Running RAxML in RStudio

[Giuliano Colosimo]

Hello,

I am trying to run RAxML from within RStudio. 

Here are some specs about my machine and the OS.

      Model Name: MacBook Pro

      Processor Name: Intel Core i5

      Processor Speed: 2.6 GHz

      Number of Processors: 1

      Total Number of Cores: 2

      L2 Cache (per Core): 256 KB

      L3 Cache: 3 MB

      Memory: 16 GB

I have installed RAxML in my Applications folder and everything seems to work fine when I try and run it from the terminal. It would be awesome if I could directly run it from within RStudio (version 1.1.463). The ips package should allow me to do that via the function raxml(). Within the function you specify the path to your RAxML executable, your input file and a bunch of other parameters. When I try to run the command, though, I get the following message:

> exec <- "/Applications/RAxML-8.0.3/raxmlHPC-PTHREADS-AVX"

> MLtree <- raxml(ccc_tree, exec)

Error in setwd(path) : cannot change working directory

These are the specs of the R session I am working on:

>sessionInfo()

R version 3.5.0 (2018-04-23)

Platform: x86_64-apple-darwin15.6.0 (64-bit)

Running under: macOS  10.14.2

Matrix products: default

BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib

LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

 [1] phyloch_1.5-3    phangorn_2.4.0   seqinr_3.4-5     phytools_0.6-60  maps_3.3.0      

 [6] bindrcpp_0.2.2   ggtree_1.14.4    treeio_1.6.1     ips_0.0-7        XML_3.98-1.16   

[11] colorspace_1.3-2 rgl_0.99.16      reshape2_1.4.3   pegas_0.10       adegenet_2.1.1  

[16] ade4_1.7-11      ape_5.1          ggforce_0.1.2    scatterpie_0.1.0 ggrepel_0.8.0   

[21] gdata_2.18.0     rgeos_0.3-26     rgdal_1.3-4      leaflet_2.0.2    ggmap_2.7.904   

[26] ggplot2_3.1.0    dplyr_0.7.8      plyr_1.8.4       raster_2.6-7     maptools_0.9-3  

[31] sp_1.3-1        

I am not sure what the issue is because I am working on my own machine and I have all the permissions required to access the folder with the executable. 

Anybody shared the same issue and have a solution?

Thanks

Giuliano

[Alexandros Stamatakis]

Dear Guiliano,

We are not really MAC experts in my lab.

However, your standard RaxML version is pretty old (latest is: v 8.2.12:
https://github.com/stamatak/standard-RAxML/releases/tag/v8.2.12)

and we have also replaced standard RAxML by RAxML-NG now:

https://github.com/amkozlov/raxml-ng

which is a complete re-design of RAxML and the version you should
actually use!

Alexis

On 31.01.19 12:10, Giuliano Colosimo wrote:
> Hello,
>
> I am trying to run RAxML from within RStudio.
>
> Here are some specs about my machine and the OS.
>
>       Model Name: MacBook Pro
>
>       Processor Name: Intel Core i5
>
>       Processor Speed: 2.6 GHz
>
>       Number of Processors: 1
>
>       Total Number of Cores: 2
>
>       L2 Cache (per Core): 256 KB
>
>       L3 Cache: 3 MB
>
>       Memory: 16 GB
>
>
> I have installed RAxML in my Applications folder and everything seems to
> work fine when I try and run it from the terminal. It would be awesome
> if I could directly run it from within RStudio (version 1.1.463). The

> ips package should allow me to do that via the function /raxml()/.

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--
Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org