VSEARCH make log

make.log

make  all-recursive
make[1]: Entering directory '/home/mys_721tx/vsearch'
Making all in src
make[2]: Entering directory '/home/mys_721tx/vsearch/src'
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -msse2 -g -march=native -MT libcpu_sse2_a-cpu.o -MD -MP -MF .deps/libcpu_sse2_a-cpu.Tpo -c -o libcpu_sse2_a-cpu.o `test -f 'cpu.cc' || echo './'`cpu.cc
mv -f .deps/libcpu_sse2_a-cpu.Tpo .deps/libcpu_sse2_a-cpu.Po
rm -f libcpu_sse2.a
ar cru libcpu_sse2.a libcpu_sse2_a-cpu.o  
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcpu_sse2.a
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -mssse3 -DSSSE3 -g -march=native -MT libcpu_ssse3_a-cpu.o -MD -MP -MF .deps/libcpu_ssse3_a-cpu.Tpo -c -o libcpu_ssse3_a-cpu.o `test -f 'cpu.cc' || echo './'`cpu.cc
mv -f .deps/libcpu_ssse3_a-cpu.Tpo .deps/libcpu_ssse3_a-cpu.Po
rm -f libcpu_ssse3.a
ar cru libcpu_ssse3.a libcpu_ssse3_a-cpu.o  
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcpu_ssse3.a
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wno-sign-compare -O3 -g -g -march=native -MT libcityhash_a-city.o -MD -MP -MF .deps/libcityhash_a-city.Tpo -c -o libcityhash_a-city.o `test -f 'city.cc' || echo './'`city.cc
mv -f .deps/libcityhash_a-city.Tpo .deps/libcityhash_a-city.Po
rm -f libcityhash.a
ar cru libcityhash.a libcityhash_a-city.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libcityhash.a
depbase=`echo abundance.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT abundance.o -MD -MP -MF $depbase.Tpo -c -o abundance.o abundance.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT align.o -MD -MP -MF $depbase.Tpo -c -o align.o align.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo align_simd.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT align_simd.o -MD -MP -MF $depbase.Tpo -c -o align_simd.o align_simd.cc &&\
mv -f $depbase.Tpo $depbase.Po
In function ‘void pushop(s16info_s*, char)’,
    inlined from ‘void backtrack16(s16info_s*, char*, uint64_t, uint64_t, uint64_t, short unsigned int*, short unsigned int*, short unsigned int*, short unsigned int*)’ at align_simd.cc:994:13:
align_simd.cc:855:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 10 bytes from a string of length 10 [-Wstringop-truncation]
           strncpy(s->cigarend, buf, len);
           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In function ‘void pushop(s16info_s*, char)’,
    inlined from ‘void backtrack16(s16info_s*, char*, uint64_t, uint64_t, uint64_t, short unsigned int*, short unsigned int*, short unsigned int*, short unsigned int*)’ at align_simd.cc:1011:13:
align_simd.cc:855:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 10 bytes from a string of length 10 [-Wstringop-truncation]
           strncpy(s->cigarend, buf, len);
           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In function ‘void pushop(s16info_s*, char)’,
    inlined from ‘void backtrack16(s16info_s*, char*, uint64_t, uint64_t, uint64_t, short unsigned int*, short unsigned int*, short unsigned int*, short unsigned int*)’ at align_simd.cc:1001:13:
align_simd.cc:855:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 10 bytes from a string of length 10 [-Wstringop-truncation]
           strncpy(s->cigarend, buf, len);
           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In function ‘void pushop(s16info_s*, char)’,
    inlined from ‘void backtrack16(s16info_s*, char*, uint64_t, uint64_t, uint64_t, short unsigned int*, short unsigned int*, short unsigned int*, short unsigned int*)’ at align_simd.cc:1021:13:
align_simd.cc:855:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 10 bytes from a string of length 10 [-Wstringop-truncation]
           strncpy(s->cigarend, buf, len);
           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In function ‘void pushop(s16info_s*, char)’,
    inlined from ‘void backtrack16(s16info_s*, char*, uint64_t, uint64_t, uint64_t, short unsigned int*, short unsigned int*, short unsigned int*, short unsigned int*)’ at align_simd.cc:1030:13:
align_simd.cc:855:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 10 bytes from a string of length 10 [-Wstringop-truncation]
           strncpy(s->cigarend, buf, len);
           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In function ‘void finishop(s16info_s*)’,
    inlined from ‘void backtrack16(s16info_s*, char*, uint64_t, uint64_t, uint64_t, short unsigned int*, short unsigned int*, short unsigned int*, short unsigned int*)’ at align_simd.cc:1033:11:
align_simd.cc:872:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 1 and 10 bytes from a string of length 10 [-Wstringop-truncation]
           strncpy(s->cigarend, buf, len);
           ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
depbase=`echo allpairs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT allpairs.o -MD -MP -MF $depbase.Tpo -c -o allpairs.o allpairs.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo arch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT arch.o -MD -MP -MF $depbase.Tpo -c -o arch.o arch.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo bitmap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT bitmap.o -MD -MP -MF $depbase.Tpo -c -o bitmap.o bitmap.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo chimera.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT chimera.o -MD -MP -MF $depbase.Tpo -c -o chimera.o chimera.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo cluster.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT cluster.o -MD -MP -MF $depbase.Tpo -c -o cluster.o cluster.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo db.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT db.o -MD -MP -MF $depbase.Tpo -c -o db.o db.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo dbhash.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT dbhash.o -MD -MP -MF $depbase.Tpo -c -o dbhash.o dbhash.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo dbindex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT dbindex.o -MD -MP -MF $depbase.Tpo -c -o dbindex.o dbindex.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo derep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT derep.o -MD -MP -MF $depbase.Tpo -c -o derep.o derep.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo dynlibs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT dynlibs.o -MD -MP -MF $depbase.Tpo -c -o dynlibs.o dynlibs.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo eestats.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT eestats.o -MD -MP -MF $depbase.Tpo -c -o eestats.o eestats.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT fasta.o -MD -MP -MF $depbase.Tpo -c -o fasta.o fasta.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo fastq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT fastq.o -MD -MP -MF $depbase.Tpo -c -o fastq.o fastq.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo fastqops.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT fastqops.o -MD -MP -MF $depbase.Tpo -c -o fastqops.o fastqops.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo fastx.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT fastx.o -MD -MP -MF $depbase.Tpo -c -o fastx.o fastx.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo kmerhash.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT kmerhash.o -MD -MP -MF $depbase.Tpo -c -o kmerhash.o kmerhash.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo linmemalign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT linmemalign.o -MD -MP -MF $depbase.Tpo -c -o linmemalign.o linmemalign.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo maps.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT maps.o -MD -MP -MF $depbase.Tpo -c -o maps.o maps.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo mask.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT mask.o -MD -MP -MF $depbase.Tpo -c -o mask.o mask.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo md5.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT md5.o -MD -MP -MF $depbase.Tpo -c -o md5.o md5.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo mergepairs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT mergepairs.o -MD -MP -MF $depbase.Tpo -c -o mergepairs.o mergepairs.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo minheap.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT minheap.o -MD -MP -MF $depbase.Tpo -c -o minheap.o minheap.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo msa.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT msa.o -MD -MP -MF $depbase.Tpo -c -o msa.o msa.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo otutable.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT otutable.o -MD -MP -MF $depbase.Tpo -c -o otutable.o otutable.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo rerep.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT rerep.o -MD -MP -MF $depbase.Tpo -c -o rerep.o rerep.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo results.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT results.o -MD -MP -MF $depbase.Tpo -c -o results.o results.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo search.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT search.o -MD -MP -MF $depbase.Tpo -c -o search.o search.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo searchcore.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT searchcore.o -MD -MP -MF $depbase.Tpo -c -o searchcore.o searchcore.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo searchexact.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT searchexact.o -MD -MP -MF $depbase.Tpo -c -o searchexact.o searchexact.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo sha1.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
gcc -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT sha1.o -MD -MP -MF $depbase.Tpo -c -o sha1.o sha1.c &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo showalign.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT showalign.o -MD -MP -MF $depbase.Tpo -c -o showalign.o showalign.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo shuffle.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT shuffle.o -MD -MP -MF $depbase.Tpo -c -o shuffle.o shuffle.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo sintax.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT sintax.o -MD -MP -MF $depbase.Tpo -c -o sintax.o sintax.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo sortbylength.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT sortbylength.o -MD -MP -MF $depbase.Tpo -c -o sortbylength.o sortbylength.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo sortbysize.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT sortbysize.o -MD -MP -MF $depbase.Tpo -c -o sortbysize.o sortbysize.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo subsample.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT subsample.o -MD -MP -MF $depbase.Tpo -c -o subsample.o subsample.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo udb.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT udb.o -MD -MP -MF $depbase.Tpo -c -o udb.o udb.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo unique.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT unique.o -MD -MP -MF $depbase.Tpo -c -o unique.o unique.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo userfields.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT userfields.o -MD -MP -MF $depbase.Tpo -c -o userfields.o userfields.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo util.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT util.o -MD -MP -MF $depbase.Tpo -c -o util.o util.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo vsearch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I. -I..    -Wall -Wsign-compare -O3 -g -g -march=native -MT vsearch.o -MD -MP -MF $depbase.Tpo -c -o vsearch.o vsearch.cc &&\
mv -f $depbase.Tpo $depbase.Po
g++ -Wall -Wsign-compare -O3 -g -g -march=native   -o ../bin/vsearch  abundance.o align.o align_simd.o allpairs.o arch.o bitmap.o chimera.o cluster.o db.o dbhash.o dbindex.o derep.o dynlibs.o eestats.o fasta.o fastq.o fastqops.o fastx.o kmerhash.o linmemalign.o maps.o mask.o md5.o mergepairs.o minheap.o msa.o otutable.o rerep.o results.o search.o searchcore.o searchexact.o sha1.o showalign.o shuffle.o sintax.o sortbylength.o sortbysize.o subsample.o udb.o unique.o userfields.o util.o vsearch.o libcityhash.a libcpu_ssse3.a libcpu_sse2.a -ldl -lpthread 
make[2]: Leaving directory '/home/mys_721tx/vsearch/src'
Making all in man
make[2]: Entering directory '/home/mys_721tx/vsearch/man'
TEMP=$(mktemp temp.XXXXXXXX) ; \
if [ $(uname) == "Darwin" ] ; then \
	sed -e 's/\\-/-/g' vsearch.1 | \
	iconv -f UTF-8 -t ISO-8859-1 > $TEMP ; \
else \
	sed -e 's/\\-/-/g' vsearch.1 > $TEMP ; \
fi ; \
man -t ./$TEMP | ps2pdf -sPAPERSIZE=a4 - vsearch_manual.pdf ; \
rm $TEMP
make[2]: Leaving directory '/home/mys_721tx/vsearch/man'
make[2]: Entering directory '/home/mys_721tx/vsearch'
make[2]: Leaving directory '/home/mys_721tx/vsearch'
make[1]: Leaving directory '/home/mys_721tx/vsearch'