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. -- ×£ÍòÊÂ˳Ò⣡ Àî ΰ ¸´µ©´óѧÉúÎïҽѧÑо¿Ôº EpiRNAʵÑéÊÒ ÉϺ£Êж«°²Â·130ºÅÎ÷13ºÅÂ¥416ÊÒ Óʱà200032 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 [[alternative HTML version deleted]]

seems to me you should ask Ben Langmead this question... https://github.com/BenLangmead/bsmooth-align *A smart man once told me you can model any algorithm by using *map* and * reduce. *But he was wrong. * Swizec Teller<http: books.google.com="" books?id="1Qm8AQAAQBAJ&amp;pg=PT117&amp;l" pg="PT117&amp;dq=a+smart+man+once+told+me+you+can+model+any+algorithm+by+us" ing+map+and+reduce.++but+he+was+wrong.&source="bl&amp;ots=Zf8PIGoLP_&amp;sig=W4" kixxf7orcyqnq0e8p88qpwyai&hl="en&amp;sa=X&amp;ei=gze3UqjvAs36oATrxYHwBA&amp;ved=0CD" 4q6aewag#v="onepage&amp;q=a%20smart%20man%20once%20told%20me%20you%20can%20" model%20any%20algorithm%20by%20using%20map%20and%20reduce.%20%20but%20="" he%20was%20wrong.&f="false"> On Wed, Dec 25, 2013 at 12:48 AM, liwei_epi <liwei_epi@fudan.edu.cn> wrote: > 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. > > > > > > -- > > ×£ÍòÊÂ˳Ò⣡ > > Àî ΰ > ¸´µ©´óѧÉúÎïҽѧÑо¿Ôº EpiRNAʵÑéÊÒ > ÉϺ£Êж«°²Â·130ºÅÎ÷13ºÅÂ¥416ÊÒ Óʱà200032 > 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 > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]