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Re: htslib: Use pkgsrc install macros instead of mkdir

Thanks for taking the time to examine this so carefully. I've taken notes on all these comments and updated my checklist for reviewing a package. Responses embedded below.

On 05/23/17 09:54, Thomas Klausner wrote:
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:

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/ 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


then you don't need the parts that change '=' to '?='.
This I was aware of, but the Makefile requires many other patches anyway and I prefer to fix everything in one place.

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

libdl is probably still needed on Linux and some other operating
systems. Look at mk/
I can verify that it's not required for CentOS or NetBSD. Would you suggest leaving it in anyway?


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.
Configure fails without these patches. 1.4 has been released, but I want to commit 1.3 due to API compatibility issues I mentioned before. I don't intend to send any 1.3 patches upstream since development has ceased on that branch. I will be working on a 1.4.x package as well and intend to send all those patches upstream.

TODO seems to be fixed (see above).

Thanks again for the feedback.


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