[Debian-med-packaging] C++ problems when upgrading bowtie2

[Andreas Tille]

Hi,

could anybody with more C++ knowledge than me have a look at my last
bowtie2 commits of the new upstream version which throws the following
problems:


make[2]: Entering directory '/build/bowtie2-2.2.7'
g++ -O3 -m64 -msse2  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2  -funroll-loops -g3 -Wl,-z,relro -DPOPCNT_CAPABILITY -DWITH_TBB\"" -Wl,-z,relro -DPOPCNT_CAPABILITY -DWITH_TBB \
        -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \
         -I third_party \
        -o bowtie2-build-s bt2_build.cpp \
        ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
        -lpthread -ltbb -ltbbmalloc_proxy 
In file included from blockwise_sa.h:29:0,
                 from bt2_idx.h:42,
                 from bt2_build.cpp:27:
diff_sample.h: In member function 'void DifferenceCoverSample<T>::build(int)':
diff_sample.h:790:31: error: 'tthread' was not declared in this scope
                     AutoArray<tthread::thread*> threads(nthreads);
                               ^
diff_sample.h:790:47: error: template argument 1 is invalid
                     AutoArray<tthread::thread*> threads(nthreads);
                                               ^
diff_sample.h:806:36: error: invalid types 'int[int]' for array subscript
                         threads[tid] = new tthread::thread(VSorting_worker<TStr>, (void*)&tparams.back());
                                    ^
diff_sample.h:806:44: error: 'tthread' does not name a type
                         threads[tid] = new tthread::thread(VSorting_worker<TStr>, (void*)&tparams.back());
                                            ^
diff_sample.h:806:51: error: expected ';' before '::' token
                         threads[tid] = new tthread::thread(VSorting_worker<TStr>, (void*)&tparams.back());
                                                   ^
diff_sample.h:809:36: error: invalid types 'int[int]' for array subscript
                         threads[tid]->join();
                                    ^
In file included from bt2_idx.h:42:0,
                 from bt2_build.cpp:27:
blockwise_sa.h: At global scope:
blockwise_sa.h:424:11: error: 'tthread' was not declared in this scope
     EList<tthread::thread*> _threads;     /// thread list
           ^
...


Thanks a lot for any hint

        Andreas.



-- 
http://fam-tille.de