[Debian-med-packaging] Latest version of gmap has build issue

[Alex Mestiashvili]

On 1/31/19 2:19 PM, Andreas Tille wrote:
> Hi Alex,
> 
> I commited latest gmap version to Git but the build runs into
> 
> ...
> gcc -DHAVE_CONFIG_H -I.   -Wdate-time -D_FORTIFY_SOURCE=2  -pthread -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -fdebug-prefix-map=/build/gmap-2019-01-24=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c
> bigendian.c:66:1: error: redefinition of 'Bigendian_fwrite_ushort'
>  Bigendian_fwrite_ushort (unsigned short value, FILE *fp) {
>  ^~~~~~~~~~~~~~~~~~~~~~~
> bigendian.c:28:1: note: previous definition of 'Bigendian_fwrite_ushort' was here
>  Bigendian_fwrite_ushort (unsigned short value, FILE *fp) {
>  ^~~~~~~~~~~~~~~~~~~~~~~
> bigendian.c:80:1: error: redefinition of 'Bigendian_fwrite_ushorts'
>  Bigendian_fwrite_ushorts (unsigned short *array, int n, FILE *fp) {
>  ^~~~~~~~~~~~~~~~~~~~~~~~
> bigendian.c:42:1: note: previous definition of 'Bigendian_fwrite_ushorts' was here
>  Bigendian_fwrite_ushorts (unsigned short *array, int n, FILE *fp) {
>  ^~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> Can you have a look?
> 
> Kind regards
> 
>        Andreas.
> 

Hi Andreas,

I'll take care. It is due to bigendian patch. Upstream send it to me in
an attempt to fix building on other architectures but it didn't work.
Finally I gave up and limited gmap to amd64 only, so this patch doesn't
make sense anymore.

Regards,
Alex