zilong-li / basevarc Goto Github PK

g++ -std=c++11 -g -O2 -Wall -Wextra  -Wno-unknown-pragmas -g -O2   -o BaseVarC BaseVarC-BaseVarC.o BaseVarC-BamProcess.o BaseVarC-BaseType.o BaseVarC-Algorithm.o ../SeqLib/src/libseqlib.a ../SeqLib/htslib/libhts.a  -lz -lbz2 -llzma
/usr/bin/ld: ../SeqLib/htslib/libhts.a(bgzf.o): undefined reference to symbol 'pthread_join@@GLIBC_2.2.5'
/usr/bin/ld: //lib/x86_64-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: Leaving directory '/home/maxh/BaseVarC/src'
make[2]: *** [Makefile:357: BaseVarC] Error 1
make[1]: *** [Makefile:358: all-recursive] Error 1
make[1]: Leaving directory '/home/maxh/BaseVarC'
make: *** [Makefile:299: all] Error 2
The command '/bin/sh -c git clone --recursive https://github.com/Zilong-Li/BaseVarC.git     && cd BaseVarC     && git checkout 7c16b05     && ./configure     && make && make install' returned a non-zero code: 2

basetype start -- Fri Jan 10 21:05:43 2020
begin to read bams and save as tmp file
./GRC194242428.bam

sam.c: In function 'bam_hdr_write':
sam.c:233:5: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
     strncpy(buf, "BAM\1", 4);

In file included from ./cram/sam_header.h:56,
                 from ./cram/cram_samtools.h:77,
                 from ./cram/cram.h:45,
                 from cram/cram_index.c:66:
In function 'kputsn',
    inlined from 'kputs' at ./htslib/kstring.h:156:9,
    inlined from 'cram_index_build' at cram/cram_index.c:519:9:
./htslib/kstring.h:148:2: warning: 'memcpy' pointer overflow between offset 0 and size [-2, 9223372036854775807] [-Warray-bounds]
  memcpy(s->s + s->l, p, l);

cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:2180:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 4096 [-Wformat-overflow=]
      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
                           ^~~~~
cram/cram_io.c:2180:24: note: using the range [0, 4294967295] for directive argument
      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
                        ^~~~~~~~~~~~~~~~~
cram/cram_io.c:2180:24: note: using the range [0, 4294967295] for directive argument
cram/cram_io.c:2180:6: note: 'sprintf' output between 11 and 4134 bytes into a destination of size 4096
      sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:2072:2: warning: 'strncpy' specified bound 4096 equals destination size [-Wstringop-truncation]
  strncpy(path, path2, PATH_MAX);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'full_path',
    inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:3750:3:
cram/cram_io.c:3675:6: warning: 'strncpy' specified bound 4096 equals destination size [-Wstringop-truncation]
      strncpy(out, in, PATH_MAX);
      ^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:3667:2: warning: 'strncpy' specified bound 4096 equals destination size [-Wstringop-truncation]
  strncpy(out, in, PATH_MAX);

jsoncpp.cpp: In member function 'bool Json::OurReader::readToken(Json::OurReader::Token&)':
jsoncpp.cpp:1417:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
     if (features_.allowSingleQuotes_) {
     ^~
jsoncpp.cpp:1422:3: note: here
   case '/':
   ^~~~

ssw_cpp.cpp: In member function 'bool StripedSmithWaterman::Aligner::ReBuild(const int8_t*, const int&, const int8_t*, const int&)':
ssw_cpp.cpp:449:19: warning: unused parameter 'score_matrix_size' [-Wunused-parameter]
     const int&    score_matrix_size,