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ryanlayer
make Error in MacOS Sierra
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.
I figured this out. I have the same problem also in Ubuntu machine. Adding -lcurl -llzma -lbz2 to the last of the code did the trick.
Change the last line, -ldl -lz -lm -pthread to -ldl -lz -lm -lcurl -llzma -lbz2 -pthread
Ah! Thanks for the update. I will try and get this fixed in the repo.
On Thu, Sep 27, 2018 at 3:22 AM mehar-GIT [email protected] wrote:
I figured this out. I have the same problem also in Ubuntu machine. Adding -lcurl -llzma -lbz2 to the last of the code did the trick.
Change the last line, -ldl -lz -lm -pthread to -ldl -lz -lm -lcurl -llzma -lbz2 -pthread
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