Entering edit mode
11.2 years ago
fo3c
▴
450
I am trying to compile somatic sniper from source but run into compilation errors.
I cloned the git repository yesterday
$ git clone --recursive git://github.com/genome/somatic-sniper.git
ran cmake
$ cmake ../somatic-sniper/ -- The C compiler identification is GNU 4.2.1 -- The CXX compiler identification is GNU 4.2.1 -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/gcc -- Check for working C compiler: /usr/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done No CMAKE_BUILD_TYPE specified, defaulting to release SAMTOOLS_ROOT is set to: /Users/xxx/samtools-0.1.16 -- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.3") -- Found Samtools - Samtools include dirs: /Users/xxx/samtools-0.1.16;/usr/include - Samtools libraries: /Users/xxx/samtools-0.1.16/libbam.a;/usr/lib/libz.dylib -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE -- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_INCLUDE_DIR GTEST_MAIN_LIBRARY) Google Test framework not found, no tests will be built GTest is available at http://code.google.com/p/googletest/ Ubuntu users can likely sudo apt-get install gtest -- Configuring done -- Generating done -- Build files have been written to: /Users/xxx/SomaticSniper
and finally make
$ make Scanning dependencies of target sniper [ 10%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/allele_util.c.o [ 20%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/dqstats.c.o [ 30%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_bed.c.o [ 40%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_classic.c.o [ 50%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_format.c.o [ 60%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/output_vcf.c.o [ 70%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_maqcns.c.o [ 80%] Building C object build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_pileup.c.o /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c: In function ‘bam_plbuf_reset’: /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:124: error: ‘bam_plbuf_t’ has no member named ‘max_tid’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:124: error: ‘bam_plbuf_t’ has no member named ‘max_pos’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:125: error: ‘bam_plbuf_t’ has no member named ‘tid’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:125: error: ‘bam_plbuf_t’ has no member named ‘pos’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:126: error: ‘bam_plbuf_t’ has no member named ‘is_eof’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:127: error: ‘bam_plbuf_t’ has no member named ‘head’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:129: error: ‘bam_plbuf_t’ has no member named ‘mp’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:132: error: ‘bam_plbuf_t’ has no member named ‘head’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:132: error: ‘bam_plbuf_t’ has no member named ‘tail’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c: In function ‘bam_plbuf_set_mapq_thresh’: /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:137: error: ‘bam_plbuf_t’ has no member named ‘mapq_thresh’ /Users/xxx/somatic-sniper/src/lib/sniper/sniper_pileup.c:138: error: ‘bam_plbuf_t’ has no member named ‘mapq_thresh’ [... and many similar ones ...] make[2]: *** [build/src/lib/sniper/CMakeFiles/sniper.dir/sniper_pileup.c.o] Error 1 make[1]: *** [build/src/lib/sniper/CMakeFiles/sniper.dir/all] Error 2 make: *** [all] Error 2
There seems to be a conflict between struct __bam_plbuf_t in sniper_pileup.c and samtool's bam.h
typedef struct {
bam_plp_t iter;
bam_pileup_f func;
void *data;
} bam_plbuf_t;
but I don't know how to solve it.
Any suggestions?
This is also addressed in SomaticSniper's README.
When I run "make", I get the following errors:
What does this mean?? Thanks, Rini
You should probably post a new question instead of replying on someone else's. It also looks like the text you pasted contains special characters so is difficult to read. The FAQ has information about how text can be styled.