[Debian-med-packaging] Bug#784929: subread: FTBFS on arm64, armel, armhf, ...

[Edmund Grimley Evans]

Source: subread
Version: 1.4.6-p2+dfsg-2

It failed to build on several architectures:

https://buildd.debian.org/status/package.php?p=subread&suite=sid

There seems to be a problem with (unsigned) char. See this file, for
example:

https://sources.debian.net/src/subread/1.4.6-p2%2Bdfsg-2/src/SNPCalling.c/

This line:

while ((c = getopt_long (argc, argv, "7:N:a:i:g:o:bQ:p:f:n:r:x:w:s:t:T:v4",snp_long_options, &optindex))!=-1)

The function getopt_long returns int, but the value is assigned to a
char c, which is unsigned on ARM architectures, so it will never be
equal to -1. That is probably the immediate cause of the failure.
However, there may be other char-related problems in there. I noticed,
for example, that mask_snp_bitmap may be incorrect according to the C
standard (signed overflow).