morrislab / phylosub Goto Github PK

When running the following command I get warnings preventing me from compiling:

$ g++ -o mh.o mh.cpp util.cpp gsl-config --cflags --libs
mh.cpp: In function ‘int main(int, char*)’:
mh.cpp:42: warning: deprecated conversion from string constant to ‘char’
mh.cpp:48: warning: deprecated conversion from string constant to ‘char*’

I suggest that the following changes should be made:

In mh.hpp and mh.cpp, change the data type of function argument fname from "char fname[]" to "const char* fname", as shown below:

void load_tree(const char* fname, struct node nodes[]);
void write_params(const char* fname, struct node nodes[], struct config conf);

This should fix the error.

Hi,

Thank you very much for developing this tool!

I did run phylosub successully and it generate the output files, one of which is the top_k_trees. Are those trees order by probability or equally likely?
Another question is what "phi" exactly means in the output?

Thanks,

Pascal

Hi,
I’m attempting to compile phylosub and get this error:

mh.cpp:38:20: error: variable length array of non-POD element type
'struct datum'
struct datum data[conf.NDATA];
^
mh.cpp:43:20: error: variable length array of non-POD element type 'struct node'
struct node nodes[conf.NNODES];

Any ideas?

KR

Matthew

Hi, thanks for sharing your nice tool! I was wondering if you could give an example of file input or a description of the data.txt input file. I could not find it in the Wiki/README.
Thanks!

Hi!
I tried to run Phylosub, but there was a problem.
I used sample data set, and the 1st command
(python evolve.py 'data.txt' 'trees' 'top_k_trees' 'clonal_frequencies' 'llh_trace' 100 100 1) was working.
However, the 2nd command
(python porder.py 'trees' 'data.txt' 'partial_order.pdf') was not working.
This is the error message
" ImportError: /usr/local/lib/liblapack.so: undefined symbol: slamch_ " (lapack-3.5.0)
I found out that there were other many undefined symbols.
I tried several ways to solve the problem, but it was not working.

Thanks.