Re: htslib: Use pkgsrc install macros instead of mkdir

[Thomas Klausner <wiz%NetBSD.org@localhost>]

On Fri, May 19, 2017 at 10:54:35AM -0500, Jason Bacon wrote:
> I had to add one more patch to htslib to solve this problem:
> 
> https://sourceforge.net/p/samtools/mailman/message/31883152/
> 
> They're using cpp pasting to simulate polymorphic functions. NetBSD was
> expanding uintXX_t to __unintXX_t in one macro, but not others.  This patch
> brings them all into agreement.

Please add a comment to the patch.

> With that, samtools should be ready for review now as well.

files/pkg-message.in looks like a leftover from the FreeBSD port;
also, it does not seem to apply to pkgsrc, so it can be removed.

I suggest making perl a runtime dependency:

USE_TOOLS+=... perl:run

About the patches:

"=" assignments in Makefiles can be overridden by
passing the appropriate values on the make command line with
MAKE_FLAGS, e.g.

MAKE_FLAGS+=	CC=${CC}

then you don't need the parts that change '=' to '?='.

-ALL_LIBS     = -lz -ldl $(LIBS)
+ALL_LIBS     = -lz $(LIBS)

libdl is probably still needed on Linux and some other operating
systems. Look at mk/dlopen.buildlink3.mk.

+m4_include([ax_with_htslib.m4])
+m4_include([ax_with_curses.m4])

If these are not needed for finding the appropriate libraries, you can
skip that parts. It is something upstream should fix, but in pkgsrc
we'll make sure the dependencies are installed anyway.

TODO seems to be fixed (see above).

Cheers,
 Thomas