Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

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

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

Dear Dan : Really appreciated for your quick respond. Instead, I am using R CMD check on my packages, I have an error. Here is whole session detail : Microsoft Windows [Version 6.3.9600] (c) 2013 Microsoft Corporation. All rights reserved. C:\Users\jvrat>cd C:\Program Files\R\R-devel\bin\x64

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

If your 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 installed when you install the package, but the inst directory

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

See below. - Original Message - > From: "Jurat Shayidin" > To: "Dan Tenenbaum" , "bioc-devel" > > Sent: Friday, December 2, 2016 8:32:35 AM > Subject: Re: [Bioc-devel] package vignette error : external data can't be

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

Dear Dan : I forgot to commit vignette file, now I pushed new changes, so now error could be something else. People in stackoverflow suggest me to put all my external data (a.k.a, bed files) into vignette folder, try to run R CMD check and see what happen, I did this solution, but it doesn't

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

On 12/02/2016 09:11 AM, Jurat Shayidin wrote: Dear Dan : I forgot to commit vignette file, now I pushed new changes, so now error could be something else. People in stackoverflow suggest me to put all my external data (a.k.a, bed files) into vignette folder, try to run R CMD check and see what

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

I tried building your package, there are a number of issues with it. I recommend that you 1) always be aware of what is and is not in github, by using the 'git status' command. Bear in mind that if files are not committed to git then we will not be able to see them and not be able to help you.

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

Dear Jurat, Maybe it'll be helpful to you if you see how other packages have their data. For example, take a look at one of my packages: https://github.com/lcolladotor/derfinder You'll see that I have two directories inside /inst/extdata with some files that I use in my vignette code. See

Re: [Bioc-devel] package vignette error : external data can't be captured when compiling package vignette

On 12/02/2016 09:26 AM, Leonardo Collado Torres wrote: Dear Jurat, Maybe it'll be helpful to you if you see how other packages have their data. For example, take a look at one of my packages: https://github.com/lcolladotor/derfinder You'll see that I have two directories inside /inst/extdata

[Bioc-devel] Dependency update propagation (rcdk on morelia)

Hi Bioc, - the Rcpi package depends on rcdk, and the rcdk package was updated last week from 3.3.6 to 3.3.8 on CRAN thanks to Zach's (cc'd) work, which removed the Java > 1.8 requirement (previously discussed in https://stat.ethz.ch/pipermail/bioc-devel/2016-October/009881.html ). I've updated