Question: Undefined reference ERROR in building the localized UCSC Genome browser with kent source
0
gravatar for 2013302630028
2.6 years ago by
201330263002810 wrote:
I want to install a localized UCSC Genome browser in my server. I try to use the Oliver's method to install it, and this is the [link][1]. When I install fixCr in $kent/src/utils/fixCr I get some undefined reference errors. My command is in the end. Thank you for your help~
sqreb@sqreb-Vostro-1450:~/genome/kent/src/utils/fixCr$ make
gcc -O -g -o /home/sqreb/bin/x86_64/fixCr fixCr.o    ../../lib/x86_64/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lstdc++ -lrt -lm ../../htslib/libhts.a -pthread -L/lib -lssl -lcrypto -lpng12 -lm
../../htslib/libhts.a(hts.o): In function `decompress_peek':
/home/sqreb/genome/kent/src/htslib/hts.c:142: undefined reference to `inflateInit2_'
/home/sqreb/genome/kent/src/htslib/hts.c:145: undefined reference to `inflate'
/home/sqreb/genome/kent/src/htslib/hts.c:148: undefined reference to `inflateEnd'
../../htslib/libhts.a(cram_io.o): In function `itf8_decode_crc':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:195: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:201: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:208: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:216: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:225: undefined reference to `crc32'
../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:537: more undefined references to `crc32' follow
../../htslib/libhts.a(cram_io.o): In function `zlib_mem_inflate':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:718: undefined reference to `inflateInit2_'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:731: undefined reference to `inflate'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:751: undefined reference to `inflateEnd'
../../htslib/libhts.a(cram_io.o): In function `zlib_mem_deflate':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:782: undefined reference to `deflateInit2_'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:796: undefined reference to `deflate'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:803: undefined reference to `deflate'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:808: undefined reference to `deflateEnd'
../../htslib/libhts.a(cram_io.o): In function `cram_read_block':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:946: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:948: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:980: undefined reference to `crc32'
../../htslib/libhts.a(cram_io.o): In function `cram_write_block':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1049: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1052: undefined reference to `crc32'
../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1054: more undefined references to `crc32' follow
../../htslib/libhts.a(zfio.o): In function `zfgets':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:69: undefined reference to `gzgets'
../../htslib/libhts.a(zfio.o): In function `zfputs':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:80: undefined reference to `gzputs'
../../htslib/libhts.a(zfio.o): In function `zfpeek':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:95: undefined reference to `gzgetc'
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:97: undefined reference to `gzungetc'
../../htslib/libhts.a(zfio.o): In function `zfeof':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:105: undefined reference to `gzeof'
../../htslib/libhts.a(zfio.o): In function `zfopen':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:165: undefined reference to `gzopen'
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:169: undefined reference to `gzopen'
../../htslib/libhts.a(zfio.o): In function `zfclose':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:180: undefined reference to `gzclose'
../../htslib/libhts.a(bgzf.o): In function `bgzf_write_init':
/home/sqreb/genome/kent/src/htslib/bgzf.c:166: undefined reference to `deflateInit2_'
../../htslib/libhts.a(bgzf.o): In function `bgzf_open':
/home/sqreb/genome/kent/src/htslib/bgzf.c:174: undefined reference to `compressBound'
../../htslib/libhts.a(bgzf.o): In function `bgzf_dopen':
/home/sqreb/genome/kent/src/htslib/bgzf.c:196: undefined reference to `compressBound'
../../htslib/libhts.a(bgzf.o): In function `bgzf_hopen':
/home/sqreb/genome/kent/src/htslib/bgzf.c:218: undefined reference to `compressBound'
../../htslib/libhts.a(bgzf.o): In function `bgzf_compress':
/home/sqreb/genome/kent/src/htslib/bgzf.c:244: undefined reference to `deflateInit2_'
/home/sqreb/genome/kent/src/htslib/bgzf.c:245: undefined reference to `deflate'
/home/sqreb/genome/kent/src/htslib/bgzf.c:246: undefined reference to `deflateEnd'
/home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32'
../../htslib/libhts.a(bgzf.o): In function `bgzf_gzip_compress':
/home/sqreb/genome/kent/src/htslib/bgzf.c:267: undefined reference to `deflate'
../../htslib/libhts.a(bgzf.o): In function `inflate_block':
/home/sqreb/genome/kent/src/htslib/bgzf.c:302: undefined reference to `inflateInit2_'
/home/sqreb/genome/kent/src/htslib/bgzf.c:306: undefined reference to `inflate'
/home/sqreb/genome/kent/src/htslib/bgzf.c:307: undefined reference to `inflateEnd'
/home/sqreb/genome/kent/src/htslib/bgzf.c:311: undefined reference to `inflateEnd'
../../htslib/libhts.a(bgzf.o): In function `inflate_gzip_block':
/home/sqreb/genome/kent/src/htslib/bgzf.c:335: undefined reference to `inflate'
../../htslib/libhts.a(bgzf.o): In function `bgzf_read_block':
/home/sqreb/genome/kent/src/htslib/bgzf.c:505: undefined reference to `inflateInit2_'
../../htslib/libhts.a(bgzf.o): In function `bgzf_close':
/home/sqreb/genome/kent/src/htslib/bgzf.c:816: undefined reference to `inflateEnd'
/home/sqreb/genome/kent/src/htslib/bgzf.c:817: undefined reference to `deflateEnd'
collect2: error: ld returned 1 exit status
../../inc/userApp.mk:31: recipe for target '/home/sqreb/bin/x86_64/fixCr' failed
make: *** [/home/sqreb/bin/x86_64/fixCr] Error 1

--This is my command.-- Set MACHTYPE

sqreb@sqreb-Vostro-1450:~$ uname -a
Linux sqreb-Vostro-1450 4.4.0-34-generic #53-Ubuntu SMP Wed Jul 27 16:06:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
sqreb@sqreb-Vostro-1450:~$ MACHTYPE=x86_64
sqreb@sqreb-Vostro-1450:~$ export MACHTYPE
sqreb@sqreb-Vostro-1450:~$ mkdir -p ~/bin/${MACHTYPE}

Download USCS source codes

sqreb@sqreb-Vostro-1450:~$ cd genome/
sqreb@sqreb-Vostro-1450:~/genome$ git clone git://genome-source.cse.ucsc.edu/kent.git 
Cloning into 'kent'...
Checking connectivity... done.
sqreb@sqreb-Vostro-1450:~/genome$ git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix
Cloning into 'samtabix'...
Checking connectivity... done.

MySQL option

sqreb@sqreb-Vostro-1450:~/genome$ mysql_config --libs
-L/usr/local/mysql/lib -lmysqlclient -lpthread -lm -lrt -ldl
sqreb@sqreb-Vostro-1450:~/genome$ mysql_config --include
-I/usr/local/mysql/include
sqreb@sqreb-Vostro-1450:~/genome$ MYSQLINC=/usr/local/mysql
sqreb@sqreb-Vostro-1450:~/genome$ MYSQLLIBS="/usr/local/mysql/lib/libmysqlclient.a -lz"
sqreb@sqreb-Vostro-1450:~/genome$ export MYSQLINC MYSQLLIBS

SSL and SAM/BAM and tabix (for VCF) option

Add those command in common.mk
USE_SSL=1
USE_SAMTABIX=1
SAMTABIXDIR=/home/sqreb/genome/samtabix

Install UCSC Genome browser

sqreb@sqreb-Vostro-1450:~/genome$ cd kent/src
sqreb@sqreb-Vostro-1450:~/genome/kent/src$ make libs
cd lib && make
make[1]: Entering directory '/home/sqreb/genome/kent/src/lib'
...
make[1]: Leaving directory '/home/sqreb/genome/kent/src/hg/lib'
sqreb@sqreb-Vostro-1450:~/genome/kent/src$ cd utils/fixCr/
sqreb@sqreb-Vostro-1450:~/genome/kent/src/utils/fixCr$ make
gcc -O -g -o /home/sqreb/bin/x86_64/fixCr fixCr.o    ../../lib/x86_64/jkweb.a /usr/local/mysql/lib/libmysqlclient.a -lz -lstdc++ -lrt -lm ../../htslib/libhts.a -pthread -L/lib -lssl -lcrypto -lpng12 -lm
../../htslib/libhts.a(hts.o): In function `decompress_peek':
/home/sqreb/genome/kent/src/htslib/hts.c:142: undefined reference to `inflateInit2_'
/home/sqreb/genome/kent/src/htslib/hts.c:145: undefined reference to `inflate'
/home/sqreb/genome/kent/src/htslib/hts.c:148: undefined reference to `inflateEnd'
../../htslib/libhts.a(cram_io.o): In function `itf8_decode_crc':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:195: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:201: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:208: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:216: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:225: undefined reference to `crc32'
../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:537: more undefined references to `crc32' follow
../../htslib/libhts.a(cram_io.o): In function `zlib_mem_inflate':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:718: undefined reference to `inflateInit2_'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:731: undefined reference to `inflate'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:751: undefined reference to `inflateEnd'
../../htslib/libhts.a(cram_io.o): In function `zlib_mem_deflate':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:782: undefined reference to `deflateInit2_'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:796: undefined reference to `deflate'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:803: undefined reference to `deflate'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:808: undefined reference to `deflateEnd'
../../htslib/libhts.a(cram_io.o): In function `cram_read_block':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:946: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:948: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:980: undefined reference to `crc32'
../../htslib/libhts.a(cram_io.o): In function `cram_write_block':
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1049: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1052: undefined reference to `crc32'
../../htslib/libhts.a(cram_io.o):/home/sqreb/genome/kent/src/htslib/cram/cram_io.c:1054: more undefined references to `crc32' follow
../../htslib/libhts.a(zfio.o): In function `zfgets':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:69: undefined reference to `gzgets'
../../htslib/libhts.a(zfio.o): In function `zfputs':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:80: undefined reference to `gzputs'
../../htslib/libhts.a(zfio.o): In function `zfpeek':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:95: undefined reference to `gzgetc'
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:97: undefined reference to `gzungetc'
../../htslib/libhts.a(zfio.o): In function `zfeof':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:105: undefined reference to `gzeof'
../../htslib/libhts.a(zfio.o): In function `zfopen':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:165: undefined reference to `gzopen'
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:169: undefined reference to `gzopen'
../../htslib/libhts.a(zfio.o): In function `zfclose':
/home/sqreb/genome/kent/src/htslib/cram/zfio.c:180: undefined reference to `gzclose'
../../htslib/libhts.a(bgzf.o): In function `bgzf_write_init':
/home/sqreb/genome/kent/src/htslib/bgzf.c:166: undefined reference to `deflateInit2_'
../../htslib/libhts.a(bgzf.o): In function `bgzf_open':
/home/sqreb/genome/kent/src/htslib/bgzf.c:174: undefined reference to `compressBound'
../../htslib/libhts.a(bgzf.o): In function `bgzf_dopen':
/home/sqreb/genome/kent/src/htslib/bgzf.c:196: undefined reference to `compressBound'
../../htslib/libhts.a(bgzf.o): In function `bgzf_hopen':
/home/sqreb/genome/kent/src/htslib/bgzf.c:218: undefined reference to `compressBound'
../../htslib/libhts.a(bgzf.o): In function `bgzf_compress':
/home/sqreb/genome/kent/src/htslib/bgzf.c:244: undefined reference to `deflateInit2_'
/home/sqreb/genome/kent/src/htslib/bgzf.c:245: undefined reference to `deflate'
/home/sqreb/genome/kent/src/htslib/bgzf.c:246: undefined reference to `deflateEnd'
/home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32'
/home/sqreb/genome/kent/src/htslib/bgzf.c:252: undefined reference to `crc32'
../../htslib/libhts.a(bgzf.o): In function `bgzf_gzip_compress':
/home/sqreb/genome/kent/src/htslib/bgzf.c:267: undefined reference to `deflate'
../../htslib/libhts.a(bgzf.o): In function `inflate_block':
/home/sqreb/genome/kent/src/htslib/bgzf.c:302: undefined reference to `inflateInit2_'
/home/sqreb/genome/kent/src/htslib/bgzf.c:306: undefined reference to `inflate'
/home/sqreb/genome/kent/src/htslib/bgzf.c:307: undefined reference to `inflateEnd'
/home/sqreb/genome/kent/src/htslib/bgzf.c:311: undefined reference to `inflateEnd'
../../htslib/libhts.a(bgzf.o): In function `inflate_gzip_block':
/home/sqreb/genome/kent/src/htslib/bgzf.c:335: undefined reference to `inflate'
../../htslib/libhts.a(bgzf.o): In function `bgzf_read_block':
/home/sqreb/genome/kent/src/htslib/bgzf.c:505: undefined reference to `inflateInit2_'
../../htslib/libhts.a(bgzf.o): In function `bgzf_close':
/home/sqreb/genome/kent/src/htslib/bgzf.c:816: undefined reference to `inflateEnd'
/home/sqreb/genome/kent/src/htslib/bgzf.c:817: undefined reference to `deflateEnd'
collect2: error: ld returned 1 exit status
../../inc/userApp.mk:31: recipe for target '/home/sqreb/bin/x86_64/fixCr' failed
make: *** [/home/sqreb/bin/x86_64/fixCr] Error 1
ucsc local make error • 1.7k views
ADD COMMENTlink written 2.6 years ago by 201330263002810

Have you solved this issue? I have a similar problem.

ADD REPLYlink written 2.4 years ago by sklages60
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