ekg/arfer

annotation of variants using genotype likelihoods

arfer's Issues

arfer does not build

When building arfer (current git master) with make, I get:

g++ -c estimators.cpp -o estimators.o -I/include -I/usr/include  -O3 -D_FILE_OFFSET_BITS=64
g++ -O3 -D_FILE_OFFSET_BITS=64   -c -o main.o main.cpp
cd vcflib && make
make[1]: Entering directory `/vol/home/koester/scms/arfer/vcflib'
cd tabixpp && make
make[2]: Entering directory `/vol/home/koester/scms/arfer/vcflib/tabixpp'
make[3]: Entering directory `/vol/home/koester/scms/arfer/vcflib/tabixpp'
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_close’:
bgzf.c:630:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  kstring.c -o kstring.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  knetfile.c -o knetfile.o
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:418:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:239:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  index.c -o index.o
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  bedidx.c -o bedidx.o
ar -cru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o
ranlib libtabix.a
gcc -c -g -Wall -O2 -fPIC  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE  main.c -o main.o
gcc -g -Wall -O2 -fPIC  -o tabix main.o -lm  -lz -L. -ltabix
./libtabix.a(bgzf.o): In function `deflate_block':
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:311: undefined reference to `deflate'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:313: undefined reference to `deflateEnd'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:305: undefined reference to `deflateInit2_'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:329: undefined reference to `deflateEnd'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:345: undefined reference to `crc32'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:346: undefined reference to `crc32'
./libtabix.a(bgzf.o): In function `inflate_block':
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:380: undefined reference to `inflateInit2_'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:385: undefined reference to `inflate'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:391: undefined reference to `inflateEnd'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bgzf.c:387: undefined reference to `inflateEnd'
./libtabix.a(bedidx.o): In function `ks_getuntil':
/vol/home/koester/scms/arfer/vcflib/tabixpp/bedidx.c:11: undefined reference to `gzread'
./libtabix.a(bedidx.o): In function `bed_read':
/vol/home/koester/scms/arfer/vcflib/tabixpp/bedidx.c:103: undefined reference to `gzdopen'
./libtabix.a(bedidx.o): In function `ks_getc':
/vol/home/koester/scms/arfer/vcflib/tabixpp/bedidx.c:11: undefined reference to `gzread'
./libtabix.a(bedidx.o): In function `bed_read':
/vol/home/koester/scms/arfer/vcflib/tabixpp/bedidx.c:138: undefined reference to `gzclose'
/vol/home/koester/scms/arfer/vcflib/tabixpp/bedidx.c:103: undefined reference to `gzopen64'
collect2: ld returned 1 exit status
make[3]: *** [tabix] Error 1
make[3]: Leaving directory `/vol/home/koester/scms/arfer/vcflib/tabixpp'
make[2]: *** [all-recur] Error 1
make[2]: Leaving directory `/vol/home/koester/scms/arfer/vcflib/tabixpp'
make[1]: *** [tabixpp/tabix.o] Error 2
make[1]: Leaving directory `/vol/home/koester/scms/arfer/vcflib'
make: *** [vcflib/tabixpp/tabix.o] Error 2

zlib.h is correctly installed and resides under /usr/include
Thanks a lot in advance for your help!