Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

2017-03-01 Thread Duncan Murdoch 

On 01/03/2017 2:17 AM, Henrik Bengtsson wrote:

On Tue, Feb 28, 2017 at 2:47 PM, Duncan Murdoch
 wrote:

On 28/02/2017 5:17 PM, Patrick Schratz wrote:


Thanks Duncan, that was the problem! Although the Rbuildignore entry
pointed to the main dir



No, it contains patterns, not paths, and is matched "case-insensitively
against the file and directory names relative to the top-level package
source directory".  Put ^ at the beginning if you want to refer to the main
dir.

Hadley, reporting what gets omitted might be a good suggestion, but it might
report too much in a package with compiled code (the .o files will generally
be omitted; rgl has 51 of those in src...).


I like this idea.  It could be done such that R CMD build lists the
files omitted based solely on the content of .Rbuildignore, which I
assume is also what Hadley meant.  This way *.o files wouldn't be
listed since they're omitted by the built-in rules of R CMD build
itself.


That makes sense.  Want to submit a patch?

Duncan Murdoch

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

Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

2017-02-28 Thread Henrik Bengtsson 
On Tue, Feb 28, 2017 at 2:47 PM, Duncan Murdoch
 wrote:
> On 28/02/2017 5:17 PM, Patrick Schratz wrote:
>>
>> Thanks Duncan, that was the problem! Although the Rbuildignore entry
>> pointed to the main dir
>
>
> No, it contains patterns, not paths, and is matched "case-insensitively
> against the file and directory names relative to the top-level package
> source directory".  Put ^ at the beginning if you want to refer to the main
> dir.
>
> Hadley, reporting what gets omitted might be a good suggestion, but it might
> report too much in a package with compiled code (the .o files will generally
> be omitted; rgl has 51 of those in src...).

I like this idea.  It could be done such that R CMD build lists the
files omitted based solely on the content of .Rbuildignore, which I
assume is also what Hadley meant.  This way *.o files wouldn't be
listed since they're omitted by the built-in rules of R CMD build
itself.

/Henrik

>
> Duncan Murdoch
>
> and my .bib file was lying under vignettes/...
>>
>> That Rbuildignore entry was a leftover when my .bib file was initially
>> lying in the top directory and hence was throwing notes during R CMD
>> check.
>>
>> Afterwards I used full paths in the vignette to specify the .bib
>> location. This approach works fine until you submit to CRAN which of
>> course cannot deal with full paths (and you forget about that you used a
>> full path when releasing).
>>
>> @hadley
>> Could be useful as most often you do not think of possible leftover
>> entries in Rbuildignore...
>>
>> 2017-02-28 18:57 GMT+01:00 Duncan Murdoch > >:
>>
>> On 28/02/2017 10:44 AM, Patrick Schratz wrote:
>>
>> When building the vignette using R CMD Build or
>> `devtools::build_vignette()` everything works fine.
>>
>> However, during R CMD check I get the following
>>
>> ** checking running R code from vignettes ...*
>> *   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
>> * NONE*
>> ** checking re-building of vignette outputs ... WARNING*
>> *Error in re-building vignettes:*
>> *  ...*
>> *pandoc-citeproc: Could not find Biblio.bib*
>> *CallStack (from HasCallStack):*
>> *  error, called at src/Text/CSL/Pandoc.hs:224:39 in
>> pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
>> *pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
>> *Filter returned error status 1*
>> *Error: processing vignette 'sperrorest-vignette.Rmd' failed with
>> diagnostics:*
>> *pandoc document conversion failed with error 83*
>> *Execution halted*
>>
>> The .bib file is lying in `/vignettes`. There is a similar
>> question on SO
>>
>> >
>> >
>> but
>> the answer does not address the problem.
>> When using full paths everything is fine. However, I cannot use
>> full paths
>> when submitting to CRAN.
>>
>> If you want to check on your own, please use the `dev` branch;
>> https://github.com/pat-s/sperrorest/tree/dev
>> 
>>
>> pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
>> pandoc: stable 1.19.2.1 (bottled), HEAD
>>
>>
>> Your .Rbuildignore file says not to include Biblio.bib.  Don't do
>> that.
>>
>> Duncan Murdoch
>>
>>
>
> __
> 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] .bib file in vignette not found during R CMD check

2017-02-28 Thread Duncan Murdoch 

On 28/02/2017 5:17 PM, Patrick Schratz wrote:

Thanks Duncan, that was the problem! Although the Rbuildignore entry
pointed to the main dir


No, it contains patterns, not paths, and is matched "case-insensitively 
against the file and directory names relative to the top-level package 
source directory".  Put ^ at the beginning if you want to refer to the 
main dir.


Hadley, reporting what gets omitted might be a good suggestion, but it 
might report too much in a package with compiled code (the .o files will 
generally be omitted; rgl has 51 of those in src...).


Duncan Murdoch

and my .bib file was lying under vignettes/...

That Rbuildignore entry was a leftover when my .bib file was initially
lying in the top directory and hence was throwing notes during R CMD check.

Afterwards I used full paths in the vignette to specify the .bib
location. This approach works fine until you submit to CRAN which of
course cannot deal with full paths (and you forget about that you used a
full path when releasing).

@hadley
Could be useful as most often you do not think of possible leftover
entries in Rbuildignore...

2017-02-28 18:57 GMT+01:00 Duncan Murdoch >:

On 28/02/2017 10:44 AM, Patrick Schratz wrote:

When building the vignette using R CMD Build or
`devtools::build_vignette()` everything works fine.

However, during R CMD check I get the following

** checking running R code from vignettes ...*
*   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
* NONE*
** checking re-building of vignette outputs ... WARNING*
*Error in re-building vignettes:*
*  ...*
*pandoc-citeproc: Could not find Biblio.bib*
*CallStack (from HasCallStack):*
*  error, called at src/Text/CSL/Pandoc.hs:224:39 in
pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
*pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
*Filter returned error status 1*
*Error: processing vignette 'sperrorest-vignette.Rmd' failed with
diagnostics:*
*pandoc document conversion failed with error 83*
*Execution halted*

The .bib file is lying in `/vignettes`. There is a similar
question on SO

>
but
the answer does not address the problem.
When using full paths everything is fine. However, I cannot use
full paths
when submitting to CRAN.

If you want to check on your own, please use the `dev` branch;
https://github.com/pat-s/sperrorest/tree/dev


pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
pandoc: stable 1.19.2.1 (bottled), HEAD


Your .Rbuildignore file says not to include Biblio.bib.  Don't do that.

Duncan Murdoch




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

Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

2017-02-28 Thread Hadley Wickham 
I wonder if it would be useful for R CMD build to list the files it
ignores? A misspecified .Rbuildignore seems to be reasonable for a
high proportion of weird errors where you have no idea what's going
wrong.

Hadley

On Tue, Feb 28, 2017 at 11:57 AM, Duncan Murdoch
 wrote:
> On 28/02/2017 10:44 AM, Patrick Schratz wrote:
>>
>> When building the vignette using R CMD Build or
>> `devtools::build_vignette()` everything works fine.
>>
>> However, during R CMD check I get the following
>>
>> ** checking running R code from vignettes ...*
>> *   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
>> * NONE*
>> ** checking re-building of vignette outputs ... WARNING*
>> *Error in re-building vignettes:*
>> *  ...*
>> *pandoc-citeproc: Could not find Biblio.bib*
>> *CallStack (from HasCallStack):*
>> *  error, called at src/Text/CSL/Pandoc.hs:224:39 in
>> pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
>> *pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
>> *Filter returned error status 1*
>> *Error: processing vignette 'sperrorest-vignette.Rmd' failed with
>> diagnostics:*
>> *pandoc document conversion failed with error 83*
>> *Execution halted*
>>
>> The .bib file is lying in `/vignettes`. There is a similar question on SO
>>
>> 
>> but
>> the answer does not address the problem.
>> When using full paths everything is fine. However, I cannot use full paths
>> when submitting to CRAN.
>>
>> If you want to check on your own, please use the `dev` branch;
>> https://github.com/pat-s/sperrorest/tree/dev
>>
>> pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
>> pandoc: stable 1.19.2.1 (bottled), HEAD
>
>
> Your .Rbuildignore file says not to include Biblio.bib.  Don't do that.
>
> Duncan Murdoch
>
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel



-- 
http://hadley.nz

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

Re: [R-pkg-devel] .bib file in vignette not found during R CMD check

2017-02-28 Thread Duncan Murdoch 

On 28/02/2017 10:44 AM, Patrick Schratz wrote:

When building the vignette using R CMD Build or
`devtools::build_vignette()` everything works fine.

However, during R CMD check I get the following

** checking running R code from vignettes ...*
*   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
* NONE*
** checking re-building of vignette outputs ... WARNING*
*Error in re-building vignettes:*
*  ...*
*pandoc-citeproc: Could not find Biblio.bib*
*CallStack (from HasCallStack):*
*  error, called at src/Text/CSL/Pandoc.hs:224:39 in
pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
*pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
*Filter returned error status 1*
*Error: processing vignette 'sperrorest-vignette.Rmd' failed with
diagnostics:*
*pandoc document conversion failed with error 83*
*Execution halted*

The .bib file is lying in `/vignettes`. There is a similar question on SO

but
the answer does not address the problem.
When using full paths everything is fine. However, I cannot use full paths
when submitting to CRAN.

If you want to check on your own, please use the `dev` branch;
https://github.com/pat-s/sperrorest/tree/dev

pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
pandoc: stable 1.19.2.1 (bottled), HEAD


Your .Rbuildignore file says not to include Biblio.bib.  Don't do that.

Duncan Murdoch

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

[R-pkg-devel] .bib file in vignette not found during R CMD check

2017-02-28 Thread Patrick Schratz 
When building the vignette using R CMD Build or
`devtools::build_vignette()` everything works fine.

However, during R CMD check I get the following

** checking running R code from vignettes ...*
*   ‘sperrorest-vignette.Rmd’ using ‘UTF-8’ ... OK*
* NONE*
** checking re-building of vignette outputs ... WARNING*
*Error in re-building vignettes:*
*  ...*
*pandoc-citeproc: Could not find Biblio.bib*
*CallStack (from HasCallStack):*
*  error, called at src/Text/CSL/Pandoc.hs:224:39 in
pandoc-citeproc-0.10.4.1-EdjBizYp62fCPHef3CymGR:Text.CSL.Pandoc*
*pandoc: Error running filter /usr/local/bin/pandoc-citeproc*
*Filter returned error status 1*
*Error: processing vignette 'sperrorest-vignette.Rmd' failed with
diagnostics:*
*pandoc document conversion failed with error 83*
*Execution halted*

The .bib file is lying in `/vignettes`. There is a similar question on SO

but
the answer does not address the problem.
When using full paths everything is fine. However, I cannot use full paths
when submitting to CRAN.

If you want to check on your own, please use the `dev` branch;
https://github.com/pat-s/sperrorest/tree/dev

pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
pandoc: stable 1.19.2.1 (bottled), HEAD

Best, Patrick

[[alternative HTML version deleted]]

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