=> 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-0.7.9anb2 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 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 bwa.c:125:18: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] w = (max_gap + abs(rlen - l_query) + 1) >> 1; ^ bwa.c:125:18: note: use function 'labs' instead w = (max_gap + abs(rlen - l_query) + 1) >> 1; ^~~ labs bwa.c:127:11: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] min_w = abs(rlen - l_query) + 3; ^ bwa.c:127:11: note: use function 'labs' instead min_w = abs(rlen - l_query) + 3; ^~~ labs clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o bwase.c:181:57: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^ bwase.c:181:57: note: use function 'labs' instead ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^~~ labs bwase.c:181:88: warning: absolute value function 'abs' given an argument of type 'long' but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^ bwase.c:181:88: note: use function 'labs' instead ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32); ^~~ labs 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 is.c -o is.o 2 warnings generated. 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 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 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 clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o 2 warnings generated. clang -c -O2 -I/usr/include -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.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:20: recipe for target 'kopen.o' failed gmake: *** [kopen.o] Error 1 gmake: *** Waiting for unfinished jobs.... bwtsw2_pair.c:239:13: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value] diff = fabs(G[0] - G[1]) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.); ^ bwtsw2_pair.c:239:13: note: use function 'abs' instead diff = fabs(G[0] - G[1]) / (opt->a + opt->b) / ((hits[i]->hits[0].len + a[1].len + hits[i+1]->hits[0].len + a[0].len) / 2.); ^~~~ abs 1 warning generated. *** Error code 2 Stop. make[1]: stopped in /data/pkgsrc/biology/bwa *** Error code 1 Stop. make: stopped in /data/pkgsrc/biology/bwa