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I was troubleshooting and looking into the error messages and I thoughts Id share some progress, well I hope progress
Looking at the error statement again
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -march=i686 -O3 -DNDEBUG -pthread -I/usr/local/boost_1_53_0/include -I/usr/local/include/bam/include -I/usr/local/include/Eigen/include -o cufflinks -L/usr/local/lib -L/usr/local/include/bam/lib cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lbam -lz
/usr/local/lib/libboost_thread.a(thread.o): In function `__gnu_cxx::__exchange_and_add_dispatch(int*, int) [clone .constprop.241]':
thread.cpp
.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4'
I noticed:
-I/usr/local/boost_1_53_0/include
-I/usr/local/include/bam/include
I noticed that while there is an include subdirectory for Eigen there was none for /boost_1_53_0 or /bam. What I did for the bam subdirectory was to copy my header files to the /usr/local/include/bam directory. I went back to the cufflinks gettign started manual
and read "Copy the samtools binary to some directory in your PATH." Would I be correct in assuming that I should copy the contents of Desktop/samtools-0.1.19 to the /usr/local/ folder ? Would it make sense to create an include folder in the /boost_1_53_0 and /bam directories and fill it with the appropriate files ?
The line that Im still trying to decipher is the
thread.cpp.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4'
I figure it has something to do with not being able to find the thread.cpp in the library directory which in the connfigure statement I defined as : --with-boost-libdir=/usr/local/lib. did a locate *read.cpp and found the following locations:
Looking at the error statement again
g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -march=i686 -O3 -DNDEBUG -pthread -I/usr/local/boost_1_53_0/include -I/usr/local/include/bam/include -I/usr/local/include/Eigen/include -o cufflinks -L/usr/local/lib -L/usr/local/include/bam/lib cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lbam -lz
/usr/local/lib/libboost_thread.a(thread.o): In function `__gnu_cxx::__exchange_and_add_dispatch(int*, int) [clone .constprop.241]':
thread.cpp
.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4'I noticed:
-I/usr/local/boost_1_53_0/include
-I/usr/local/include/bam/include
I noticed that while there is an include subdirectory for Eigen there was none for /boost_1_53_0 or /bam. What I did for the bam subdirectory was to copy my header files to the /usr/local/include/bam directory. I went back to the cufflinks gettign started manual
and read "Copy the samtools binary to some directory in your PATH." Would I be correct in assuming that I should copy the contents of Desktop/samtools-0.1.19 to the /usr/local/ folder ? Would it make sense to create an include folder in the /boost_1_53_0 and /bam directories and fill it with the appropriate files ?
The line that Im still trying to decipher is the
thread.cpp
.text.unlikely+0x22): undefined reference to `__atomic_fetch_add_4' I figure it has something to do with not being able to find the thread.cpp in the library directory which in the connfigure statement I defined as : --with-boost-libdir=/usr/local/lib. did a locate *read.cpp and found the following locations:
/usr/local/boost_1_53_0/libs/thread/example/thread.cpp
/usr/local/boost_1_53_0/libs/thread/src/pthread/thread.cpp
/usr/local/boost_1_53_0/libs/thread/src/win32/thread.cpp
/usr/local/boost_1_53_0/libs/thread/src/pthread/thread.cpp
/usr/local/boost_1_53_0/libs/thread/src/win32/thread.cpp
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