what I can see you only get the --lua-filter
if pandoc 2.0 is available:
https://github.com/rstudio/rmarkdown/blob/66d27e09befd5f0579f0f4e27c4b9325284b9b15/R/pandoc.R#L719
I think this is the current rmarkdown version.
Duncan Murdoch
Maybe we would need to pass the minimum version check into rmarkdown as an
option so that rmarkdown knows not to ask for `--lua-filter` on setups where
rmarkdown knows pandoc is too old? Or maybe make the vignette builder barf?
| This makes the test happy, though it also makes the vignette pretty
| useless on systems that don't meet the stated requirements. Since
| SystemRequirements is free-form, I can see why CRAN doesn't do automatic
| interpretation of it, but it would be nice if they did.
Alas, the free-form requirement has been a constraint for a long time indeed.
Dirk
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] CRAN Windows failure due to old pandoc ?
On 26 September 2020 at 14:20, Duncan Murdoch wrote: | On 26/09/2020 12:54 p.m., Dirk Eddelbuettel wrote: | Hmmm, that's strange. From what I can see you only get the --lua-filter | if pandoc 2.0 is available: | | https://github.com/rstudio/rmarkdown/blob/66d27e09befd5f0579f0f4e27c4b9325284b9b15/R/pandoc.R#L719 | | I think this is the current rmarkdown version. I was using a different document driver which may not make that check. In the meantime, I think I will just follow the usual advice 'stop doing that then' after complaining that it hurts and may just switch to a pdf vignette. Dirk -- https://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-pkg-devel] rtiff Build failure on r-release-macos-x86_64
Good afternoon. Forgive me if this belongs on R-SIG-Mac. I am the maintainer of the rtiff package. It has come to my attention that binaries are not being successfully built on CRAN, although build succeeds on r-oldrel-macos-x86_64. The error is: checking for TIFFOpen in -ltiff... no Try static libs needed on OS X checking for TIFFOpen in -ltiff... no Error: Could not find libtiff. ERROR: configuration failed for package ‘rtiff’ * removing ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/rtiff.Rcheck/rtiff’ Is it an option to include libtiff in the new build environment for Mac OS? Thanks, Eric __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] rtiff Build failure on r-release-macos-x86_64
Ideally send a note to Imion Urbanek, the Mac maintainer. Best, Uwe Ligges On 25.09.2020 19:40, Kort, Eric wrote: Good afternoon. Forgive me if this belongs on R-SIG-Mac. I am the maintainer of the rtiff package. It has come to my attention that binaries are not being successfully built on CRAN, although build succeeds on r-oldrel-macos-x86_64. The error is: checking for TIFFOpen in -ltiff... no Try static libs needed on OS X checking for TIFFOpen in -ltiff... no Error: Could not find libtiff. ERROR: configuration failed for package ‘rtiff’ * removing ‘/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/rtiff.Rcheck/rtiff’ Is it an option to include libtiff in the new build environment for Mac OS? Thanks, Eric __ 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
