Hi，
 according to the readme file, there are someting wrong in the bsmooth-align-0.8.1 install. the detail in the following:
g++  -DUSE_PTHREADS -DMERMAN_VERSION="\"0.4.1-beta1\"" -lpthread -Wall -g -DNDEBUG -O3 -o merman mer_index.cpp alphabet.cpp check.cpp merman.cpp qual.cpp read.cpp seeds.cpp edit.cpp hit_set.cpp refmap.cpp annot.cpp threading.cpp color_dec.cpp color.cpp output.cpp align_sw.cpp align_naive.cpp ref.cpp orient.cpp merman_main.cpp
In file included from edit.h:27,
                 from hit_set.h:26,
                 from read.h:28,
                 from mer_index.h:28,
                 from mer_index.cpp:25:
sstring.h:492: error: explicit template specialization cannot have a storage class
In file included from mer_index.cpp:30:
parsort.h: In member function \u2018void DivideMergeSortThread<T>::run(T*, T*, int, int)\u2019:
parsort.h:44: error: \u2018tid1\u2019 was not declared in this scope
parsort.h: In member function \u2018void DivideMergeMergeThread<T>::run(T*, T*, int, int)\u2019:
parsort.h:92: error: \u2018tid1\u2019 was not declared in this scope
parsort.h:95: error: \u2018tid2\u2019 was not declared in this scope
parsort.h: In function \u2018void workingListParallelSort(const EList<std::pair<T*, T*> >&, int)\u2019:
parsort.h:253: error: \u2018auto_ptr\u2019 was not declared in this scope
parsort.h:253: error: expected primary-expression before \u2018>\u2019 token
parsort.h:253: error: there are no arguments to \u2018wlpsLock\u2019 that depend on a template parameter, so a declaration of \u2018wlpsLock\u2019 must be available


     if possible, could you help me to solve the problem? looking forward to your replying.
    




--

祝万事顺意！ 

李 伟 
复旦大学生物医学研究院 EpiRNA实验室
上海市东安路130号西13号楼416室    邮编200032
Regards!
Wei Li
EpiRNA Lab, Institues of Biomedical Sciences, Fudan University
130 # Dongan Road, West 13# Building, Room 416,Shanghai 200032, P.R.China, 
Phone number(Lab):+86-21-54237977
Fax number: +86-21-54237339
E-mail（optional）: liwei_epi@fudan.edu.cn
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