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thibautjombart / apex

Phylogenetic Methods for Multiple Gene Data
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Make markdown vignette #6

Closed thibautjombart closed 9 years ago

thibautjombart commented 9 years ago

Doesn't need to be fancy, just to go over the main functionalities. Could be basically what we have in our README.md

thibautjombart commented 9 years ago

@KlausVigo @zkamvar @jgx65 Added now. The cool thing is the README.Rmd can now be used to compile README.md, which will include the freshly recompiled vignette. So we now have one doc for the package and the github project.

KlausVigo commented 9 years ago

That is really great!!

thibautjombart commented 9 years ago

As of 52c06ad1bce84ff671ee9e8caa3e9aa8bfcbcdb5, I get:

> build_vignettes()
Building apex vignettes
Quitting from lines 162-172 (apex.Rmd) 
Error: processing vignette 'apex.Rmd' failed with diagnostics:
subscript out of bounds

@KlausVigo is this the final version or are you still working on it?

KlausVigo commented 9 years ago

@thibautjombart This was the the final version. Can you check the phangorn version, should be 1.99-13 now. build_vignettes() works fine also on my machine, maybe should put the dependency in the DESCRIPTION file. 

> build_vignettes()
Building apex vignettes
Hit <Return> to see next plot: 
Hit <Return> to see next plot: 
Moving apex.html, apex.R to inst/doc/
Copying apex.Rmd to inst/doc/

NJ still issue needs to be addressed, but setting edge length to 0 should do the trick for now.

thibautjombart commented 9 years ago

Will do!

On Fri, Apr 10, 2015 at 4:38 PM, klash notifications@github.com wrote:

@thibautjombart https://github.com/thibautjombart This was the the final version. Can you check the phangorn version, should be 1.99-13 now. build_vignettes() works fine also on my machine, maybe should put the dependency in the DESCRIPTION file.

build_vignettes() Building apex vignettes Hit to see next plot: Hit to see next plot: Moving apex.html, apex.R to inst/doc/ Copying apex.Rmd to inst/doc/

NJ still issue needs to be addressed, but setting edge length to 0 should do the trick for now.

— Reply to this email directly or view it on GitHub https://github.com/thibautjombart/apex/issues/6#issuecomment-91595138.

thibautjombart commented 9 years ago

I think it is all good now. We could still put a bit more meat around the bone, but that's good enough for a first release.