Question: Bam-Readcount Git Installation
0
gravatar for Karol Pal jr.
5.2 years ago by
Czech Republic
Karol Pal jr.20 wrote:

Hi,

I'm trying to install bam-readcount. Following the git installation instructions I get stuck in the 'make' step. Here is the somewhat long error message. I'd like to ask anyone willing to help me decipher it. (Also I'm on a 64 bit ubuntu 3.8.0-27-generic machine).

Thanks

Error log:

../../../../vendor/gtest160-build/libgtest.a(gtest-all.cc.o): In function `testing::internal::ThreadLocal<testing::TestPartResultReporterInterface*>::~ThreadLocal()':
gtest-all.cc:(.text._ZN7testing8internal11ThreadLocalIPNS_31TestPartResultReport
erInterfaceEED2Ev[_ZN7testing8internal11ThreadLocalIPNS_31TestPartResultReporter
InterfaceEED5Ev]+0x16): undefined reference to `pthread_getspecific'
gtest-all.cc:(.text._ZN7testing8internal11ThreadLocalIPNS_31TestPartResultReport
erInterfaceEED2Ev[_ZN7testing8internal11ThreadLocalIPNS_31TestPartResultReporter
InterfaceEED5Ev]+0x2b): undefined reference to `pthread_key_delete'
../../../../vendor/gtest160-build/libgtest.a(gtest-all.cc.o): In function `testing::internal::ThreadLocal<std::vector<testing::internal::TraceInfo, std::allocator<testing::internal::TraceInfo> > >::~ThreadLocal()':
gtest-all.cc:(.text._ZN7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoES
aIS3_EEED2Ev[_ZN7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoESaIS3_EE
ED5Ev]+0x16): undefined reference to `pthread_getspecific'
gtest-all.cc:(.text._ZN7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoES
aIS3_EEED2Ev[_ZN7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoESaIS3_EE
ED5Ev]+0x2b): undefined reference to `pthread_key_delete'
../../../../vendor/gtest160-build/libgtest.a(gtest-all.cc.o): In function `testi
ng::internal::ThreadLocal<std::vector<testing::internal::TraceInfo, std::allocator<testing::internal::TraceInfo> > >::GetOrCreateValue() const':
gtest-all.cc:(.text._ZNK7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoE
SaIS3_EEE16GetOrCreateValueEv[_ZNK7testing8internal11ThreadLocalISt6vectorINS0_9
TraceInfoESaIS3_EEE16GetOrCreateValueEv]+0x18): undefined reference to `pthread_getspecific'
gtest-all.cc:(.text._ZNK7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoE
SaIS3_EEE16GetOrCreateValueEv[_ZNK7testing8internal11ThreadLocalISt6vectorINS0_9
TraceInfoESaIS3_EEE16GetOrCreateValueEv]+0x7c): undefined reference to `pthread_setspecific'
../../../../vendor/gtest160-build/libgtest.a(gtest-all.cc.o): In function `testing::internal::ThreadLocal<testing::TestPartResultReporterInterface*>::CreateKey()':
gtest-all.cc:(.text._ZN7testing8internal11ThreadLocalIPNS_31TestPartResultReport
erInterfaceEE9CreateKeyEv[_ZN7testing8internal11ThreadLocalIPNS_31TestPartResult
ReporterInterfaceEE9CreateKeyEv]+0x16): undefined reference to `pthread_key_create'
../../../../vendor/gtest160-build/libgtest.a(gtest-all.cc.o): In function `testing::internal::ThreadLocal<std::vector<testing::internal::TraceInfo,std::allocator<testing::internal::TraceInfo> > >::CreateKey()':
gtest-all.cc:(.text._ZN7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoES
aIS3_EEE9CreateKeyEv[_ZN7testing8internal11ThreadLocalISt6vectorINS0_9TraceInfoE    
SaIS3_EEE9CreateKeyEv]+0x16): undefined reference to `pthread_key_create'
../../../../vendor/gtest160-build/libgtest.a(gtest-all.cc.o): In function `testing::internal::ThreadLocal<testing::TestPartResultReporterInterface*>::GetOrCreateValue() const':
gtest-all.cc:(.text._ZNK7testing8internal11ThreadLocalIPNS_31TestPartResultReporterInterfaceEE16GetOrCreateValueEv[_ZNK7testing8internal11ThreadLocalIPNS_31Test
PartResultReporterInterfaceEE16GetOrCreateValueEv]+0x16): undefined reference to`pthread_getspecific'
gtest-all.cc:(.text._ZNK7testing8internal11ThreadLocalIPNS_31TestPartResultReporterInterfaceEE16GetOrCreateValueEv[_ZNK7testing8internal11ThreadLocalIPNS_31Test
PartResultReporterInterfaceEE16GetOrCreateValueEv]+0x7a): undefined reference to `pthread_setspecific'
collect2: error: ld returned 1 exit status
make[2]: *** [build/test/lib/bamrc/TestAuxFields] Error 1
make[1]: *** [build/test/lib/bamrc/CMakeFiles/TestAuxFields.dir/all] Error 2
make: *** [all] Error 2
installation • 1.8k views
ADD COMMENTlink modified 5.2 years ago by Zev.Kronenberg11k • written 5.2 years ago by Karol Pal jr.20
0
gravatar for Zev.Kronenberg
5.2 years ago by
United States
Zev.Kronenberg11k wrote:

This is just a place to start looking and I'm not guaranteeing this is correct.

collect2: error: ld returned 1 exit status -- Looks like the compiler cannot find the pthread library

On my OS the pthread library is here: /usr/lib64/libpthread.so

Install pthreads using your package manager. I think it is part of glib.

http://blenderartists.org/forum/archive/index.php/t-130400.html

http://stackoverflow.com/questions/5153096/pthread-library-location

If the library is installed but the compiler isn't find it try adding this to your bash profile:

export CPATH=/xxx-path-to-library/:$CPATH

export LD_LIBRARY_PATH=/xxx-path-to-library/:$LD_LIBARARY_PATH

export LIBRARY_PATH=/xxx-path-to-library/:$LIBARARY_PATH

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Zev.Kronenberg11k

thanks for the suggestion, so, I think the library is installed since

find / -name 'libpthread.*' -print

returns: /usr/lib/x86_64-linux-gnu/libpthread.so

do I need to tell the compiler somehow where to look for it?

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Karol Pal jr.20

see edits above.

ADD REPLYlink written 5.2 years ago by Zev.Kronenberg11k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 943 users visited in the last hour