Description
i get install by this Fast and dirty install:
git clone --recursive https://github.com/zeeev/wham.git
cd wham
make
and i get this problem:
`g++ -fstack-protector-all -Wall -DVERSION="v1.7.0-311-g4e8c-dirty" -std=c++0x -Wno-sign-compare -O3 -Isrc/lib -Isrc/bamtools/include -Isrc/bamtools/src -Isrc/ -Isrc/fastahack -Isrc/Complete-Striped-Smith-Waterman-Library/src/ src/bin/whamg.cpp src/bamtools/lib/libbamtools.a src/obj/entropy.o src/obj/split.o src/obj/read_pileup.o src/obj/readPileUp.o src/obj/flag.o src/fastahack/Fasta.o src/Complete-Striped-Smith-Waterman-Library/src/ssw_cpp.o src/Complete-Striped-Smith-Waterman-Library/src/ssw.o -o bin/whamg -fopenmp -lz -lm
src/bin/whamg.cpp: In function ‘void findPairs(std::vector<node*>&, breakpoint*, std::map<int, std::map<int, breakpoint*> >&)’:
src/bin/whamg.cpp:1706:9: warning: variable ‘lmax’ set but not used [-Wunused-but-set-variable]
int lmax = 0;
^~~~
src/bin/whamg.cpp:1707:9: warning: variable ‘rmax’ set but not used [-Wunused-but-set-variable]
int rmax = 0;
^~~~
src/bin/whamg.cpp:1709:9: warning: variable ‘edsn’ set but not used [-Wunused-but-set-variable]
int edsn = 0;
^~~~
/var/tmp/ccBfD5UZ.o: In function _ZNK8BamTools12BamAlignment6GetTagINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_RT_.part.23': whamg.cpp:(.text+0x73): undefined reference to BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char*&, unsigned int const&, unsigned int&) const'
/var/tmp/ccBfD5UZ.o: In function loadBam(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)': whamg.cpp:(.text+0x4d7f): undefined reference to BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
whamg.cpp:(.text+0x4ec2): undefined reference to BamTools::BamReader::OpenIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /var/tmp/ccBfD5UZ.o: In function gatherBamStats(std::__cxx11::basic_string<char, std::char_traits, std::allocator >&)':
whamg.cpp:(.text+0x9ac5): undefined reference to BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' whamg.cpp:(.text+0x9bbc): undefined reference to BamTools::BamReader::OpenIndex(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
/var/tmp/ccBfD5UZ.o: In function runRegion(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, int, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)': whamg.cpp:(.text+0xd388): undefined reference to BamTools::BamReader::Open(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
whamg.cpp:(.text+0xd461): undefined reference to BamTools::BamReader::OpenIndex(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /var/tmp/ccBfD5UZ.o: In function main':
whamg.cpp:(.text.startup+0xca): undefined reference to BamTools::BamMultiReader::Open(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)' src/obj/readPileUp.o: In function readPileUp::processPileup(long*)':
readPileUp.cpp:(.text+0x30c4): undefined reference to BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, char*&, unsigned int const&, unsigned int&) const' collect2: error: ld returned 1 exit status make: *** [Makefile:38: bin/whamg] Error 1
i already have all you require:
gcc (GCC) 7.2.0
cmake version 3.16.0
pip install -U numpy scipy scikit-learn argparse
Requirement already up-to-date: numpy in (1.16.6)
Requirement already up-to-date: scipy in (1.2.2)
Requirement already up-to-date: scikit-learn in (0.20.4)
Requirement already up-to-date: argparse in (1.4.0)
and i also try to install bamtools by anaconda in python2.7 and python3.7 env.
please help me.