cant make about bri HOT 8 CLOSED

Did you use the same compiler/machine to build libhts as bri?

from bri.

I believe so, yes.

from bri.

1)When trying to make bri, I pointed at the htslib found in nanopolish's install directory.
2)It's possible/probable that I ran the make of nanopolish with the "HDF5=noinstall, EIGEN=noinstall or HTS=noinstall" since I share the machine with others and there was a comment on the nanopolish page about "Some users however may want to use system-wide versions of the libraries".
Is this relevant/connected/the cause? Many thanks in advance

from bri.

It looks like libhts compiled, since you get symbol undefined errors instead of a file-not-found error. The symbols that it is complaining about should be provided by -lz and -lpthread so I'm not sure what the problem is.

from bri.

Can you try running this command:

cc -o bri -O3 -std=c99 -fsigned-char -D_FILE_OFFSET_BITS=64 -g -I/home/mike.harbour/nanopolish/htslib/ -fPIC src/bri_index.o src/bri_main.o src/bri_test.o src/bri_get.o /home/mike.harbour/nanopolish/htslib/libhts.a -lpthread -lz

from bri.

ran that command, completed ok, no errors reported. I have an executable bri now, which gives....
prompt:/bri/bri$ ./bri
[bri] usage bri [...]
prompt:/bri/bri$

...will test it.... but... Many Thanks!

from bri.

er... there was some strange strikethroughs added there that shouldnt have been, that wasnt me, it was github :)

from bri.

Thanks, the problem was the order that the libraries were linked in. I have fixed this in the Makefile.

from bri.