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ultimatesource / denovogear

A program to detect denovo-variants using next-generation sequencing data.
http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2611.html
GNU General Public License v3.0
49 stars 25 forks source link

Compiling DeNovoGear on CentOS 6.6 #267

Closed aschoenr closed 6 years ago

aschoenr commented 6 years ago

Hi, I'm trying to compile denovogear 1.1.1 on CentOS. I believe I have all the dependencies (gcc 7.2.1, CMake 3.11.1, HTSlib 1.8, Eigen 3, Boost 1.67). Here is exactly what I've done, any healp would be greatly appreciated.

[aschoenr@bratty apps]$ tar -xvf v1.1.1.tar.gz ... [aschoenr@bratty apps]$ cd denovogear-1.1.1/build/ [aschoenr@bratty build]$ cmake .. -- The CXX compiler identification is GNU 7.2.1 -- The C compiler identification is GNU 7.2.1 -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- Check for working C compiler: /opt/rh/devtoolset-7/root/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Found Git: /usr/bin/git (found version "1.7.1") -- DeNovoGear version is 1.1.1 -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3") -- Boost version: 1.67.0 -- Found the following Boost libraries: -- program_options -- filesystem -- system -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") CMake Warning at Modules/LibFindMacros.cmake:191 (message): The find module for HTSLIB does not provide version information, so we'll just assume that it is OK. Please fix the module or remove package version requirements to get rid of this warning. Call Stack (most recent call first): Modules/FindHTSLIB.cmake:11 (libfind_process) Modules/ExternalDep.cmake:127 (FIND_PACKAGE) src/CMakeLists.txt:15 (INCLUDE)

-- Found HTSLIB -- Configuring done -- Generating done -- Build files have been written to: /home/aschoenr/work/apps/denovogear-1.1.1/build [aschoenr@bratty build]$ make Scanning dependencies of target dngutils [ 1%] Building C object src/utils/CMakeFiles/dngutils.dir/bgzf.c.o [ 2%] Building C object src/utils/CMakeFiles/dngutils.dir/dict.c.o [ 4%] Building C object src/utils/CMakeFiles/dngutils.dir/array.c.o [ 5%] Building C object src/utils/CMakeFiles/dngutils.dir/kstring.c.o [ 7%] Building C object src/utils/CMakeFiles/dngutils.dir/bcf.c.o [ 8%] Building C object src/utils/CMakeFiles/dngutils.dir/knetfile.c.o [ 10%] Building C object src/utils/CMakeFiles/dngutils.dir/vcf.c.o [ 11%] Building C object src/utils/CMakeFiles/dngutils.dir/bcfutils.c.o [ 13%] Building C object src/utils/CMakeFiles/dngutils.dir/sam_view.c.o [ 14%] Building C object src/utils/CMakeFiles/dngutils.dir/sam.c.o [ 15%] Building C object src/utils/CMakeFiles/dngutils.dir/bam.c.o [ 17%] Building C object src/utils/CMakeFiles/dngutils.dir/bedidx.c.o [ 18%] Building C object src/utils/CMakeFiles/dngutils.dir/bam_aux.c.o [ 20%] Building C object src/utils/CMakeFiles/dngutils.dir/sam_header.c.o [ 21%] Building C object src/utils/CMakeFiles/dngutils.dir/bam_import.c.o [ 23%] Building C object src/utils/CMakeFiles/dngutils.dir/bam_pileup.c.o [ 24%] Building C object src/utils/CMakeFiles/dngutils.dir/bam_index.c.o [ 26%] Building C object src/utils/CMakeFiles/dngutils.dir/faidx.c.o [ 27%] Building C object src/utils/CMakeFiles/dngutils.dir/razf.c.o [ 28%] Building C object src/utils/CMakeFiles/dngutils.dir/index.c.o [ 30%] Linking C static library libdngutils.a [ 30%] Built target dngutils Scanning dependencies of target newmat [ 31%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat1.cpp.o [ 33%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat2.cpp.o [ 34%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat3.cpp.o [ 36%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat4.cpp.o [ 37%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat5.cpp.o In file included from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:14:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat5.cpp:13: /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat5.cpp: In destructor ‘MatrixInput::~MatrixInput()’: /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat5.cpp:494:69: warning: throw will always call terminate() [-Wterminate] if (n!=0) Throw(ProgramException("A list of values was too short")); ^ /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/myexcept.h:193:24: note: in definition of macro ‘Throw’

define Throw(E) throw E

^ /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat5.cpp:494:69: note: in C++11 destructors default to noexcept if (n!=0) Throw(ProgramException("A list of values was too short")); ^ /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/myexcept.h:193:24: note: in definition of macro ‘Throw’

define Throw(E) throw E

^ [ 39%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat6.cpp.o [ 40%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat7.cpp.o [ 42%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat8.cpp.o [ 43%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmatex.cpp.o [ 44%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/bandmat.cpp.o [ 46%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/submat.cpp.o [ 47%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/myexcept.cpp.o [ 49%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/cholesky.cpp.o [ 50%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/evalue.cpp.o [ 52%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/fft.cpp.o [ 53%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/hholder.cpp.o [ 55%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/jacobi.cpp.o [ 56%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newfft.cpp.o [ 57%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/sort.cpp.o [ 59%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/svd.cpp.o [ 60%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/nm_misc.cpp.o [ 62%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmatrm.cpp.o [ 63%] Building CXX object src/contrib/newmat/CMakeFiles/newmat.dir/newmat9.cpp.o [ 65%] Linking CXX static library libnewmat.a [ 65%] Built target newmat Scanning dependencies of target dng-phaser [ 66%] Building CXX object src/CMakeFiles/dng-phaser.dir/dng-phaser.cc.o [ 68%] Building CXX object src/CMakeFiles/dng-phaser.dir/snpLike.cc.o [ 69%] Building CXX object src/CMakeFiles/dng-phaser.dir/indelLike.cc.o [ 71%] Building CXX object src/CMakeFiles/dng-phaser.dir/pairLike.cc.o [ 72%] Building CXX object src/CMakeFiles/dng-phaser.dir/makeLookup.cc.o [ 73%] Building CXX object src/CMakeFiles/dng-phaser.dir/pedParser.cc.o [ 75%] Building CXX object src/CMakeFiles/dng-phaser.dir/bcf2Qcall.cc.o [ 76%] Building CXX object src/CMakeFiles/dng-phaser.dir/bcf2Paired.cc.o [ 78%] Linking CXX executable dng-phaser [ 78%] Built target dng-phaser Scanning dependencies of target dng-dnm [ 79%] Building CXX object src/CMakeFiles/dng-dnm.dir/dng-dnm.cc.o /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc: In function ‘int writeVCFHeader(std::ofstream&, std::string, std::string, std::string, std::string)’: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:13: error: no match for ‘operator==’ (operand types are ‘std::ofstream {aka std::basic_ofstream}’ and ‘long int’) if(fo_vcf == NULL) { ^ /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:13: note: candidate: operator==(int, long int) /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:13: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘int’ In file included from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/lookup.h:23, from /home/aschoenr/work/apps/denovogear-1.1.1/src/makeLookup.h:25, from /home/aschoenr/work/apps/denovogear-1.1.1/src/denovogear.h:29, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:41: /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:2074:6: note: candidate: bool operator==(const GeneralMatrix&, const GeneralMatrix&) bool operator==(const GeneralMatrix& A, const GeneralMatrix& B); ^~~~ /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:2074:6: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const GeneralMatrix&’ /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:2075:6: note: candidate: bool operator==(const BaseMatrix&, const BaseMatrix&) bool operator==(const BaseMatrix& A, const BaseMatrix& B); ^~~~ /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:2075:6: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const BaseMatrix&’ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_conv.h:41:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/locale:43, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iomanip:43, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/include.h:92, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:12, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12, from /home/aschoenr/work/apps/denovogear-1.1.1/src/lookup.h:23, from /home/aschoenr/work/apps/denovogear-1.1.1/src/makeLookup.h:25, from /home/aschoenr/work/apps/denovogear-1.1.1/src/denovogear.h:29, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:41: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/unique_ptr.h:694:5: note: candidate: template<class _Tp,="" class="" _Dp=""> bool std::operator==(std::nullptr_t, const std::unique_ptr<_Tp, _Dp>&) operator==(nullptr_t, const unique_ptr<_Tp, _Dp>& x) noexcept ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/unique_ptr.h:694:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: mismatched types ‘const std::unique_ptr<_Tp, _Dp>’ and ‘long int’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_conv.h:41:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/locale:43, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iomanip:43, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/include.h:92, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:12, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12, from /home/aschoenr/work/apps/denovogear-1.1.1/src/lookup.h:23, from /home/aschoenr/work/apps/denovogear-1.1.1/src/makeLookup.h:25, from /home/aschoenr/work/apps/denovogear-1.1.1/src/denovogear.h:29, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:41: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/unique_ptr.h:689:5: note: candidate: template<class _Tp,="" class="" _Dp=""> bool std::operator==(const std::unique_ptr<_Tp, _Dp>&, std::nullptr_t) operator==(const unique_ptr<_Tp, _Dp>& x, nullptr_t) noexcept ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/unique_ptr.h:689:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::unique_ptr<_Tp, _Dp>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_conv.h:41:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/locale:43, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iomanip:43, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/include.h:92, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmat.h:12, from /home/aschoenr/work/apps/denovogear-1.1.1/src/contrib/newmat/newmatap.h:12, from /home/aschoenr/work/apps/denovogear-1.1.1/src/lookup.h:23, from /home/aschoenr/work/apps/denovogear-1.1.1/src/makeLookup.h:25, from /home/aschoenr/work/apps/denovogear-1.1.1/src/denovogear.h:29, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:41: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/unique_ptr.h:683:5: note: candidate: template<class _Tp,="" class="" _Dp,="" class="" _Up,="" class="" _Ep=""> bool std::operator==(const std::unique_ptr<_Tp, _Dp>&, const std::unique_ptr<_Up, _Ep>&) operator==(const unique_ptr<_Tp, _Dp>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/unique_ptr.h:683:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::unique_ptr<_Tp, _Dp>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/map:62:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:28: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_multimap.h:1045:5: note: candidate: template<class _Key,="" class="" _Tp,="" class="" _Compare,="" class="" _Alloc=""> bool std::operator==(const std::multimap<_Key, _Tp, _Compare, _Alloc>&, const std::multimap<_Key, _Tp, _Compare, _Alloc>&) operator==(const multimap<_Key, _Tp, _Compare, _Alloc>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_multimap.h:1045:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::multimap<_Key, _Tp, _Compare, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/map:61:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:28: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_map.h:1380:5: note: candidate: template<class _Key,="" class="" _Tp,="" class="" _Compare,="" class="" _Alloc=""> bool std::operator==(const std::map<_Key, _Tp, _Compare, _Alloc>&, const std::map<_Key, _Tp, _Compare, _Alloc>&) operator==(const map<_Key, _Tp, _Compare, _Alloc>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_map.h:1380:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::map<_Key, _Tp, _Compare, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_map.h:63:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/map:61, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:28: /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:1397:5: note: candidate: template<class ...="" _TElements,="" class="" ...="" _UElements=""> constexpr bool std::operator==(const std::tuple<_Tps ...>&, const std::tuple<_Args2 ...>&) operator==(const tuple<_TElements...>& t, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:1397:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::tuple<_Tps ...>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/tuple:39:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_map.h:63, from /opt/rh/devtoolset-7/root/usr/include/c++/7/map:61, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:28: /opt/rh/devtoolset-7/root/usr/include/c++/7/array:252:5: note: candidate: template<class _Tp,="" long="" unsigned="" int="" _Nm=""> bool std::operator==(const std::array<_Tp, _Nm>&, const std::array<_Tp, _Nm>&) operator==(const array<_Tp, _Nm>& one, const array<_Tp, _Nm>& two) ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/array:252:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::array<_Tp, _Nm>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/map:60:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:28: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_tree.h:1533:5: note: candidate: template<class _Key,="" class="" _Val,="" class="" _KeyOfValue,="" class="" _Compare,="" class="" _Alloc=""> bool std::operator==(const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&, const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>&) operator==(const _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_tree.h:1533:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/map:60:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:28: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_tree.h:406:5: note: candidate: template bool std::operator==(const std::_Rb_tree_iterator<_Tp>&, const std::_Rb_tree_const_iterator<_Val>&) operator==(const _Rb_tree_iterator<_Val>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_tree.h:406:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::_Rb_tree_iterator<_Tp>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_facets.h:48:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_ios.h:37, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ios:44, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ostream:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iostream:39, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:25: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/streambuf_iterator.h:204:5: note: candidate: template<class _CharT,="" class="" _Traits=""> bool std::operator==(const std::istreambuf_iterator<_CharT, _Traits>&, const std::istreambuf_iterator<_CharT, _Traits>&) operator==(const istreambuf_iterator<_CharT, _Traits>& a, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/streambuf_iterator.h:204:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::istreambuf_iterator<_CharT, _Traits>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/ios_base.h:46:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ios:42, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ostream:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iostream:39, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:25: /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:311:3: note: candidate: bool std::operator==(const std::error_condition&, const std::error_condition&) operator==(const error_condition& lhs, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:311:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_condition&’ /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:304:3: note: candidate: bool std::operator==(const std::error_condition&, const std::error_code&) operator==(const error_condition& lhs, const error_code& rhs) noexcept ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:304:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_condition&’ /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:297:3: note: candidate: bool std::operator==(const std::error_code&, const std::error_condition&) operator==(const error_code& lhs, const error_condition& rhs) noexcept ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:297:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_code&’ /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:292:3: note: candidate: bool std::operator==(const std::error_code&, const std::error_code&) operator==(const error_code& lhs, const error_code& rhs) noexcept ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/system_error:292:3: note: no known conversion for argument 1 from ‘std::ofstream {aka std::basic_ofstream}’ to ‘const std::error_code&’ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_classes.h:40, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/ios_base.h:41, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ios:42, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ostream:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iostream:39, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:25: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5841:5: note: candidate: template<class _CharT,="" class="" _Traits,="" class="" _Alloc=""> bool std::operator==(const std::basic_string<_CharT, _Traits, _Alloc>&, const _CharT) operator==(const basic_string<_CharT, _Traits, _Alloc>& lhs, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5841:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::basic_string<_CharT, _Traits, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_classes.h:40, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/ios_base.h:41, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ios:42, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ostream:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iostream:39, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:25: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5829:5: note: candidate: template<class _CharT,="" class="" _Traits,="" class="" _Alloc=""> bool std::operator==(const _CharT, const std::basic_string<_CharT, _Traits, _Alloc>&) operator==(const _CharT lhs, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5829:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: mismatched types ‘const _CharT’ and ‘std::basic_ofstream’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_classes.h:40, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/ios_base.h:41, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ios:42, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ostream:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iostream:39, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:25: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5815:5: note: candidate: template typename gnu_cxx::enable_if<std::__is_char<_Tp>::value, bool>::type std::operator==(const std::basic_string<_CharT>&, const std::basic_string<_CharT>&) operator==(const basic_string<_CharT>& lhs, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5815:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::basic_string<_CharT>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/string:52:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/locale_classes.h:40, from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/ios_base.h:41, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ios:42, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ostream:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iostream:39, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:25: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5807:5: note: candidate: template<class _CharT,="" class="" _Traits,="" class="" _Alloc=""> bool std::operator==(const std::basic_string<_CharT, _Traits, _Alloc>&, const std::basic_string<_CharT, _Traits, _Alloc>&) operator==(const basic_string<_CharT, _Traits, _Alloc>& lhs, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/basic_string.h:5807:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::basic_string<_CharT, _Traits, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/iosfwd:40:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ios:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/ostream:38, from /opt/rh/devtoolset-7/root/usr/include/c++/7/iostream:39, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:25: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/postypes.h:216:5: note: candidate: template bool std::operator==(const std::fpos<_StateT>&, const std::fpos<_StateT>&) operator==(const fpos<_StateT>& lhs, const fpos<_StateT>& rhs) ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/postypes.h:216:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::fpos<_StateT>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:64:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_vector.h:1596:5: note: candidate: template<class _Tp,="" class="" _Alloc=""> bool std::operator==(const std::vector<_Tp, _Alloc>&, const std::vector<_Tp, _Alloc>&) operator==(const vector<_Tp, _Alloc>& x, const vector<_Tp, _Alloc>& y) ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_vector.h:1596:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::vector<_Tp, _Alloc>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:61:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/allocator.h:152:5: note: candidate: template bool std::operator==(const std::allocator<_Tp1>&, const std::allocator<_Tp1>&) operator==(const allocator<_Tp>&, const allocator<_Tp>&) ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/allocator.h:152:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::allocator<_Tp1>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:61:0, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/allocator.h:146:5: note: candidate: template<class _T1,="" class="" _T2=""> bool std::operator==(const std::allocator<_Tp1>&, const std::allocator<_T2>&) operator==(const allocator<_T1>&, const allocator<_T2>&) ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/allocator.h:146:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::allocator<_Tp1>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_algobase.h:67:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:60, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:1124:5: note: candidate: template bool std::operator==(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorL>&) operator==(const move_iterator<_Iterator>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:1124:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::move_iterator<_IteratorL>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_algobase.h:67:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:60, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:1118:5: note: candidate: template<class _IteratorL,="" class="" _IteratorR=""> bool std::operator==(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorR>&) operator==(const move_iterator<_IteratorL>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:1118:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::move_iterator<_IteratorL>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_algobase.h:67:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:60, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:337:5: note: candidate: template<class _IteratorL,="" class="" _IteratorR=""> bool std::operator==(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_IteratorR>&) operator==(const reverse_iterator<_IteratorL>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:337:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::reverse_iterator<_Iterator>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_algobase.h:67:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:60, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:299:5: note: candidate: template bool std::operator==(const std::reverse_iterator<_Iterator>&, const std::reverse_iterator<_Iterator>&) operator==(const reverse_iterator<_Iterator>& x, ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_iterator.h:299:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::reverse_iterator<_Iterator>’ if(fo_vcf == NULL) { ^ In file included from /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_algobase.h:64:0, from /opt/rh/devtoolset-7/root/usr/include/c++/7/vector:60, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:24: /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h:443:5: note: candidate: template<class _T1,="" class="" _T2=""> constexpr bool std::operator==(const std::pair<_T1, _T2>&, const std::pair<_T1, _T2>&) operator==(const pair<_T1, _T2>& x, const pair<_T1, _T2>& y) ^~~~ /opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h:443:5: note: template argument deduction/substitution failed: In file included from /usr/include/unistd.h:227:0, from /usr/include/zconf.h:289, from /usr/include/zlib.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/utils/bcf.h:34, from /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:39: /home/aschoenr/work/apps/denovogear-1.1.1/src/dng-dnm.cc:164:16: note: ‘std::ofstream {aka std::basic_ofstream}’ is not derived from ‘const std::pair<_T1, _T2>’ if(fo_vcf == NULL) { ^ make[2]: [src/CMakeFiles/dng-dnm.dir/dng-dnm.cc.o] Error 1 make[1]: [src/CMakeFiles/dng-dnm.dir/all] Error 2 make: *** [all] Error 2

reedacartwright commented 6 years ago

Thanks for posting the entire output. Can you try compiling from the develop branch to see if you are still having the issue? I suspect that something that worked a few years ago is no longer working and I want to see if it is fixed in the develop branch.

aschoenr commented 6 years ago

Hi,

I downloaded the development branch code from here: https://github.com/denovogear/denovogear/archive/develop.tar.gz. On my first attempt to build it, it complained that I only had HTSlib 1.2 installed (not 1.8 like I thought). I installed 1.8 and then retried building v1.1.1. I got the same results as before. I then built the development version with no problems. I ran the tests and all 39 passed.

Is there any reason for me to not use this version and persist with v1.1.1? If not, I guess I'm good to go. Thanks for your help.

jgarciamesa commented 6 years ago

Hello @aschoenr , if, as of my understanding, you successfully installed the develop branch you are good to go. This version includes upgrades made after the v1.1.1 release. Please feel free to open a new issue if you encounter problems using DeNovoGear. I am now closing this issue and marking it as resolved in develop branch.