=> Bootstrap dependency digest>=20010302: found digest-20160304
===> Skipping vulnerability checks.
WARNING: No /var/db/pkg/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /var/db/pkg fetch-pkg-vulnerabilities'.
=> Checksum SHA1 OK for bwa-0.7.9a.tar.bz2
=> Checksum RMD160 OK for bwa-0.7.9a.tar.bz2
=> Checksum SHA512 OK for bwa-0.7.9a.tar.bz2
===> Installing dependencies for bwa-0.7.9anb2
=> Tool dependency gmake>=3.81: found gmake-4.1nb3
=> Tool dependency checkperms>=1.1: found checkperms-1.11nb1
=> Build dependency cwrappers>=20150314: found cwrappers-20170112
=> Full dependency perl>=5.0: found perl-5.24.1
===> Overriding tools for bwa-0.7.9anb2
===> Extracting for bwa-0.7.9anb2
===> Patching for bwa-0.7.9anb2
=> Applying pkgsrc patches for bwa-0.7.9anb2
=> Verifying /data/pkgsrc/biology/bwa/patches/patch-Makefile
=> Applying pkgsrc patch /data/pkgsrc/biology/bwa/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.1 2015/12/12 16:56:04 wiedi Exp $
|
|Don't overwrite pkgsrc CC and CFLAGS
|
|--- Makefile.orig	2014-05-19 13:11:41.000000000 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 1.
Hunk #2 succeeded at 11.
done
===> Creating toolchain wrappers for bwa-0.7.9anb2
===> Configuring for bwa-0.7.9anb2
=> Replacing Perl interpreter in *.pl.
=> Checking for portability problems in extracted files