=> 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'.
===> Building for bwa-0.7.17
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  utils.c -o utils.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kthread.c -o kthread.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kstring.c -o kstring.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  ksw.c -o ksw.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt.c -o bwt.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bntseq.c -o bntseq.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwa.c -o bwa.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem.c -o bwamem.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_pair.c -o bwamem_pair.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwamem_extra.c -o bwamem_extra.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  malloc_wrap.c -o malloc_wrap.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  QSufSort.c -o QSufSort.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_gen.c -o bwt_gen.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  rope.c -o rope.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  rle.c -o rle.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  is.c -o is.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtindex.c -o bwtindex.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwashm.c -o bwashm.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwase.c -o bwase.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwaseqio.c -o bwaseqio.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtgap.c -o bwtgap.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtaln.c -o bwtaln.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bamlite.c -o bamlite.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwape.c -o bwape.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  kopen.c -o kopen.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  pemerge.c -o pemerge.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  maxk.c -o maxk.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_core.c -o bwtsw2_core.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_main.c -o bwtsw2_main.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_aux.c -o bwtsw2_aux.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwt_lite.c -o bwt_lite.o
clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS  bwtsw2_chain.c -o bwtsw2_chain.o
kopen.c:29:17: error: variable has incomplete type 'struct timeval'
        struct timeval tv;
                       ^
kopen.c:29:9: note: forward declaration of 'struct timeval'
        struct timeval tv;
               ^
kopen.c:36:8: warning: implicit declaration of function 'select' is invalid in C99 [-Wimplicit-function-declaration]
        ret = select(fd+1, fdr, fdw, 0, &tv);
              ^
1 warning and 1 error generated.
Makefile:28: recipe for target 'kopen.o' failed
gmake: *** [kopen.o] Error 1
gmake: *** Waiting for unfinished jobs....
*** Error code 2

Stop.
make[1]: stopped in /data/pkgsrc/biology/bwa
*** Error code 1

Stop.
make: stopped in /data/pkgsrc/biology/bwa