Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

installation fails #54

Open
masen1991 opened this issue Jan 11, 2020 · 0 comments
Open

installation fails #54

masen1991 opened this issue Jan 11, 2020 · 0 comments

Comments

@masen1991
Copy link

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant