How to install this software?

[Microkiller]

Hi, I have downloaded the code from your repository. How do I install it on Ubuntu?
Thank you.

[ekg]

You should git clone --recursive when you download it, or manually download
bamtools into bamtools directory. It's better to use the --recursive flag.

Now, just type "make" and if compilation progresses correctly you'll get
the bamaddrg executable in the project root directory.

On Thu, Jul 25, 2013 at 7:10 PM, Jiayi Zhou [email protected]:

Hi, I have downloaded the code from your repository. How do I install it
on Ubuntu?
Thank you.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/1
.

[Microkiller]

According to your method, I successfully installed the bamaddrg on my ubuntu.
Now I am trying to install it on RHEL5 system. I was doing the compile process.
I have already downloaded bamtools into the bamtools directory and run the following command to compile the bamtools.
mkdir build
cd build
cmake ..
cd ..
make

The above command all ran successfully. So I think I have installed bamtools.

However, when I type make under bamaddrg directory, i got the following error msg.
g++ -O3 -Ibamtools/include -L./ bamaddrg.cpp -o bamaddrg -lbamtools -lz
.//libbamtools.a(SamProgramChain.cpp.o): In function BamTools::SamProgramChain::First()': SamProgramChain.cpp:(.text+0x1be): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamProgramChain.cpp:(.text+0x202): undefined reference to std::ctype<char>::_M_widen_init() const' .//libbamtools.a(SamProgramChain.cpp.o): In functionBamTools::SamProgramChain::First() const':
SamProgramChain.cpp:(.text+0x27e): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' SamProgramChain.cpp:(.text+0x2c2): undefined reference to std::ctype::_M_widen_init() const'
.//libbamtools.a(SamProgramChain.cpp.o): In functionBamTools::SamProgramChain::Last()': SamProgramChain.cpp:(.text+0x44e): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
SamProgramChain.cpp:(.text+0x492): undefined reference tostd::ctype<char>::_M_widen_init() const' .//libbamtools.a(SamProgramChain.cpp.o): In function BamTools::SamProgramChain::Last() const':
SamProgramChain.cpp:(.text+0x50e): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' SamProgramChain.cpp:(.text+0x552): undefined reference to std::ctype::_M_widen_init() const'
.//libbamtools.a(BamMultiReader_p.cpp.o): In functionBamTools::Internal::BamMultiReaderPrivate::ValidateReaders() const': BamMultiReader_p.cpp:(.text+0x2ec1): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x2eda): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' BamMultiReader_p.cpp:(.text+0x2ef1): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x3296): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BamMultiReader_p.cpp:(.text+0x32ad): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
BamMultiReader_p.cpp:(.text+0x32da): undefined reference tostd::ctype<char>::_M_widen_init() const' BamMultiReader_p.cpp:(.text+0x3365): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
BamMultiReader_p.cpp:(.text+0x3416): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BamMultiReader_p.cpp:(.text+0x342d): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x3463): undefined reference to std::ctype<char>::_M_widen_init() const' BamMultiReader_p.cpp:(.text+0x379c): undefined reference tostd::ctype::_M_widen_init() const'
BamMultiReader_p.cpp:(.text+0x37b8): undefined reference to std::ctype<char>::_M_widen_init() const' BamMultiReader_p.cpp:(.text+0x3aef): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x3b08): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BamMultiReader_p.cpp:(.text+0x3b1f): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
BamMultiReader_p.cpp:(.text+0x3b42): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' .//libbamtools.a(BgzfStream_p.cpp.o): In function BamTools::Internal::BgzfStream::FlushBlock()':
BgzfStream_p.cpp:(.text+0x16a7): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BgzfStream_p.cpp:(.text+0x16b4): undefined reference to std::basic_ostream<char, std::char_traits >& std::basic_ostream<char, std::char_traits >::_M_insert(unsigned long)'
BgzfStream_p.cpp:(.text+0x16cb): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BgzfStream_p.cpp:(.text+0x16d6): undefined reference to std::basic_ostream<char, std::char_traits >& std::basic_ostream<char, std::char_traits >::_M_insert(long)'
.//libbamtools.a(SamFormatParser_p.cpp.o): In functionBamTools::Internal::SamFormatParser::Parse(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': SamFormatParser_p.cpp:(.text+0x1c24): undefined reference to std::ctype::_M_widen_init() const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintHD(std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&) const': SamFormatPrinter_p.cpp:(.text+0x137): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x148): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' SamFormatPrinter_p.cpp:(.text+0x22c): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x310): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' SamFormatPrinter_p.cpp:(.text+0x364): undefined reference to std::ctype::_M_widen_init() const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintSQ(std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&) const': SamFormatPrinter_p.cpp:(.text+0x72c): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
SamFormatPrinter_p.cpp:(.text+0x73d): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' SamFormatPrinter_p.cpp:(.text+0x74e): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x83d): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' SamFormatPrinter_p.cpp:(.text+0x91e): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
.//libbamtools.a(SamFormatPrinter_p.cpp.o):SamFormatPrinter_p.cpp:(.text+0x9ff): more undefined references to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' follow .//libbamtools.a(SamFormatPrinter_p.cpp.o): In function BamTools::Internal::SamFormatPrinter::PrintSQ(std::basic_stringstream<char, std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0xb1a): undefined reference tostd::ctype<char>::_M_widen_init() const' .//libbamtools.a(SamFormatPrinter_p.cpp.o): In function BamTools::Internal::SamFormatPrinter::PrintRG(std::basic_stringstream<char, std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x10c4): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' SamFormatPrinter_p.cpp:(.text+0x10d5): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x11b2): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' SamFormatPrinter_p.cpp:(.text+0x128b): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x1368): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' .//libbamtools.a(SamFormatPrinter_p.cpp.o):SamFormatPrinter_p.cpp:(.text+0x1445): more undefined references to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)' follow
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintRG(std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&) const': SamFormatPrinter_p.cpp:(.text+0x1a8a): undefined reference to std::ctype::_M_widen_init() const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintPG(std::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >&) const': SamFormatPrinter_p.cpp:(.text+0x253c): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
SamFormatPrinter_p.cpp:(.text+0x254d): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' SamFormatPrinter_p.cpp:(.text+0x262a): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x2703): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' SamFormatPrinter_p.cpp:(.text+0x27e0): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
.//libbamtools.a(SamFormatPrinter_p.cpp.o):SamFormatPrinter_p.cpp:(.text+0x28bd): more undefined references to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' follow .//libbamtools.a(SamFormatPrinter_p.cpp.o): In function BamTools::Internal::SamFormatPrinter::PrintPG(std::basic_stringstream<char, std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x28f7): undefined reference tostd::ctype<char>::_M_widen_init() const' .//libbamtools.a(SamFormatPrinter_p.cpp.o): In function BamTools::Internal::SamFormatPrinter::PrintCO(std::basic_stringstream<char, std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x2cdf): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' SamFormatPrinter_p.cpp:(.text+0x2cf6): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x2d06): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' SamFormatPrinter_p.cpp:(.text+0x2d2b): undefined reference tostd::ctype::_M_widen_init() const'
.//libbamtools.a(SamHeaderValidator_p.cpp.o): In function BamTools::Internal::SamHeaderValidator::PrintErrorMessages(std::basic_ostream<char, std::char_traits<char> >&)': SamHeaderValidator_p.cpp:(.text+0x251): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamHeaderValidator_p.cpp:(.text+0x263): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)' SamHeaderValidator_p.cpp:(.text+0x27a): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamHeaderValidator_p.cpp:(.text+0x2cf): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' SamHeaderValidator_p.cpp:(.text+0x2ec): undefined reference tostd::ctype::_M_widen_init() const'
.//libbamtools.a(SamHeaderValidator_p.cpp.o): In function BamTools::Internal::SamHeaderValidator::PrintWarningMessages(std::basic_ostream<char, std::char_traits<char> >&)': SamHeaderValidator_p.cpp:(.text+0x341): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamHeaderValidator_p.cpp:(.text+0x353): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)' SamHeaderValidator_p.cpp:(.text+0x36a): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
SamHeaderValidator_p.cpp:(.text+0x3bf): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' SamHeaderValidator_p.cpp:(.text+0x3dc): undefined reference tostd::ctype::_M_widen_init() const'
.//libbamtools.a(SamHeaderValidator_p.cpp.o): In function BamTools::Internal::SamHeaderValidator::CheckLengthInRange(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': SamHeaderValidator_p.cpp:(.text+0xf51): undefined reference tostd::basic_istream<char, std::char_traits >& std::basic_istream<char, std::char_traits >::_M_extract(unsigned int&)'
.//libbamtools.a(BamRandomAccessController_p.cpp.o): In function BamTools::Internal::BamRandomAccessController::CreateIndex(BamTools::Internal::BamReaderPrivate*, BamTools::BamIndex::IndexType const&)': BamRandomAccessController_p.cpp:(.text+0x11d8): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In function BamTools::Internal::BamStandardIndex::CheckBufferSize(unsigned char_&, unsigned int&, unsigned int const&)': BamStandardIndex_p.cpp:(.text+0x1906): undefined reference to std::basic_ostream<char, std::char_traits >& std::basic_ostream<char, std::char_traits >::_M_insert(unsigned long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In functionBamTools::Internal::BamStandardIndex::CheckBufferSize(char_&, unsigned int&, unsigned int const&)': BamStandardIndex_p.cpp:(.text+0x1ab6): undefined reference to std::basic_ostream<char, std::char_traits >& std::basic_ostream<char, std::char_traits >::_M_insert(unsigned long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In functionBamTools::Internal::BamStandardIndex::ReadIntoBuffer(unsigned int const&)': BamStandardIndex_p.cpp:(.text+0x1c49): undefined reference to std::basic_ostream<char, std::char_traits >& std::basic_ostream<char, std::char_traits >::_M_insert(unsigned long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In functionBamTools::Internal::BamStandardIndex::Create()': BamStandardIndex_p.cpp:(.text+0x455d): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
BamStandardIndex_p.cpp:(.text+0x45b7): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' BamStandardIndex_p.cpp:(.text+0x45d8): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
BamStandardIndex_p.cpp:(.text+0x45fa): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BamStandardIndex_p.cpp:(.text+0x494d): undefined reference to std::ctype::_M_widen_init() const'
BamStandardIndex_p.cpp:(.text+0x4968): undefined reference tostd::ctype<char>::_M_widen_init() const' .//libbamtools.a(BamFtp_p.cpp.o): In function BamTools::Internal::BamFtp::ConnectDataSocket()':
BamFtp_p.cpp:(.text+0x28cc): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<long>(long)' .//libbamtools.a(BamHttp_p.cpp.o): In function BamTools::Internal::BamHttp::SendGetRequest(unsigned long)':
BamHttp_p.cpp:(.text+0x24f8): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BamHttp_p.cpp:(.text+0x2503): undefined reference to std::basic_ostream<char, std::char_traits >& std::basic_ostream<char, std::char_traits >::_M_insert(long)'
BamHttp_p.cpp:(.text+0x251a): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' BamHttp_p.cpp:(.text+0x2525): undefined reference to std::basic_ostream<char, std::char_traits >& std::basic_ostream<char, std::char_traits >::_M_insert(long)'
.//libbamtools.a(HttpHeader_p.cpp.o): In functionBamTools::Internal::HttpResponseHeader::ToString() const': HttpHeader_p.cpp:(.text+0x71b): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
HttpHeader_p.cpp:(.text+0x73e): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' HttpHeader_p.cpp:(.text+0x760): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
HttpHeader_p.cpp:(.text+0x783): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' HttpHeader_p.cpp:(.text+0x794): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
.//libbamtools.a(HttpHeader_p.cpp.o):HttpHeader_p.cpp:(.text+0x7a7): more undefined references to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' follow .//libbamtools.a(TcpSocket_p.cpp.o): In function BamTools::Internal::TcpSocket::ConnectImpl(BamTools::Internal::HostInfo const&, std::basic_string<char, std::char_traits, std::allocator > const&, BamTools::IBamIODevice::OpenMode)':
TcpSocket_p.cpp:(.text+0xb9c): undefined reference tostd::basic_istream<char, std::char_traits<char> >& std::basic_istream<char, std::char_traits<char> >::_M_extract<unsigned short>(unsigned short&)' .//libbamtools.a(TcpSocket_p.cpp.o): In function BamTools::Internal::TcpSocket::ConnectToHost(std::basic_string<char, std::char_traits, std::allocator > const&, unsigned short, BamTools::IBamIODevice::OpenMode)':
TcpSocket_p.cpp:(.text+0x1418): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)' .//libbamtools.a(TcpSocketEngine_unix_p.cpp.o): In function BamTools::Internal::TcpSocketEngine::nativeSelect(int, bool) const':
TcpSocketEngine_unix_p.cpp:(.text+0x42b): undefined reference to__fdelt_chk' .//libbamtools.a(HostAddress_p.cpp.o): In function BamTools::Internal::HostAddress::GetIPString() const':
HostAddress_p.cpp:(.text+0x925): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)' HostAddress_p.cpp:(.text+0x93c): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
HostAddress_p.cpp:(.text+0x946): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)' HostAddress_p.cpp:(.text+0x95d): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
HostAddress_p.cpp:(.text+0x969): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)' HostAddress_p.cpp:(.text+0x980): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
HostAddress_p.cpp:(.text+0x98b): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::basic_ostream<char, std::char_traits<char> >::_M_insert<unsigned long>(unsigned long)' HostAddress_p.cpp:(.text+0x9fe): undefined reference to std::basic_ostream<char, std::char_traits >& std::__ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const*, long)'
HostAddress_p.cpp:(.text+0xa48): undefined reference tostd::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const_, long)' HostAddress_p.cpp:(.text+0xa92): undefined reference to std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
HostAddress_p.cpp:(.text+0xadc): undefined reference to std::basic_ostream<char, std::char_traits<char> >& std::__ostream_insert<char, std::char_traits<char> >(std::basic_ostream<char, std::char_traits<char> >&, char const*, long)' HostAddress_p.cpp:(.text+0xb26): undefined reference tostd::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)'
.//libbamtools.a(HostAddress_p.cpp.o):HostAddress_p.cpp:(.text+0xb70): more undefined references to `std::basic_ostream<char, std::char_traits >& std::_ostream_insert<char, std::char_traits >(std::basic_ostream<char, std::char_traits >&, char const, long)' follow
collect2: ld returned 1 exit status
make: *** [bamaddrg] Error 1

Do you know how to solve this problem?

[ekg]

It should be necessary to use git clone --recursive at first, rather than
manually downloading bamtools. This way the correct version is pulled.
Please try using git clone --recursive!
On Dec 12, 2013 4:29 PM, "Jiayi Zhou" [email protected] wrote:

According to your method, I successfully installed the bamaddrg on my
ubuntu.
Now I am trying to install it on RHEL5 system. I was doing the compile
process.
I have already downloaded bamtools into the bamtools directory and run the
following command to compile the bamtools.
mkdir build
cd build
cmake ..
cd ..
make

The above command all ran successfully. So I think I have installed
bamtools.

However, when I type make under bamaddrg directory, i got the following
error msg.
g++ -O3 -Ibamtools/include -L./ bamaddrg.cpp -o bamaddrg -lbamtools -lz
.//libbamtools.a(SamProgramChain.cpp.o): In function
BamTools::SamProgramChain::First()':
SamProgramChain.cpp:(.text+0x1be): undefined reference tostd::basic_ostream

& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamProgramChain.cpp:(.text+0x202): undefined reference to
std::ctype::_M_widen_init() const'
.//libbamtools.a(SamProgramChain.cpp.o): In
functionBamTools::SamProgramChain::First() const':
SamProgramChain.cpp:(.text+0x27e): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamProgramChain.cpp:(.text+0x2c2): undefined reference
tostd::ctype::Mwiden_init() const' .//libbamtools.a(SamProgramChain.cpp.o):
In function BamTools::SamProgramChain::Last()':
SamProgramChain.cpp:(.text+0x44e): undefined reference tostd::basic_ostream
& std::ostream_insert >(std::basic_ostream >&, char const, long)'
SamProgramChain.cpp:(.text+0x492): undefined reference to std::ctype::_M_widen_init()
const'
.//libbamtools.a(SamProgramChain.cpp.o): In functionBamTools::SamProgramChain::Last()
const':
SamProgramChain.cpp:(.text+0x50e): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
SamProgramChain.cpp:(.text+0x552): undefined reference tostd::ctype::_M_widen_init()
const'
.//libbamtools.a(BamMultiReader_p.cpp.o): In function BamTools::Internal::BamMultiReaderPrivate::ValidateReaders()
const':
BamMultiReader_p.cpp:(.text+0x2ec1): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x2eda): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
BamMultiReader_p.cpp:(.text+0x2ef1): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
BamMultiReader_p.cpp:(.text+0x3296): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
BamMultiReader_p.cpp:(.text+0x32ad): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x32da): undefined reference to
std::ctype::_M_widen_init() const'
BamMultiReader_p.cpp:(.text+0x3365): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
BamMultiReader_p.cpp:(.text+0x3416): undefined reference to std::basic_ostream<char,
std::char_traits >& std::__ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits

&, char const*, long)'
BamMultiReader_p.cpp:(.text+0x342d): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x3463): undefined reference to
std::ctype::_M_widen_init() const'
BamMultiReader_p.cpp:(.text+0x379c): undefined reference
tostd::ctype::Mwiden_init() const' BamMultiReader_p.cpp:(.text+0x37b8):
undefined reference to std::ctype::_M_widen_init() const'
BamMultiReader_p.cpp:(.text+0x3aef): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
BamMultiReader_p.cpp:(.text+0x3b08): undefined reference to std::basic_ostream<char,
std::char_traits >& std::__ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits

&, char const*, long)'
BamMultiReader_p.cpp:(.text+0x3b1f): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
BamMultiReader_p.cpp:(.text+0x3b42): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
.//libbamtools.a(BgzfStream_p.cpp.o): In
functionBamTools::Internal::BgzfStream::FlushBlock()':
BgzfStream_p.cpp:(.text+0x16a7): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::_ostream_insert<char, std::char_traits
(std::basic_ostream<char, std::char_traits >&, char const, long)'
BgzfStream_p.cpp:(.text+0x16b4): undefined reference tostd::basic_ostream
& std::basic_ostream >::Minsert(unsigned long)'
BgzfStream_p.cpp:(.text+0x16cb): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::_ostream_insert<char, std::char_traits
(std::basic_ostream<char, std::char_traits >&, char const, long)'
BgzfStream_p.cpp:(.text+0x16d6): undefined reference tostd::basic_ostream
& std::basic_ostream >::Minsert(long)'
.//libbamtools.a(SamFormatParser_p.cpp.o): In function
BamTools::Internal::SamFormatParser::Parse(std::basic_string<char,
std::char_traits, std::allocator > const&)':
SamFormatParser_p.cpp:(.text+0x1c24): undefined reference
tostd::ctype::Mwiden_init() const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In function
BamTools::Internal::SamFormatPrinter::PrintHD(std::basic_stringstream<char,
std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x137): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
SamFormatPrinter_p.cpp:(.text+0x148): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x22c): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x310): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamFormatPrinter_p.cpp:(.text+0x364): undefined reference
tostd::ctype::Mwiden_init() const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In function
BamTools::Internal::SamFormatPrinter::PrintSQ(std::basic_stringstream<char,
std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x72c): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
SamFormatPrinter_p.cpp:(.text+0x73d): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x74e): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x83d): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamFormatPrinter_p.cpp:(.text+0x91e): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
.//libbamtools.a(SamFormatPrinter_p.cpp.o):SamFormatPrinter_p.cpp:(.text+0x9ff):
more undefined references to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)' follow
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintSQ(std::basic_stringstream,
std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0xb1a): undefined reference to std::ctype::_M_widen_init()
const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintRG(std::basic_stringstream,
std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x10c4): undefined reference to std::basic_ostream<char,
std::char_traits >& std::__ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const*, long)'
SamFormatPrinter_p.cpp:(.text+0x10d5): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x11b2): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamFormatPrinter_p.cpp:(.text+0x128b): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
SamFormatPrinter_p.cpp:(.text+0x1368): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
.//libbamtools.a(SamFormatPrinter_p.cpp.o):SamFormatPrinter_p.cpp:(.text+0x1445):
more undefined references tostd::basic_ostream >& std::

ostream_insert >(std::basic_ostream >&, char const, long)' follow
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In function
BamTools::Internal::SamFormatPrinter::PrintRG(std::basic_stringstream<char,
std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x1a8a): undefined reference
tostd::ctype::Mwiden_init() const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In function
BamTools::Internal::SamFormatPrinter::PrintPG(std::basic_stringstream<char,
std::char_traits, std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x253c): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
SamFormatPrinter_p.cpp:(.text+0x254d): undefined reference to std::basic_ostream<char,
std::char_traits >& std::__ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits

&, char const*, long)'
SamFormatPrinter_p.cpp:(.text+0x262a): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x2703): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamFormatPrinter_p.cpp:(.text+0x27e0): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
.//libbamtools.a(SamFormatPrinter_p.cpp.o):SamFormatPrinter_p.cpp:(.text+0x28bd):
more undefined references to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)' follow
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintPG(std::basic_stringstream,
std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x28f7): undefined reference to std::ctype::_M_widen_init()
const'
.//libbamtools.a(SamFormatPrinter_p.cpp.o): In functionBamTools::Internal::SamFormatPrinter::PrintCO(std::basic_stringstream,
std::allocator >&) const':
SamFormatPrinter_p.cpp:(.text+0x2cdf): undefined reference to std::basic_ostream<char,
std::char_traits >& std::__ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const*, long)'
SamFormatPrinter_p.cpp:(.text+0x2cf6): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamFormatPrinter_p.cpp:(.text+0x2d06): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamFormatPrinter_p.cpp:(.text+0x2d2b): undefined reference
tostd::ctype::Mwiden_init() const'
.//libbamtools.a(SamHeaderValidator_p.cpp.o): In function
BamTools::Internal::SamHeaderValidator::PrintErrorMessages(std::basic_ostream<char,
std::char_traits >&)': SamHeaderValidator_p.cpp:(.text+0x251):
undefined reference tostd::basic_ostream >& std::_ostream_insert
(std::basic_ostream >&, char const*, long)'
SamHeaderValidator_p.cpp:(.text+0x263): undefined reference to std::basic_ostream<char,
std::char_traits >& std::basic_ostream<char, std::char_traits
::_M_insert(unsigned long)'
SamHeaderValidator_p.cpp:(.text+0x27a): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamHeaderValidator_p.cpp:(.text+0x2cf): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamHeaderValidator_p.cpp:(.text+0x2ec): undefined reference
tostd::ctype::Mwiden_init() const'
.//libbamtools.a(SamHeaderValidator_p.cpp.o): In function
BamTools::Internal::SamHeaderValidator::PrintWarningMessages(std::basic_ostream<char,
std::char_traits >&)': SamHeaderValidator_p.cpp:(.text+0x341):
undefined reference tostd::basic_ostream >& std::_ostream_insert
(std::basic_ostream >&, char const*, long)'
SamHeaderValidator_p.cpp:(.text+0x353): undefined reference to std::basic_ostream<char,
std::char_traits >& std::basic_ostream<char, std::char_traits
::_M_insert(unsigned long)'
SamHeaderValidator_p.cpp:(.text+0x36a): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
SamHeaderValidator_p.cpp:(.text+0x3bf): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
SamHeaderValidator_p.cpp:(.text+0x3dc): undefined reference
tostd::ctype::Mwiden_init() const'
.//libbamtools.a(SamHeaderValidator_p.cpp.o): In function
BamTools::Internal::SamHeaderValidator::CheckLengthInRange(std::basic_string<char,
std::char_traits, std::allocator > const&)':
SamHeaderValidator_p.cpp:(.text+0xf51): undefined reference
tostd::basic_istream >& std::basic_istream >::Mextract(unsigned int&)'
.//libbamtools.a(BamRandomAccessController_p.cpp.o): In function
BamTools::Internal::BamRandomAccessController::CreateIndex(BamTools::Internal::BamReaderPrivate_,
BamTools::BamIndex::IndexType const&)':
BamRandomAccessController_p.cpp:(.text+0x11d8): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In function BamTools::Internal::BamStandardIndex::CheckBufferSize(unsigned
char_&, unsigned int&, unsigned int const&)':
BamStandardIndex_p.cpp:(.text+0x1906): undefined reference tostd::basic_ostream
& std::basic_ostream >::M_insert(unsigned long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In function BamTools::Internal::BamStandardIndex::CheckBufferSize(char&,
unsigned int&, unsigned int const&)':
BamStandardIndex_p.cpp:(.text+0x1ab6): undefined reference tostd::basic_ostream
& std::basic_ostream >::_M_insert(unsigned long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In function BamTools::Internal::BamStandardIndex::ReadIntoBuffer(unsigned
int const&)':
BamStandardIndex_p.cpp:(.text+0x1c49): undefined reference tostd::basic_ostream
& std::basic_ostream >::_M_insert(unsigned long)'
.//libbamtools.a(BamStandardIndex_p.cpp.o): In function
BamTools::Internal::BamStandardIndex::Create()':
BamStandardIndex_p.cpp:(.text+0x455d): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
BamStandardIndex_p.cpp:(.text+0x45b7): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
BamStandardIndex_p.cpp:(.text+0x45d8): undefined reference
tostd::basic_ostream >& std::ostream_insert >(std::basic_ostream >&,
char const, long)'
BamStandardIndex_p.cpp:(.text+0x45fa): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
BamStandardIndex_p.cpp:(.text+0x494d): undefined reference tostd::ctype::
_M_widen_init() const'
BamStandardIndex_p.cpp:(.text+0x4968): undefined reference to std::ctype::_M_widen_init()
const'
.//libbamtools.a(BamFtp_p.cpp.o): In function
BamTools::Internal::BamFtp::ConnectDataSocket()':
BamFtp_p.cpp:(.text+0x28cc): undefined reference to std::basic_ostream<char,
std::char_traits >& std::basic_ostream<char, std::char_traits
::_M_insert(long)'
.//libbamtools.a(BamHttp_p.cpp.o): In functionBamTools::Internal::BamHttp::SendGetRequest(unsigned
long)':
BamHttp_p.cpp:(.text+0x24f8): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
BamHttp_p.cpp:(.text+0x2503): undefined reference tostd::basic_ostream >&
std::basic_ostream >::_M_insert(long)'
BamHttp_p.cpp:(.text+0x251a): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
BamHttp_p.cpp:(.text+0x2525): undefined reference tostd::basic_ostream >&
std::basic_ostream >::_M_insert(long)'
.//libbamtools.a(HttpHeader_p.cpp.o): In function BamTools::Internal::HttpResponseHeader::ToString()
const':
HttpHeader_p.cpp:(.text+0x71b): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
HttpHeader_p.cpp:(.text+0x73e): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
HttpHeader_p.cpp:(.text+0x760): undefined reference tostd::basic_ostream >&
std::ostream_insert >(std::basic_ostream >&, char const, long)'
HttpHeader_p.cpp:(.text+0x783): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
HttpHeader_p.cpp:(.text+0x794): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
.//libbamtools.a(HttpHeader_p.cpp.o):HttpHeader_p.cpp:(.text+0x7a7): more
undefined references to std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
follow .//libbamtools.a(TcpSocket_p.cpp.o): In
functionBamTools::Internal::TcpSocket::ConnectImpl(BamTools::Internal::HostInfo
const&, std::basic_string, std::allocator > const&,
BamTools::IBamIODevice::OpenMode)': TcpSocket_p.cpp:(.text+0xb9c):
undefined reference to std::basic_istream<char, std::char_traits >&
std::basic_istream<char, std::char_traits >::_M_extract(unsigned short&)' .//libbamtools.a(TcpSocket_p.cpp.o): In
functionBamTools::Internal::TcpSocket::ConnectToHost(std::basic_string,
std::allocator > const&, unsigned short,
BamTools::IBamIODevice::OpenMode)': TcpSocket_p.cpp:(.text+0x1418):
undefined reference to std::basic_ostream<char, std::char_traits >&
std::basic_ostream<char, std::char_traits >::_M_insert(unsigned long)' .//libbamtools.a(TcpSocketEngine_unix_p.cpp.o): In
functionBamTools::Internal::TcpSocketEngine::nativeSelect(int, bool)
const': TcpSocketEngine_unix_p.cpp:(.text+0x42b): undefined reference to
__fdelt_chk' .//libbamtools.a(HostAddress_p.cpp.o): In
functionBamTools::Internal::HostAddress::GetIPString() const':
HostAddress_p.cpp:(.text+0x925): undefined reference to
std::basic_ostream<char, std::char_traits >& std::basic_ostream<char,
std::char_traits >::_M_insert(unsigned long)'
HostAddress_p.cpp:(.text+0x93c): undefined reference tostd::basic_ostream
& std::_ostream_insert >(std::basic_ostream >&, char const*, long)'
HostAddress_p.cpp:(.text+0x946): undefined reference to std::basic_ostream<char,
std::char_traits >& std::basic_ostream<char, std::char_traits
::_M_insert(unsigned long)'
HostAddress_p.cpp:(.text+0x95d): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
HostAddress_p.cpp:(.text+0x969): undefined reference to
std::basic_ostream<char, std::char_traits >& std::basic_ostream<char,
std::char_traits >::_M_insert(unsigned long)'
HostAddress_p.cpp:(.text+0x980): undefined reference tostd::basic_ostream

& std::ostream_insert >(std::basic_ostream >&, char const, long)'
HostAddress_p.cpp:(.text+0x98b): undefined reference to std::basic_ostream<char,
std::char_traits >& std::basic_ostream<char, std::char_traits
::_M_insert(unsigned long)'
HostAddress_p.cpp:(.text+0x9fe): undefined reference tostd::basic_ostream
& std::

ostream_insert >(std::basic_ostream >&, char const, long)'
HostAddress_p.cpp:(.text+0xa48): undefined reference to
std::basic_ostream<char, std::char_traits >&
std::__ostream_insert<char, std::char_traits

(std::basic_ostream<char, std::char_traits >&, char const_, long)'
HostAddress_p.cpp:(.text+0xa92): undefined reference tostd::basic_ostream
& std::ostream_insert >(std::basic_ostream >&, char const, long)'
HostAddress_p.cpp:(.text+0xadc): undefined reference to std::basic_ostream<char,
std::char_traits >& std::_ostream_insert<char,
std::char_traits >(std::basic_ostream<char, std::char_traits
&, char const, long)'
HostAddress_p.cpp:(.text+0xb26): undefined reference tostd::basic_ostream
& std::
ostream_insert >(std::basic_ostream >&, char const, long)'
.//libbamtools.a(HostAddress_p.cpp.o):HostAddress_p.cpp:(.text+0xb70): more
undefined references to `std::basic_ostream >& std::ostream_insert
(std::basic_ostream >&, char const, long)' follow
collect2: ld returned 1 exit status
make: *** [bamaddrg] Error 1

Do you know how to solve this problem?

�
Reply to this email directly or view it on GitHubhttps://github.com//issues/1#issuecomment-30463683
.

[Microkiller]

Thank you.
I did use the git clone --recursive.
But when I tried to compile the samtools, I got some warnings as
"/data/zj_AIF9_analytics/bamaddrg-master/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendGetRequest(size_t)’:
/data/zj_AIF9_analytics/bamaddrg-master/bamtools/src/api/internal/io/BamHttp_p.cpp:409: warning: comparison between signed and unsigned integer expressions
/data/zj_AIF9_analytics/bamaddrg-master/bamtools/src/api/internal/io/BamHttp_p.cpp: In member function ‘bool BamTools::Internal::BamHttp::SendHeadRequest()’:
/data/zj_AIF9_analytics/bamaddrg-master/bamtools/src/api/internal/io/BamHttp_p.cpp:501: warning: comparison between signed and unsigned integer expressions
"
But the compile still finished successfully.
Is this caused problem?

[hirenbioinfo]

DETECTED_VERSION = v1.0.2-29-g41c1313
CURRENT_VERSION = v1.0.2-29-g41c1313
g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../ttmath -I../bamtools/src/ -I../vcflib/src/ -I../vcflib/tabixpp/ -I../vcflib/smithwaterman/ -I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/tabixpp/htslib/ freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o ../vcflib/tabixpp/tabix.o ../vcflib/tabixpp/htslib/bgzf.o ../vcflib/smithwaterman/SmithWatermanGotoh.o ../vcflib/smithwaterman/disorder.cpp ../vcflib/smithwaterman/LeftAlign.o ../vcflib/smithwaterman/Repeats.o ../vcflib/smithwaterman/IndelAllele.o Variant.o ../bamtools/lib/libbamtools.a ../vcflib/tabixpp/htslib/libhts.a -o ../bin/freebayes -lz -lm -lpthread
AlleleParser.o: In function AlleleParser::loadReferenceSequence(std::string&)': /home/biotools/freebayes/src/AlleleParser.cpp:611: undefined reference toBamTools::BamMultiReader::GetReferenceID(std::string const&) const'
AlleleParser.o: In function AlleleParser::loadTarget(BedTarget*)': /home/biotools/freebayes/src/AlleleParser.cpp:2618: undefined reference toBamTools::BamMultiReader::GetErrorString() const'
AlleleParser.o: In function AlleleParser::openBams()': /home/biotools/freebayes/src/AlleleParser.cpp:56: undefined reference toBamTools::BamMultiReader::Open(std::vector<std::string, std::allocatorstd::string > const&)'
/home/hiren/biotools/freebayes/src/AlleleParser.cpp:89: undefined reference to BamTools::BamMultiReader::GetHeaderText() const' /home/biotools/freebayes/src/AlleleParser.cpp:62: undefined reference toBamTools::BamMultiReader::Open(std::vector<std::string, std::allocatorstd::string > const&)'
/home/biotools/freebayes/src/AlleleParser.cpp:69: undefined reference to BamTools::BamMultiReader::GetErrorString() const' /home/hiren/biotools/freebayes/src/AlleleParser.cpp:82: undefined reference toBamTools::BamMultiReader::GetErrorString() const'
/home/biotools/freebayes/src/AlleleParser.cpp:64: undefined reference to BamTools::BamMultiReader::GetErrorString() const' /home/biotools/freebayes/src/AlleleParser.cpp:58: undefined reference toBamTools::BamMultiReader::GetErrorString() const'
AlleleParser.o: In function AlleleParser::getInputVariantsInRegion(std::string&, long, long)': /home/biotools/freebayes/src/AlleleParser.cpp:2223: undefined reference toBamTools::BamMultiReader::GetReferenceID(std::string const&) const'
AlleleParser.o: In function AlleleParser::updateInputVariants(long, int)': /home/biotools/freebayes/src/AlleleParser.cpp:2353: undefined reference toBamTools::BamMultiReader::GetReferenceID(std::string const&) const'
AlleleParser.o: In function GetTag<std::basic_string<char> >': /home/biotools/freebayes/src/../bamtools/src/api/BamAlignment.h:517: undefined reference toBamTools::BamAlignment::FindTag(std::string const&, char_&, unsigned int const&, unsigned int&) const'
/home/biotools/freebayes/src/../bamtools/src/api/BamAlignment.h:517: undefined reference to `BamTools::BamAlignment::FindTag(std::string const&, char_&, unsigned int const&, unsigned int&) const'
collect2: error: ld returned 1 exit status
Makefile:85: recipe for target '../bin/freebayes' failed
make[1]: *** [../bin/freebayes] Error 1
make[1]: Leaving directory '/home/hiren/biotools/freebayes/src'
Makefile:2: recipe for target 'all' failed
make: *** [all] Error 2

[ekg]

@hirenbioinfo is this a freebayes or bamaddrg issue?

[hirenbioinfo]

Issue reported here : freebayes/freebayes#298

On 16 June 2016 at 14:00, Erik Garrison [email protected] wrote:

@hirenbioinfo https://github.com/hirenbioinfo is this a freebayes or
bamaddrg issue?

—
You are receiving this because you were mentioned.
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Hiren Ghosh, Doctoral Research Scholar Biomedizinisches Forschungszentrum
SeltersbergInstitut für Medizinische
MikrobiologieJustus-Liebig-UniversitätSchubertstr. 8135392 Gießen , Germany

Mobile No: 017672157634

Email:[email protected]
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[cramirezs]

Hello Erik,

I've trying to compile bamaddrg in a cluster, but I've got this error (whether it's dowloaded with the --recursive flag or not). So, I' coping with the end of bamtools compilation. Also, I'm adding some warnings bamtools had.
Could you help me with this?

Thank you very much!

WARNINGS
1.- src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/depend.make' has modification time 32 s in the future
2.- comparison between signed and unsigned integer expressions [-Wsign-compare] return ( WriteToSocket(requestHeader.c_str(), headerSize) == headerSize );
3.- warning: Clock skew detected. Your build may be incomplete.
...

ERROR
[100%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o
Linking CXX executable ../../../bin/bamtools
make[3]: warning: Clock skew detected. Your build may be incomplete.
make[3]: Leaving directory /home/ciro/bin/bamaddrg/bamtools/build' [100%] Built target bamtools_cmd make[2]: warning: Clock skew detected. Your build may be incomplete. make[2]: Leaving directory /home/ciro/bin/bamaddrg/bamtools/build'
make[1]: warning: Clock skew detected. Your build may be incomplete.
make[1]: Leaving directory /home/ciro/bin/bamaddrg/bamtools/build' cp bamtools/lib/libbamtools.a ./ g++ -O3 -Ibamtools/include -L./ bamaddrg.cpp -o bamaddrg -lbamtools -lz /scratch/ccPIjr4p.o: In function main':
bamaddrg.cpp:(.text.startup+0x6e4): undefined reference to BamTools::SamReadGroup::SamReadGroup(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' bamaddrg.cpp:(.text.startup+0x76f): undefined reference to BamTools::BamMultiReader::Open(std::vector<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::allocator<std::__cxx11::basic_string<char, std::char_traits, std::allocator > > > const&)'
bamaddrg.cpp:(.text.startup+0xc08): undefined reference to BamTools::SamHeader::ToString[abi:cxx11]() const' bamaddrg.cpp:(.text.startup+0xc3c): undefined reference to BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::vector<BamTools::RefData, std::allocatorBamTools::RefData > const&)'
bamaddrg.cpp:(.text.startup+0xd7e): undefined reference to BamTools::BamAlignment::HasTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' bamaddrg.cpp:(.text.startup+0xdb1): undefined reference to BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
bamaddrg.cpp:(.text.startup+0xe77): 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' bamaddrg.cpp:(.text.startup+0x1037): undefined reference to BamTools::BamAlignment::RemoveTag(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
collect2: error: ld returned 1 exit status
make: *** [bamaddrg] Error 1

[cramirezs]

Hi,

The time clock skew is fixed, but still getting this error and warnings.

WARNING
comparison between signed and unsigned integer expressions
ERROR
g++ -O3 -Ibamtools/include -L./ bamaddrg.cpp -o bamaddrg -lbamtools -lz
/scratch/ccoUWhPV.o: In function main': bamaddrg.cpp:(.text.startup+0x6e4): undefined reference to BamTools::SamReadGroup::SamReadGroup(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
bamaddrg.cpp:(.text.startup+0x76f): 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&)' bamaddrg.cpp:(.text.startup+0xc08): undefined reference to BamTools::SamHeader::ToStringabi:cxx11 const'
bamaddrg.cpp:(.text.startup+0xc3c): undefined reference to BamTools::BamWriter::Open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::vector<BamTools::RefData, std::allocator<BamTools::RefData> > const&)' bamaddrg.cpp:(.text.startup+0xd7e): undefined reference to BamTools::BamAlignment::HasTag(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const'
bamaddrg.cpp:(.text.startup+0xdb1): undefined reference to BamTools::BamAlignment::IsValidSize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' bamaddrg.cpp:(.text.startup+0xe77): undefined reference to BamTools::BamAlignment::FindTag(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, char*&, unsigned int const&, unsigned int&) const'
bamaddrg.cpp:(.text.startup+0x1037): undefined reference to `BamTools::BamAlignment::RemoveTag(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)'
collect2: error: ld returned 1 exit status
make: *** [bamaddrg] Error 1

[janxkoci]

Hi @cramirezs,

you can try using conda manager like this.

Hope it helps.

[lufuhao]

well, I am not the owner of bamaddrg. From your error log, you may need to install cmake first before install bamtools Cheers Fuhao 发自我的iPhone 在 2020年3月18日，00:51，Sabhrina Aninta <[email protected]> 写道：  Hi, I have used this for installing bamaddrg on a remote server git clone --recursive https://github.com/ekg/bamaddrg.git Resulted in this message: Cloning into 'bamaddrg'... remote: Enumerating objects: 33, done. remote: Total 33 (delta 0), reused 0 (delta 0), pack-reused 33 Unpacking objects: 100% (33/33), done. Submodule 'bamtools' (git://github.com/pezmaster31/bamtools.git) registered for path 'bamtools' Cloning into 'bamtools'... remote: Enumerating objects: 281, done. remote: Counting objects: 100% (281/281), done. remote: Compressing objects: 100% (184/184), done. remote: Total 5138 (delta 168), reused 158 (delta 93), pack-reused 4857 Receiving objects: 100% (5138/5138), 6.28 MiB | 6.56 MiB/s, done. Resolving deltas: 100% (3541/3541), done. Submodule path 'bamtools': checked out '6111130f6d7b1ae06ac25178f8dc5006f0754cfc' then I did this: cd bamaddrg/ make but the following message occur instead: cd bamtools && mkdir -p build && cd build && cmake .. && make /bin/sh: cmake: command not found make: *** [libbamtools.a] Error 127 Could someone tell me where I did wrong? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABRLTFSEU5LSO5B4NQ734QDRH6TBLANCNFSM4AGY2M2Q>.