g: running command
>> > '"C:/PROGRA~1/R/R-devel/bin/x64/Rscript" --vanilla --default-packages=
>> -e
>> > "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1
>> > ERROR
>> > Warning in engine$weave(file, quiet = quiet, enc
> > Quitting from lines 60-64 (vignette.Rmd)
> > Error: processing vignette 'vignette.Rmd' failed with diagnostics:
> > subscript out of bounds
> > Execution halted
> >
> > C:\Program Files\R\R-devel\bin\x64>
> >
> >
> > How I fix R CMD ch
"Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel"
> <bioc-devel@r-project.org>
> Sent: Sunday, December 4, 2016 5:12:50 AM
> Subject: Re: [Bioc-devel] package vignette error : external data can't be
> captured when compiling package vignette
&g
DESCRIPTION, etc.
>
> Dan
>
>
>
> - Original Message -
> > From: "Jurat Shayidin" <juratb...@gmail.com>
> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
> bioc-devel@r-project.org>
> > Sent: Frid
atb...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel"
> <bioc-devel@r-project.org>
> Sent: Friday, December 2, 2016 9:11:29 AM
> Subject: Re: [Bioc-devel] package vignette error : external data can't be
> captured when compili
installed when you install the
package, but the inst directory itself goes away.
If in your package source you have the following structure:
inst/extdata/
inst/foo.txt
In the installed package you end up with:
extdata/
foo.txt
HTH
Dan
----- Original Message -----
From: "Jurat Shay
t;
>
> How I fix R CMD check error above ? system.file() still can't detect
> external data. Any idea please ? Thanks a lot
>
> Best regards :
>
> Jurat
>
>
> On Fri, Dec 2, 2016 at 5:43 PM, Dan Tenenbaum <dtene...@fredhutch.org>
> wrote:
>
>> See below.
&g
ssage -
From: "Jurat Shayidin" <juratb...@gmail.com>
To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" <
bioc-devel@r-project.org>
Sent: Friday, December 2, 2016 8:32:35 AM
Subject: Re: [Bioc-devel] package vignette error : external data can't
b
our package is in github at https://github.com/julaiti/MSPC , it
> >> looks like there is no inst or extdata folder in that repository.
> >>
> >> Maybe it has not yet been added/committed/pushed to git?
> >>
> >> Note that everything _under_ inst gets insta
when you install the
>> package, but the inst directory itself goes away.
>>
>> If in your package source you have the following structure:
>>
>> inst/extdata/
>> inst/foo.txt
>>
>> In the installed package you end up with:
>>
>> extdata/
&
al Message -
> > From: "Jurat Shayidin" <juratb...@gmail.com>
> > To: "Hervé Pagès" <hpa...@fredhutch.org>, "bioc-devel" <
> bioc-devel@r-project.org>
> > Sent: Friday, December 2, 2016 5:36:28 AM
> > Subject: Re: [Bio
agès" <hpa...@fredhutch.org>, "bioc-devel"
> <bioc-devel@r-project.org>
> Sent: Friday, December 2, 2016 5:36:28 AM
> Subject: Re: [Bioc-devel] package vignette error : external data can't be
> captured when compiling package vignette
> Dear Hervé :
>
&
Dear Hervé :
Thanks again for your response on my issue. I've read your message very
carefully and did all you suggested to me, still can't fix the vignette
compilation error. I have developed my package on windows machine under
devel version of R and Bioc, all unit test works fine to me. I don't
Hi,
Make sure you understand the difference between the *package source
tree*, which you control and where you must create the inst/ folder,
and the *package installation folder*, which gets created and
populated by 'R CMD INSTALL'. The exact location of the *package
installation folder* doesn't
Hi BiocDevel :
I am getting vignette error when I building my packages, and external data
can't be captured by system.file() . I did unit test all function of my
packages, it works fine. When I am going to compile package vignette, test
input bed file can't be detected. However, I used
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