Tests fail when mafft is not installed.

[knausb]

When running tests I receive:

Error: MAFFT not found in the specified path: '//mafft'
 Please check your MAFFT installation.
In addition: Warning messages:
1: running command 'which mafft' had status 1 
2: running command 'which hmmsearch' had status 1 
Execution halted

Exited with status 1.

This is reproduced as follows.

source('~/gits/effectR/tests/testthat/test_effector_summary.R')

Which dumps me into the browser on my system. Here I see:

Browse[1]> mafft.path
[1] "/"

which may be an unanticipated value?

[zachary-foster]

This is due to this line:

effectR/tests/testthat/test_effector_summary.R

Line 8 in d72fae3

mafft.path <- paste0(dirname(system("which mafft", intern = T)), "/")

dirname(system("which mafft", intern = T)) is returning nothing, which is then appended to "/" and passed to get_mafft_path, which interprets it as a user-defined path to a directory and adds "mafft" to it.

[Tabima]

@knausb Can you test again? The new commit should address that