ekg / arfer Goto Github PK
View Code? Open in Web Editor NEWannotation of variants using genotype likelihoods
License: MIT License
annotation of variants using genotype likelihoods
License: MIT License
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!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.