=> Bootstrap dependency digest>=20010302: found digest-20190127
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Building for minimap2-2.18nb1
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  main.c -o main.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  kthread.c -o kthread.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  kalloc.c -o kalloc.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  misc.c -o misc.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  bseq.c -o bseq.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  sketch.c -o sketch.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  sdust.c -o sdust.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  options.c -o options.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  index.c -o index.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  chain.c -o chain.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  align.c -o align.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  hit.c -o hit.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  map.c -o map.o
map.c: In function 'mm_map_frag':
map.c:385:20: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t {aka unsigned int}' [-Wformat=]
    fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
                    ^
map.c:385:20: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t {aka unsigned int}' [-Wformat=]
map.c:385:20: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t {aka unsigned int}' [-Wformat=]
map.c:385:20: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t {aka unsigned int}' [-Wformat=]
map.c:385:20: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t {aka unsigned int}' [-Wformat=]
map.c:385:20: warning: format '%ld' expects argument of type 'long int', but argument 7 has type 'size_t {aka unsigned int}' [-Wformat=]
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  format.c -o format.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  pe.c -o pe.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  esterr.c -o esterr.o
gcc -c -g -Wall -O2 -Wc++-compat  -DHAVE_KALLOC  splitidx.c -o splitidx.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse2 -DHAVE_KALLOC  ksw2_ll_sse.c -o ksw2_ll_sse.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_extz2_sse.c -o ksw2_extz2_sse41.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_extd2_sse.c -o ksw2_extd2_sse41.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_exts2_sse.c -o ksw2_exts2_sse41.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY  ksw2_extz2_sse.c -o ksw2_extz2_sse2.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY  ksw2_extd2_sse.c -o ksw2_extd2_sse2.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse2 -mno-sse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH -DKSW_SSE2_ONLY  ksw2_exts2_sse.c -o ksw2_exts2_sse2.o
gcc -c -g -Wall -O2 -Wc++-compat  -msse4.1 -DHAVE_KALLOC -DKSW_CPU_DISPATCH  ksw2_dispatch.c -o ksw2_dispatch.o
ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o
gcc -g -Wall -O2 -Wc++-compat  main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
./libminimap2.a(index.o): In function `mm_idx_cal_max_occ':
/scratch/work/biology/minimap2/work/minimap2-2.18/index.c:182: undefined reference to `ks_ksmall_uint32_t'
gmake: *** [Makefile:46: minimap2] Error 1
*** Error code 2

Stop.
make[1]: stopped in /tree/pkgsrc/biology/minimap2
*** Error code 1

Stop.
make: stopped in /tree/pkgsrc/biology/minimap2