Strange behaviour (possible failure) on ubuntu

[dfalster]

@richfitz -- I'm hoping you might be able to test this on another linux machine. If the results below extend to other linux boxes then dockertest may not be working as hoped on linux.

@jscamac and I were trying to use dockerest on linux box to run some analyses for our mortality analysis and encountered some strange behaviours. Initially, we encountered the error that file remake.yml does not exist in the current wd when clearly it does:

@SCI-6297:~/mortality_bci$ remake fulldata_models_precompiled_docker
[  LOAD ] 
[  READ ]                                       |  # loading sources
<  MAKE > fulldata_models_precompiled_docker
[ BUILD ] fulldata_models_precompiled_docker    |  fulldata_models_precompil...
[  READ ]                                       |  # loading packages
Error: while reading 'remake.yml'
The file 'remake.yml' does not exist
jscamac@SCI-6297:~/mortality_bci$ ls
data    downloads  ms          R          remake_sources.yml
docker  figures    precompile  README.md  remake.yml

But what is actually happening in building the fulldata_models_precompiled_docker target is that we are loading a docker container and compiling models inside, with directory mapped back to the current wd. (This works fine on imac but failed on the linux machine.)

Using the dry-run argument of dockertest reveals the code that call that is made to docker. I then ran a simplified version of that to highlight why the above error is not working.

Basically it seems like the directory mapping is not working as it should. Running the following should map our current wd onto the folder /home/data in the docker container. That's what happens on the mac:

✗ /usr/local/bin/docker run -v /Users/dfalster/Dropbox/_research/SIEF/mortality_bci:/home/data -it traitecoevo/mortality_bci
root@246b720e3d9e:/home/data# ls
data  docker  downloads  ignore  ms  ms.pdf  Notes.md  R  README.md  remake_sources.yml  remake.yml  results

But running the equivalent on linux does not produce the desired result (note calling ls returns an empty folder):

jscamac@SCI-6297:~/mortality_bci$ /usr/bin/docker run -v /home/jscamac/mortality_bci:/home/data -it traitecoevo/mortality_bci 
root@df98b8b9fa61:/home/data# ls
root@df98b8b9fa61:/home/data# 

I got a similar result using the base ubuntu container:

jscamac@SCI-6297:~/mortality_bci$ /usr/bin/docker run -v /home/jscamac:/home/data -it ubuntu
root@6ed0501b533c:/home/data# ls
root@6ed0501b533c:/home/data# 

The machine we using is running Ubuntu 14.04.2 (LTS).