gqt icon indicating copy to clipboard operation
gqt copied to clipboard

make Error in MacOS Sierra

Open arumds opened this issue 5 years ago • 2 comments

I am compiling a gqt in mac and met with the below error. I have installed htslib succesfully and added the path in the gqt src/Makefile. Can anyone help to fix this?

$ make cd src; /Applications/Xcode.app/Contents/Developer/usr/bin/make flex -oparse_q.yy.c parse_q.l gcc -c -g -D_FILE_OFFSET_BITS=64 -o ../obj/parse_q.yy.o parse_q.yy.c
-I/Users/xxxx/db/htslib-1.9 -I/Users/xxxx/db/sqlite-amalgamation-3080701 gcc -g -D_FILE_OFFSET_BITS=64 -o ../bin/read_binary_uints read_binary_uints.c ../obj/timer.o ../obj/misc.o ../obj/query.o ../obj/pop.o ../obj/bim.o ../obj/vid.o ../obj/off.o ../obj/parse_q.yy.o ../obj/parse_q.o ../obj/ped.o ../obj/pq.o ../obj/bcf.o ../obj/quick_file.o ../obj/output_buffer.o ../obj/pthread_pool.o ../obj/genotq.o ../obj/convert.o ../obj/plt.o ../obj/wah.o ../obj/wahbm.o ../obj/wahbm_in_place.o ../obj/wahbm_compressed_in_place.o ../obj/ubin.o ../obj/view.o ../obj/sort.o ../obj/count.o ../obj/sandbox.o
-I/Users/xxxx/db/htslib-1.9
-I/Users/xxxx/db/sqlite-amalgamation-3080701
-DSAMTOOLS=1
/Users/xxxx/db/htslib-1.9/libhts.a
/Users/xxxx/db/sqlite-amalgamation-3080701/sqlite3.o
-ldl -lz -lm -pthread Undefined symbols for architecture x86_64: "_BZ2_bzBuffToBuffCompress", referenced from: _cram_compress_block in libhts.a(cram_io.o) _cram_compress_by_method in libhts.a(cram_io.o) "_BZ2_bzBuffToBuffDecompress", referenced from: _cram_uncompress_block in libhts.a(cram_io.o) "_curl_easy_cleanup", referenced from: _libcurl_open in libhts.a(hfile_libcurl.o) _libcurl_close in libhts.a(hfile_libcurl.o) _restart_from_position in libhts.a(hfile_libcurl.o) "_curl_easy_duphandle", referenced from: _restart_from_position in libhts.a(hfile_libcurl.o) "_curl_easy_getinfo", referenced from: _easy_errno in libhts.a(hfile_libcurl.o) _libcurl_open in libhts.a(hfile_libcurl.o) "_curl_easy_init", referenced from: _libcurl_open in libhts.a(hfile_libcurl.o) "_curl_easy_pause", referenced from: _libcurl_read in libhts.a(hfile_libcurl.o) _libcurl_write in libhts.a(hfile_libcurl.o) _libcurl_close in libhts.a(hfile_libcurl.o) _restart_from_position in libhts.a(hfile_libcurl.o) "_curl_easy_reset", referenced from: _restart_from_position in libhts.a(hfile_libcurl.o) "_curl_easy_setopt", referenced from: _libcurl_open in libhts.a(hfile_libcurl.o) _restart_from_position in libhts.a(hfile_libcurl.o) "_curl_global_cleanup", referenced from: _hfile_plugin_init_libcurl in libhts.a(hfile_libcurl.o) _libcurl_exit in libhts.a(hfile_libcurl.o) "_curl_global_init", referenced from: _hfile_plugin_init_libcurl in libhts.a(hfile_libcurl.o) "_curl_multi_add_handle", referenced from: _libcurl_open in libhts.a(hfile_libcurl.o) _restart_from_position in libhts.a(hfile_libcurl.o) "_curl_multi_cleanup", referenced from: _libcurl_open in libhts.a(hfile_libcurl.o) _libcurl_close in libhts.a(hfile_libcurl.o) "_curl_multi_fdset", referenced from: _wait_perform in libhts.a(hfile_libcurl.o) "_curl_multi_info_read", referenced from: _wait_perform in libhts.a(hfile_libcurl.o) "_curl_multi_init", referenced from: _libcurl_open in libhts.a(hfile_libcurl.o) "_curl_multi_perform", referenced from: _wait_perform in libhts.a(hfile_libcurl.o) "_curl_multi_remove_handle", referenced from: _libcurl_open in libhts.a(hfile_libcurl.o) _libcurl_close in libhts.a(hfile_libcurl.o) _restart_from_position in libhts.a(hfile_libcurl.o) "_curl_multi_timeout", referenced from: _wait_perform in libhts.a(hfile_libcurl.o) "_curl_share_cleanup", referenced from: _hfile_plugin_init_libcurl in libhts.a(hfile_libcurl.o) _libcurl_exit in libhts.a(hfile_libcurl.o) "_curl_share_init", referenced from: _hfile_plugin_init_libcurl in libhts.a(hfile_libcurl.o) "_curl_share_setopt", referenced from: _hfile_plugin_init_libcurl in libhts.a(hfile_libcurl.o) "_curl_version_info", referenced from: _hfile_plugin_init_libcurl in libhts.a(hfile_libcurl.o) "_lzma_code", referenced from: _cram_uncompress_block in libhts.a(cram_io.o) "_lzma_easy_buffer_encode", referenced from: _cram_compress_block in libhts.a(cram_io.o) _cram_compress_by_method in libhts.a(cram_io.o) "_lzma_easy_decoder_memusage", referenced from: _cram_uncompress_block in libhts.a(cram_io.o) "_lzma_end", referenced from: _cram_uncompress_block in libhts.a(cram_io.o) "_lzma_stream_buffer_bound", referenced from: _cram_compress_block in libhts.a(cram_io.o) _cram_compress_by_method in libhts.a(cram_io.o) "_lzma_stream_decoder", referenced from: _cram_uncompress_block in libhts.a(cram_io.o) ld: symbol(s) not found for architecture x86_64 collect2: error: ld returned 1 exit status make[1]: *** [../bin/read_binary_uints] Error 1 make: *** [all] Error 2

$ gcc --version gcc (MacPorts gcc5 5.5.0_1) 5.5.0 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

arumds avatar Sep 26 '18 18:09 arumds