Re: [Help] Failed to upgrade bcftools to version 1.5
On Mon, Jul 24, 2017 at 12:12:04AM -0400, Afif Elghraoui wrote:
> I was under the impression that htslib 1.5, required for bcftools 1.5,
> has a soname bump. There is no pysam release yet to wrap htslib 1.5, so
> I think upgrading bcftools/samtools/htslib right now to 1.5 will just
> make it impossible to use pysam until a new release comes out, right?
I have no idea - I just realised that I'm unable to build latest
python-pysam which ends up in
pysam/libcutils.c:10574:20: warning: ‘__pyx_v_retval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
return PyInt_FromLong((long) value);
pysam/libcutils.c:5493:7: note: ‘__pyx_v_retval’ was declared here
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -g -O2 -fdebug-prefix-map=/build/python-pysam-0.11.2.2+ds=. -fstack-protector-strong -Wf
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
/usr/bin/ld: cannot find -lcsamtools
/usr/bin/ld: cannot find -lcbcftools
collect2: error: ld returned 1 exit status
I simply assumed that the cause would be that those missing libs are
part of new upstream versions of the dependencies.
> I did not get through updating pysam since my time became scarce and the
> time I did spend on it was not so effecient with a slow laptop.
I would be really happy if somebody more educated than me in the
field of bcftools/htslib/samtools would step in and fix all bugs
(whatever version - I do not care as long as it is done).