echo '#define CTX_VERSION "v0.0.3-599-g97aba19"' > src/global/version.h
mkdir -p bin
mkdir -p build/kmer31
mkdir -p build/global
mkdir -p build/basic
mkdir -p build/paths
mkdir -p build/graph31
mkdir -p build/graph_paths31
mkdir -p build/alignment31
mkdir -p build/tools31
mkdir -p build/commands31
mkdir -p build/tests31
cc -O3 -m64 -std=c99 -Wall -Wextra -Wshadow -Wstrict-aliasing=2 -Winit-self -Wmissing-include-dirs -Wdiv-by-zero -Wsign-compare -Wmissing-noreturn -Wreturn-type -Wwrite-strings -Wundef -Wpointer-arith -Wfloat-equal -Wbad-function-cast   -D_USESAM=1 -DCTXCHECKS=1  -c -o libs/string_buffer/string_buffer.o libs/string_buffer/string_buffer.c
cc -O3 -m64 -std=c99 -Wall -Wextra -Wshadow -Wstrict-aliasing=2 -Winit-self -Wmissing-include-dirs -Wdiv-by-zero -Wsign-compare -Wmissing-noreturn -Wreturn-type -Wwrite-strings -Wundef -Wpointer-arith -Wfloat-equal -Wbad-function-cast   -D_USESAM=1 -DCTXCHECKS=1  -c -o libs/carrays/carrays.o libs/carrays/carrays.c
cc -o libs/cJSON/cJSON.o -O3 -m64 -std=c99 -Wall -Wextra -Wshadow -Wstrict-aliasing=2 -Winit-self -Wmissing-include-dirs -Wdiv-by-zero -Wsign-compare -Wmissing-noreturn -Wreturn-type -Wwrite-strings -Wundef -Wpointer-arith -Wfloat-equal -Wbad-function-cast  -c libs/cJSON/cJSON.c
cd libs && make core
make[1]: Entering directory '/usr/local/apps/bioapps/mccortex/mccortex/libs'
# Run configure if config makefile not created
cd htslib && ( if ! [ -f config.mk ]; then autoreconf && ./configure --disable-lzma --disable-bz2 --disable-libcurl; fi; make -e )
configure.ac:26: error: possibly undefined macro: m4_esyscmd_s
      If this token and others are legitimate, please use m4_pattern_allow.
      See the Autoconf documentation.
autoreconf: /usr/bin/autoconf failed with exit status: 1
make[2]: Entering directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib'
echo '/* Default config.h generated by Makefile */' > config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#define HAVE_FSEEKO 1' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
gcc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.8-17-g699ed53"' > version.h
gcc -g -Wall -O2 -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -I.  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
ranlib libhts.a
gcc -g -Wall -O2 -I.  -fpic -c -o kfunc.pico kfunc.c
gcc -g -Wall -O2 -I.  -fpic -c -o knetfile.pico knetfile.c
gcc -g -Wall -O2 -I.  -fpic -c -o kstring.pico kstring.c
gcc -g -Wall -O2 -I.  -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -Wall -O2 -I.  -fpic -c -o bgzf.pico bgzf.c
gcc -g -Wall -O2 -I.  -fpic -c -o errmod.pico errmod.c
gcc -g -Wall -O2 -I.  -fpic -c -o faidx.pico faidx.c
gcc -g -Wall -O2 -I.  -fpic -c -o hfile.pico hfile.c
gcc -g -Wall -O2 -I.  -fpic -c -o hfile_net.pico hfile_net.c
gcc -g -Wall -O2 -I.  -fpic -c -o hts.pico hts.c
gcc -g -Wall -O2 -I.  -fpic -c -o hts_os.pico hts_os.c
gcc -g -Wall -O2 -I.  -fpic -c -o md5.pico md5.c
gcc -g -Wall -O2 -I.  -fpic -c -o multipart.pico multipart.c
gcc -g -Wall -O2 -I.  -fpic -c -o probaln.pico probaln.c
gcc -g -Wall -O2 -I.  -fpic -c -o realn.pico realn.c
gcc -g -Wall -O2 -I.  -fpic -c -o regidx.pico regidx.c
gcc -g -Wall -O2 -I.  -fpic -c -o sam.pico sam.c
gcc -g -Wall -O2 -I.  -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -Wall -O2 -I.  -fpic -c -o tbx.pico tbx.c
gcc -g -Wall -O2 -I.  -fpic -c -o textutils.pico textutils.c
gcc -g -Wall -O2 -I.  -fpic -c -o thread_pool.pico thread_pool.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcf.pico vcf.c
gcc -g -Wall -O2 -I.  -fpic -c -o vcfutils.pico vcfutils.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/files.pico cram/files.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -Wall -O2 -I.  -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -shared -Wl,-soname,libhts.so.2  -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread
ln -sf libhts.so libhts.so.2
gcc -g -Wall -O2 -I.  -c -o bgzip.o bgzip.c
gcc  -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o htsfile.o htsfile.c
gcc  -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o tabix.o tabix.c
gcc  -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/hts_endian.o test/hts_endian.c
gcc  -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma
gcc -g -Wall -O2 -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc  -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/hfile.o test/hfile.c
gcc  -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/sam.o test/sam.c
gcc  -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test_bgzf.o test/test_bgzf.c
gcc  -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test_realn.o test/test_realn.c
gcc  -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc  -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test_view.o test/test_view.c
gcc  -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc  -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc  -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc  -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
gcc -g -Wall -O2 -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc  -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
make[2]: Leaving directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib'
cd string_buffer && make all
make[2]: Entering directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/string_buffer'
ar -csru libstrbuf.a string_buffer.o
cc -Wall -Wextra -pedantic -std=c99 -O4  strbuf_test.c -o strbuf_test -L. -lstrbuf -lz
make[2]: Leaving directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/string_buffer'
cd bit_array && make all
make[2]: Entering directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/bit_array'
cc -Wall -Wextra -Wc++-compat -I. -O4 -fPIC -c bit_array.c -o bit_array.o
ar -csru libbitarr.a bit_array.o
cd dev && make
make[3]: Entering directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/bit_array/dev'
cc -O3 -Wall -Wextra -Wc++-compat -I.. -L.. -o bit_array_test bit_array_test.c -lbitarr
cc -O3 -Wall -Wextra -Wc++-compat -I.. -o bitlock_test bitlock_test.c -lpthread
cc -O3 -Wall -Wextra -Wc++-compat -I.. -o bitlock_try_test bitlock_try_test.c -lpthread
cc -O3 -Wall -Wextra -Wc++-compat -o bit_array_generate bit_array_generate.c
make[3]: Leaving directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/bit_array/dev'
cd examples && make
make[3]: Entering directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/bit_array/examples'
g++ -Wall -Wextra -I.. -L.. -o example_cpp example.cpp -lbitarr
cc -Wall -Wextra -I.. -L.. -Wc++-compat -o example_c example.c -lbitarr
make[3]: Leaving directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/bit_array/examples'
make[2]: Leaving directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/bit_array'
cd seq_file && make HTSLIB=../htslib all
make[2]: Entering directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/seq_file'
mkdir -p bin
cc -Wall -Wextra -std=c99 -pedantic -I. -O3 -o bin/dnacat tools/dna_cat.c -I ../htslib -D_USESAM=1 ../htslib/libhts.a -lm -lpthread -lz -lm
In file included from ./seq_file.h:27,
                 from tools/dna_cat.c:23:
../htslib/htslib/hfile.h: In function 'hwrite':
../htslib/htslib/hfile.h:245: warning: comparison between signed and unsigned integer expressions
../htslib/libhts.a(cram_io.o): In function `lzma_mem_deflate':
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:678: undefined reference to `lzma_stream_buffer_bound'
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:684: undefined reference to `lzma_easy_buffer_encode'
../htslib/libhts.a(cram_io.o): In function `cram_compress_by_method':
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:1040: undefined reference to `BZ2_bzBuffToBuffCompress'
../htslib/libhts.a(cram_io.o): In function `cram_uncompress_block':
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:966: undefined reference to `BZ2_bzBuffToBuffDecompress'
../htslib/libhts.a(cram_io.o): In function `lzma_mem_inflate':
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:700: undefined reference to `lzma_easy_decoder_memusage'
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:700: undefined reference to `lzma_stream_decoder'
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:715: undefined reference to `lzma_code'
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:728: undefined reference to `lzma_code'
/usr/local/apps/bioapps/mccortex/mccortex/libs/htslib/cram/cram_io.c:737: undefined reference to `lzma_end'
collect2: ld returned 1 exit status
Makefile:32: recipe for target 'bin/dnacat' failed
make[2]: *** [bin/dnacat] Error 1
make[2]: Leaving directory '/usr/local/apps/bioapps/mccortex/mccortex/libs/seq_file'
Makefile:49: recipe for target 'seq_file' failed
make[1]: *** [seq_file] Error 2
make[1]: Leaving directory '/usr/local/apps/bioapps/mccortex/mccortex/libs'
Makefile:238: recipe for target 'libs-core' failed
make: *** [libs-core] Error 2