# macOS Version 11.6 "BigSur"
$ bash build_ngsLCA.sh
Cloning into 'htslib'...
remote: Enumerating objects: 15018, done.
remote: Counting objects: 100% (673/673), done.
remote: Compressing objects: 100% (281/281), done.
remote: Total 15018 (delta 439), reused 490 (delta 392), pack-reused 14345
Receiving objects: 100% (15018/15018), 11.35 MiB | 12.29 MiB/s, done.
Resolving deltas: 100% (10819/10819), done.
Submodule 'htscodecs' (https://github.com/samtools/htscodecs.git) registered for path 'htscodecs'
Cloning into '/Users/maxime/Desktop/ngsLCA/test_compilation/htslib/htscodecs'...
remote: Enumerating objects: 1381, done.
remote: Counting objects: 100% (210/210), done.
remote: Compressing objects: 100% (141/141), done.
remote: Total 1381 (delta 132), reused 129 (delta 69), pack-reused 1171
Receiving objects: 100% (1381/1381), 19.87 MiB | 14.67 MiB/s, done.
Resolving deltas: 100% (944/944), done.
Submodule path 'htscodecs': checked out 'c6a459a4488624d5e4b2d4d642febbd55a78a9b1'
Cloning into 'ngsLCA'...
remote: Enumerating objects: 727, done.
remote: Counting objects: 100% (64/64), done.
remote: Compressing objects: 100% (64/64), done.
remote: Total 727 (delta 32), reused 1 (delta 0), pack-reused 663
Receiving objects: 100% (727/727), 194.22 MiB | 8.41 MiB/s, done.
Resolving deltas: 100% (407/407), done.
Updating files: 100% (24/24), done.
Makefile:122: htscodecs.mk: No such file or directory
echo '# Default htscodecs.mk generated by Makefile' > htscodecs.mk
echo 'include $(HTSPREFIX)htscodecs_bundled.mk' >> htscodecs.mk
echo '/* Default config.h generated by Makefile */' > config.h
echo '#ifndef _XOPEN_SOURCE' >> config.h
echo '#define _XOPEN_SOURCE 600' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_LIBBZ2 1' >> config.h
echo '#define HAVE_LIBLZMA 1' >> config.h
echo '#ifndef __APPLE__' >> config.h
echo '#define HAVE_LZMA_H 1' >> config.h
echo '#endif' >> config.h
echo '#define HAVE_DRAND48 1' >> config.h
echo '#define HAVE_LIBCURL 1' >> config.h
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o errmod.o errmod.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o header.o header.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o hfile.o hfile.c
echo '#define HTS_VERSION_TEXT "1.15-7-g8caa1db"' > version.h
echo '#define HTS_CC "gcc"' > config_vars.h
echo '#define HTS_CPPFLAGS ""' >> config_vars.h
echo '#define HTS_CFLAGS "-g -Wall -O2 -fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LDFLAGS "-fvisibility=hidden"' >> config_vars.h
echo '#define HTS_LIBS "-lz -lm -lbz2 -llzma -lcurl"' >> config_vars.h
Updating htscodecs/htscodecs/version.h : #define HTSCODECS_VERSION_TEXT "1.2.1"
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o hts_expr.o hts_expr.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o hts_os.o hts_os.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o multipart.o multipart.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o probaln.o probaln.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o realn.o realn.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o region.o region.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o textutils.o textutils.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o thread_pool.o thread_pool.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/arith_dynamic.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/fqzcomp_qual.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/htscodecs.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/pack.o htscodecs/htscodecs/pack.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static4x16pr.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rANS_static.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/rle.o htscodecs/htscodecs/rle.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htscodecs/htscodecs/tokenise_name3.o htscodecs/htscodecs/tokenise_name3.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o
ranlib libhts.a
gcc -dynamiclib -install_name /usr/local/lib/libhts.3.dylib -current_version 3.1.15 -compatibility_version 3.1.15 -fvisibility=hidden -o libhts.dylib kfunc.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hts.o hts_expr.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o region.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_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/string_alloc.o htscodecs/htscodecs/arith_dynamic.o htscodecs/htscodecs/fqzcomp_qual.o htscodecs/htscodecs/htscodecs.o htscodecs/htscodecs/pack.o htscodecs/htscodecs/rANS_static4x16pr.o htscodecs/htscodecs/rANS_static.o htscodecs/htscodecs/rle.o htscodecs/htscodecs/tokenise_name3.o hfile_libcurl.o -lz -lm -lbz2 -llzma -lcurl
ln -sf libhts.dylib libhts.3.dylib
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o bgzip.o bgzip.c
gcc -fvisibility=hidden -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o htsfile.o htsfile.c
gcc -fvisibility=hidden -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o tabix.o tabix.c
gcc -fvisibility=hidden -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/hts_endian.o test/hts_endian.c
gcc -fvisibility=hidden -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma -lcurl
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/fieldarith.o test/fieldarith.c
gcc -fvisibility=hidden -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/hfile.o test/hfile.c
gcc -fvisibility=hidden -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/pileup.o test/pileup.c
gcc -fvisibility=hidden -o test/pileup test/pileup.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/pileup_mod.o test/pileup_mod.c
gcc -fvisibility=hidden -o test/pileup_mod test/pileup_mod.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/plugins-dlhts.o test/plugins-dlhts.c
gcc -fvisibility=hidden -o test/plugins-dlhts test/plugins-dlhts.o -lz -lm -lbz2 -llzma -lcurl
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/sam.o test/sam.c
gcc -fvisibility=hidden -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_bgzf.o test/test_bgzf.c
gcc -fvisibility=hidden -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_expr.o test/test_expr.c
gcc -fvisibility=hidden -o test/test_expr test/test_expr.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_kfunc.o test/test_kfunc.c
gcc -fvisibility=hidden -o test/test_kfunc test/test_kfunc.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_kstring.o test/test_kstring.c
gcc -fvisibility=hidden -o test/test_kstring test/test_kstring.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_mod.o test/test_mod.c
gcc -fvisibility=hidden -o test/test_mod test/test_mod.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_realn.o test/test_realn.c
gcc -fvisibility=hidden -o test/test_realn test/test_realn.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test-regidx.o test/test-regidx.c
gcc -fvisibility=hidden -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_str2int.o test/test_str2int.c
gcc -fvisibility=hidden -o test/test_str2int test/test_str2int.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_view.o test/test_view.c
gcc -fvisibility=hidden -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_index.o test/test_index.c
gcc -fvisibility=hidden -o test/test_index test/test_index.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test-vcf-api.o test/test-vcf-api.c
gcc -fvisibility=hidden -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
gcc -fvisibility=hidden -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test-bcf-sr.o test/test-bcf-sr.c
gcc -fvisibility=hidden -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test-bcf-translate.o test/test-bcf-translate.c
gcc -fvisibility=hidden -o test/test-bcf-translate test/test-bcf-translate.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test-parse-reg.o test/test-parse-reg.c
gcc -fvisibility=hidden -o test/test-parse-reg test/test-parse-reg.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
gcc -g -Wall -O2 -fvisibility=hidden -I.  -c -o test/test_introspection.o test/test_introspection.c
gcc -fvisibility=hidden -o test/test_introspection test/test_introspection.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread
sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma -lcurl/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp
sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
sed -e 's#@-includedir@#'`pwd`'#g;s#@-libdir@#'`pwd`'#g' htslib.pc.tmp > htslib-uninstalled.pc
HTSSRC defined
c++ -c  -O3   -I/Users/maxime/Desktop/ngsLCA/test_compilation/htslib ngsLCA.cpp
ngsLCA.cpp:100:24: error: use of undeclared identifier 'basename'
int dodump = !fexists3(basename(acc2taxfile),basename(bamfile),".bin");
                       ^
ngsLCA.cpp:100:46: error: use of undeclared identifier 'basename'
int dodump = !fexists3(basename(acc2taxfile),basename(bamfile),".bin");
                                             ^
ngsLCA.cpp:107:17: error: use of undeclared identifier 'basename'
  fp = getbgzf3(basename(acc2taxfile),basename(bamfile),".bin","wb",4);
                ^
ngsLCA.cpp:107:39: error: use of undeclared identifier 'basename'
  fp = getbgzf3(basename(acc2taxfile),basename(bamfile),".bin","wb",4);
                                      ^
ngsLCA.cpp:109:19: error: use of undeclared identifier 'basename'
   fp =  getbgzf3(basename(acc2taxfile),basename(bamfile),".bin","rb",4);
                  ^
ngsLCA.cpp:109:41: error: use of undeclared identifier 'basename'
   fp =  getbgzf3(basename(acc2taxfile),basename(bamfile),".bin","rb",4);
                                        ^
ngsLCA.cpp:138:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
      bgzf_write(fp,&valinbam,sizeof(int));
      ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~
ngsLCA.cpp:139:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
      bgzf_write(fp,&val,sizeof(int));
      ^~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~
ngsLCA.cpp:151:1: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result]
bgzf_read(fp,&val,sizeof(int));
^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~
3 warnings and 6 errors generated.
make: *** [ngsLCA.o] Error 1