Re: [R-pkg-devel] R CMD check not finding my vignettes

[David Hugh-Jones]

 Okay, so this got tumbleweeded... so should I file a bug?

D

On Thu, 6 Apr 2017 at 15:37, David Hugh-Jones 
wrote:

>
> Before building my package, I manually place both pdf and html versions of
> my vignettes into inst/doc. I then build the package with `devtools::check`.
>
> Listing of the resulting tarball:
>
> -rw-r--r--  0 david  staff1692  6 Apr 15:10
> huxtable/inst/doc/design-principles.R
>
> -rw-r--r--  0 david  staff6697  6 Apr 15:10
> huxtable/inst/doc/design-principles.Rmd
>
> -rw-r--r--  0 david  staff  899765  6 Apr 15:10
> huxtable/inst/doc/design-principles.html
>
> -rw-r--r--  0 david  staff  213776  6 Apr 15:10
> huxtable/inst/doc/design-principles.pdf
>
> -rw-r--r--  0 david  staff3009  6 Apr 15:10 huxtable/inst/doc/huxreg.R
>
> -rw-r--r--  0 david  staff5521  6 Apr 15:10
> huxtable/inst/doc/huxreg.Rmd
>
> -rw-r--r--  0 david  staff  940955  6 Apr 15:10
> huxtable/inst/doc/huxreg.html
>
> -rw-r--r--  0 david  staff  237771  6 Apr 15:10
> huxtable/inst/doc/huxreg.pdf
>
> -rw-r--r--  0 david  staff   10473  6 Apr 15:11
> huxtable/inst/doc/huxtable.R
>
> -rw-r--r--  0 david  staff   20552  6 Apr 15:11
> huxtable/inst/doc/huxtable.Rmd
>
> -rw-r--r--  0 david  staff  925373  6 Apr 15:11
> huxtable/inst/doc/huxtable.html
>
> -rw-r--r--  0 david  staff  284978  6 Apr 15:11
> huxtable/inst/doc/huxtable.pdf
>
> However, R CMD check then complains:
>
> * checking package vignettes in ‘inst/doc’ ... WARNING
> Package vignettes without corresponding PDF/HTML:
>‘design-principles.Rmd’
>‘huxreg.Rmd’
>‘huxtable.Rmd’
>
> What gives?
>
> Cheers,
> David
>
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Re: [R-pkg-devel] maintainer built vignette

[Ian Carroll]

With `BuildVignettes: no` in my DESCRIPTION and `^vignettes` in my 
.Rbuildignore, I can squeak through a normal build (no `r_build_args` or 
`r_check_args`) on travis with just this note:

* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘rslurm.Rmd’
A ‘vignettes’ directory is required as from R 3.1.0
and these will not be indexed nor checked

I’ll take a NOTE over an ERROR, so I’ll try to submit like this with an 
explanation. It seems to me like `BuildVignettes: no` should also disable 
re-building them under R CMD check, but I think R CMD check --as-cran clobbers 
it.

-Original Message-
From: Dirk Eddelbuettel  on behalf of Dirk 
Eddelbuettel 
Date: Thursday, April 6, 2017 at 9:23 PM
To: Ian Carroll 
Cc: "r-package-devel@r-project.org" 
Subject: Re: [R-pkg-devel] maintainer built vignette


On 6 April 2017 at 20:17, Ian Carroll wrote:
| How do I package an rmarkdown vignette that cannot be built on 
win-builder? The vignette in question demonstrates interaction with a SLURM 
cluster, which is not available to win-builder or travis. In my `.travis.yml` I 
can include `r_build_args: "--no-build-vignettes"` and `r_check_args: 
"--no-vignettes"` to skip the build and re-build steps respectively. I don’t 
know how to do that with win-builder, so I cannot pass the incoming pretest on 
package submission. The extra steps make me feel like I’m doing something wrong 
regardless.
| 
| So, what’s the appropriate way to include vignettes that should not be 
hammered with attempts to build at every turn? Some old advice seemed to 
suggest going straight to inst/docs, but newer rules are that inclusion in 
vignettes/ is mandatory.

I think if you adjust .Rbuildignore to NOT include the source but just the
pdf then you will have documentation present -- without the risk of 'cannot
be computed here' on some platforms.

Dirk

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Re: [R-pkg-devel] maintainer built vignette

[Dirk Eddelbuettel]

On 6 April 2017 at 20:17, Ian Carroll wrote:
| How do I package an rmarkdown vignette that cannot be built on win-builder? 
The vignette in question demonstrates interaction with a SLURM cluster, which 
is not available to win-builder or travis. In my `.travis.yml` I can include 
`r_build_args: "--no-build-vignettes"` and `r_check_args: "--no-vignettes"` to 
skip the build and re-build steps respectively. I don’t know how to do that 
with win-builder, so I cannot pass the incoming pretest on package submission. 
The extra steps make me feel like I’m doing something wrong regardless.
| 
| So, what’s the appropriate way to include vignettes that should not be 
hammered with attempts to build at every turn? Some old advice seemed to 
suggest going straight to inst/docs, but newer rules are that inclusion in 
vignettes/ is mandatory.

I think if you adjust .Rbuildignore to NOT include the source but just the
pdf then you will have documentation present -- without the risk of 'cannot
be computed here' on some platforms.

Dirk

-- 
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Re: [R-pkg-devel] Help with Windows build failure

[Dirk Eddelbuettel]

On 2 April 2017 at 17:21, Alexandre Sieira wrote:
| Hi, everyone.
| 
| I have done some work this weekend to allow the SnakeCharmR package (
| https://github.com/asieira/SnakeCharmR) to be compiled under Windows. For
| reference, this is an Rcpp-based packages that links to the system's
| libpython.
| 
| I have been able to test it on my box using Windows 10 and several Python
| versions:
| 
| * Rtools mingw_64/opt Python 2.7.9;
| * python.org 2.7.13 64-bit;
| * python.org 3.6.1 64-bit;
| * python.org 2.7.x 32-bit on Appveyor (
| https://ci.appveyor.com/project/asieira/SnakeCharmR).
| 
| Still, when I submit my source package to win-builder I get an error:
| https://win-builder.r-project.org/9aqdlW0D6e3m/
| 
| https://win-builder.r-project.org/9aqdlW0D6e3m/00install.out shows some
| warnings on header files that are outside of my control, but ends with a
| successful compilation. However, it compiles only the 64-bit version of the
| DLL and gives me this warning:
| 
| Warning: this package has a non-empty 'configure.win' file,
| so building only the main architecture
| 
| 
| Finally, when we look at
| https://win-builder.r-project.org/9aqdlW0D6e3m/00check.log we see an error
| due to the fact that the package can’t be tested on i386:
| 
| ** checking whether the package can be loaded ... ERROR
| Loading this package had a fatal error status code 1
| Loading log:
| Error: package 'SnakeCharmR' is not installed for 'arch = i386'
| Execution halted
| ** DONE
| Status: 1 ERROR, 1 NOTE
| 
| 
| I apologize if this is a beginner’s problem, but this is my first R package
| ever and I’m not really used to working with R on Windows. Would appreciate
| any guidance and pointers on how to address this and get the package to
| pass the necessary CRAN automated tests.

I tried to make Python and R co-exist at some point; my conclusion was there
aren't enough days in the week to figure out how to do it on Windows.  It's
easy to do on Linux, and I don't personally have OS X / macOS use cases but
here it's feasible if you're careful about your toolchain.

I think you should just consider 'OS_type: unix' in your DESCRIPTION.  A
working and uploaded package on two OSs beats an "almost there but never
finished" package on three in my book.

Dirk

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[R-pkg-devel] maintainer built vignette

[Ian Carroll]

Hello,

First post to r-package-devel, thanks for your help.

How do I package an rmarkdown vignette that cannot be built on win-builder? The 
vignette in question demonstrates interaction with a SLURM cluster, which is 
not available to win-builder or travis. In my `.travis.yml` I can include 
`r_build_args: "--no-build-vignettes"` and `r_check_args: "--no-vignettes"` to 
skip the build and re-build steps respectively. I don’t know how to do that 
with win-builder, so I cannot pass the incoming pretest on package submission. 
The extra steps make me feel like I’m doing something wrong regardless.

So, what’s the appropriate way to include vignettes that should not be hammered 
with attempts to build at every turn? Some old advice seemed to suggest going 
straight to inst/docs, but newer rules are that inclusion in vignettes/ is 
mandatory.

Thanks,
Ian



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[R-pkg-devel] R CMD check not finding my vignettes

[David Hugh-Jones]

Before building my package, I manually place both pdf and html versions of
my vignettes into inst/doc. I then build the package with `devtools::check`.

Listing of the resulting tarball:

-rw-r--r--  0 david  staff1692  6 Apr 15:10
huxtable/inst/doc/design-principles.R

-rw-r--r--  0 david  staff6697  6 Apr 15:10
huxtable/inst/doc/design-principles.Rmd

-rw-r--r--  0 david  staff  899765  6 Apr 15:10
huxtable/inst/doc/design-principles.html

-rw-r--r--  0 david  staff  213776  6 Apr 15:10
huxtable/inst/doc/design-principles.pdf

-rw-r--r--  0 david  staff3009  6 Apr 15:10 huxtable/inst/doc/huxreg.R

-rw-r--r--  0 david  staff5521  6 Apr 15:10 huxtable/inst/doc/huxreg.Rmd

-rw-r--r--  0 david  staff  940955  6 Apr 15:10
huxtable/inst/doc/huxreg.html

-rw-r--r--  0 david  staff  237771  6 Apr 15:10 huxtable/inst/doc/huxreg.pdf

-rw-r--r--  0 david  staff   10473  6 Apr 15:11 huxtable/inst/doc/huxtable.R

-rw-r--r--  0 david  staff   20552  6 Apr 15:11
huxtable/inst/doc/huxtable.Rmd

-rw-r--r--  0 david  staff  925373  6 Apr 15:11
huxtable/inst/doc/huxtable.html

-rw-r--r--  0 david  staff  284978  6 Apr 15:11
huxtable/inst/doc/huxtable.pdf

However, R CMD check then complains:

* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignettes without corresponding PDF/HTML:
   ‘design-principles.Rmd’
   ‘huxreg.Rmd’
   ‘huxtable.Rmd’

What gives?

Cheers,
David

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