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grenaud / glactools

command-line tools for the management of genotype likelihoods and allele counts
http://grenaud.github.io/glactools/
GNU General Public License v3.0
29 stars 2 forks source link

curl error during make: install failure #7

Closed pbpearman closed 5 years ago

pbpearman commented 5 years ago

I am on Ubuntu 16.04. Late in make, I get the following errors:

/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:171: undefined reference to curl_easy_getinfo' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:185: undefined reference tocurl_easy_getinfo' htslib/libhts.a(hfile_libcurl.o): In function wait_perform': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:693: undefined reference tocurl_multi_fdset' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:714: undefined reference to curl_multi_perform' htslib/libhts.a(hfile_libcurl.o): In functionprocess_messages': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:669: undefined reference to curl_multi_info_read' htslib/libhts.a(hfile_libcurl.o): In functionwait_perform': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:696: undefined reference to curl_multi_timeout' htslib/libhts.a(hfile_libcurl.o): In functionlibcurl_close': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1073: undefined reference to curl_easy_pause' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1082: undefined reference tocurl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1086: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1087: undefined reference tocurl_multi_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1082: undefined reference to curl_multi_remove_handle' htslib/libhts.a(hfile_libcurl.o): In functionlibcurl_write': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:845: undefined reference to curl_easy_pause' htslib/libhts.a(hfile_libcurl.o): In functionlibcurl_exit': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:274: undefined reference to curl_share_cleanup' htslib/libhts.a(hfile_libcurl.o): In functionrestart_from_position': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:950: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:969: undefined reference tocurl_easy_duphandle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:973: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:974: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:975: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1052: undefined reference tocurl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:985: undefined reference to curl_multi_add_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1052: undefined reference tocurl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1052: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:992: undefined reference tocurl_easy_pause' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1012: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1015: undefined reference tocurl_easy_reset' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1016: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1044: undefined reference tocurl_easy_reset' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1045: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1025: undefined reference tocurl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1027: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1028: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1018: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1031: undefined reference tocurl_easy_reset' htslib/libhts.a(hfile_libcurl.o): In function libcurl_open': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1148: undefined reference tocurl_multi_init' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1151: undefined reference to curl_easy_init' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1155: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1159: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1167: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1168: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1169: undefined reference tocurl_easy_setopt' htslib/libhts.a(hfile_libcurl.o):/home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1176: more undefined references to curl_easy_setopt' follow htslib/libhts.a(hfile_libcurl.o): In functionlibcurl_open': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1207: undefined reference to curl_multi_add_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1215: undefined reference tocurl_easy_getinfo' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1235: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1236: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1237: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1248: undefined reference tocurl_easy_getinfo' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1258: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1259: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1286: undefined reference to curl_easy_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1287: undefined reference tocurl_multi_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1279: undefined reference to curl_multi_remove_handle' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1162: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1163: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1202: undefined reference tocurl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1194: undefined reference to curl_easy_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1269: undefined reference tocurl_easy_getinfo' htslib/libhts.a(hfile_libcurl.o): In function libcurl_read': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:786: undefined reference tocurl_easy_pause' htslib/libhts.a(hfile_libcurl.o): In function hfile_plugin_init_libcurl': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1447: undefined reference tocurl_global_init' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1450: undefined reference to curl_share_init' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1452: undefined reference tocurl_share_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1453: undefined reference to curl_share_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1454: undefined reference tocurl_share_setopt' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1480: undefined reference to curl_version_info' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1456: undefined reference tocurl_share_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1457: undefined reference to curl_global_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1469: undefined reference tocurl_share_cleanup' /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:1470: undefined reference to curl_global_cleanup' htslib/libhts.a(hfile_libcurl.o): In functionlibcurl_exit': /home/bgppermp/Downloads/glactools/htslib/hfile_libcurl.c:296: undefined reference to `curl_global_cleanup' collect2: error: ld returned 1 exit status Makefile:54: recipe for target 'glactools' failed make: *** [glactools] Error 1 glactools$

And I have: glactools$ curl --version curl 7.47.0 (x86_64-pc-linux-gnu) libcurl/7.47.0 GnuTLS/3.4.10 zlib/1.2.8 libidn/1.32 librtmp/2.3 Protocols: dict file ftp ftps gopher http https imap imaps ldap ldaps pop3 pop3s rtmp rtsp smb smbs smtp smtps telnet tftp Features: AsynchDNS IDN IPv6 Largefile GSS-API Kerberos SPNEGO NTLM NTLM_WB SSL libz TLS-SRP UnixSockets

Have I missed something?

grenaud commented 5 years ago

just so I can diagnose a bit better, could you go in the glactools directory, then do:

cd htslib
make clean
make
pbpearman commented 5 years ago

Here is what I got:

glactools$ cd htslib htslib$ make clean rm -f test/.tmp test/.tmp. test/tabix/.tmp. test/tabix/FAIL rm -f .o .pico cram/.o cram/.pico test/.o test/.dSYM version.h rm -f libhts.so libhts.so.* rm -f libhts.a bgzip htsfile tabix test/hts_endian test/fieldarith test/hfile test/pileup test/sam test/test_bgzf test/test_kstring test/test_realn test/test-regidx test/test_view test/test_index test/test-vcf-api test/test-vcf-sweep test/test-bcf-sr test/fuzz/hts_open_fuzzer.o test/test-bcf-translate test/test-parse-reg test/thrash_threads1 test/thrash_threads2 test/thrash_threads3 test/thrash_threads4 test/thrash_threads5 test/thrash_threads6 test/thrash_threads7 htslib$ make 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 header.o header.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 "1.9-288-g830c061"' > 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 region.o region.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/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/string_alloc.o cram/string_alloc.c gcc -g -Wall -O2 -I. -c -o hfile_libcurl.o hfile_libcurl.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o header.o hfile.o hfile_net.o hts.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_samtools.o cram/cram_stats.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/string_alloc.o hfile_libcurl.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 header.pico header.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 region.pico region.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/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/string_alloc.pico cram/string_alloc.c gcc -g -Wall -O2 -I. -fpic -c -o hfile_libcurl.pico hfile_libcurl.c gcc -shared -Wl,-soname,libhts.so.2to3part10 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico header.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico region.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/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/string_alloc.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread ln -sf libhts.so libhts.so.2to3part10 gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lcurl -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 -lcurl 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 -lcurl -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 -lcurl -lpthread gcc -g -Wall -O2 -I. -c -o test/pileup.o test/pileup.c gcc -o test/pileup test/pileup.o libhts.a -lz -lm -lbz2 -llzma -lcurl -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 -lcurl -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 -lcurl -lpthread gcc -g -Wall -O2 -I. -c -o test/test_kstring.o test/test_kstring.c gcc -o test/test_kstring test/test_kstring.o libhts.a -lz -lz -lm -lbz2 -llzma -lcurl -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 -lcurl -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 -lcurl -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 -lcurl -lpthread gcc -g -Wall -O2 -I. -c -o test/test_index.o test/test_index.c gcc -o test/test_index test/test_index.o libhts.a -lz -lm -lbz2 -llzma -lcurl -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 -lcurl -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 -lcurl -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 -lcurl -lpthread gcc -g -Wall -O2 -I. -c -o test/fuzz/hts_open_fuzzer.o test/fuzz/hts_open_fuzzer.c 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 -lcurl -lpthread gcc -g -Wall -O2 -I. -c -o test/test-parse-reg.o test/test-parse-reg.c gcc -o test/test-parse-reg test/test-parse-reg.o libhts.a -lz -lm -lbz2 -llzma -lcurl -lpthread htslib$

grenaud commented 5 years ago

so htslib has built successfully?

pbpearman commented 5 years ago

Well, no errors were produced... So I guess that means Yes

grenaud commented 5 years ago

it seems to have worked, from there, can you do a cd .. and

make and post the output?

pbpearman commented 5 years ago

You wrote email to say you updated the makefile. I re-cloned the repo and then compiled. It finished without errors :-) I will test this as soon as I get the chance. Thanks for addressing this issue. Cheers, Peter