not installing on macOS
jkobject opened this issue · 6 comments
jkobject commented
After running:
git clone git://github.com/nygenome/lancet.git
cd lancet
makeOn macOS catalina
receiving:
mkdir /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/build; cd /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/build; cmake -DCMAKE_INSTALL_PREFIX=../ ..; make; make install; cd ../../
mkdir: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/build: File exists
CMake Deprecation Warning at CMakeLists.txt:20 (cmake_policy):
The OLD behavior for policy CMP0042 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
-- Checking for one of the modules 'jsoncpp>=1'
Did NOT find system JsonCpp, instead using bundled version
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/build
[ 0%] Built target SharedHeaders
[ 0%] Built target APIHeaders
[ 0%] Built target AlgorithmsHeaders
[ 63%] Built target BamTools
[ 67%] Built target jsoncpp
[ 75%] Built target BamTools-utils
[100%] Built target bamtools_cmd
[ 0%] Built target SharedHeaders
[ 0%] Built target APIHeaders
[ 0%] Built target AlgorithmsHeaders
[ 63%] Built target BamTools
[ 67%] Built target jsoncpp
[ 75%] Built target BamTools-utils
[100%] Built target bamtools_cmd
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/shared/bamtools_global.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib/pkgconfig/bamtools-1.pc
-- Installing: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib/libbamtools.a
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/api_global.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamAlgorithms.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamAlignment.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamAux.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamConstants.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamIndex.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamMultiReader.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamReader.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/BamWriter.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/IBamIODevice.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamConstants.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamHeader.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamProgram.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamProgramChain.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamReadGroup.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamReadGroupDictionary.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamSequence.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/SamSequenceDictionary.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools/api/algorithms/Sort.h
-- Up-to-date: /Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/bin/bamtools
cd /Users/jeremie/Documents/logiciels/lancet/htslib-1.8; ./configure; make; cd ../
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for grep that handles long lines and -e... /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for _LARGEFILE_SOURCE value needed for large files... no
checking shared library type for unknown-Darwin... Darwin dylib
checking how to run the C preprocessor... gcc -E
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for fsync... yes
checking for drand48... yes
checking whether fdatasync is declared... no
checking for library containing log... none required
checking for zlib.h... yes
checking for inflate in -lz... yes
checking for library containing recv... none required
checking for bzlib.h... yes
checking for BZ2_bzBuffToBuffCompress in -lbz2... yes
checking for lzma.h... yes
checking for lzma_easy_buffer_encode in -llzma... yes
checking for libdeflate.h... no
checking for libdeflate_deflate_compress in -ldeflate... no
checking for curl_easy_pause in -lcurl... yes
checking for CCHmac... yes
checking whether PTHREAD_MUTEX_RECURSIVE is declared... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating htslib.pc.tmp
config.status: creating config.h
config.status: config.h is unchanged
make[1]: Nothing to be done for `all'.
cd src; make; cp lancet ../; cd ../
g++ -std=c++0x -Wno-deprecated -Wall -O3 -fexceptions -g -Wl,-rpath,/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib64/ -I/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools -I/Users/jeremie/Documents/logiciels/lancet/htslib-1.8/ -L/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib64/ -L/Users/jeremie/Documents/logiciels/lancet/htslib-1.8/ Lancet.cc Edge.cc Node.cc Graph.cc Microassembler.cc Ref.cc Path.cc ContigLink.cc align.cc util.cc sha256.cc VariantDB.cc Variant.cc -o lancet /Users/jeremie/Documents/logiciels/lancet/htslib-1.8/libhts.a -llzma -lbz2 -lz -ldl -lpthread -lcurl -lcrypto -lbamtools
In file included from Lancet.cc:1:
In file included from ./Lancet.hh:27:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:91:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Lancet.cc:1:
In file included from ./Lancet.hh:27:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:92:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Lancet.cc:1:
In file included from ./Lancet.hh:27:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:93:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Lancet.cc:1:
In file included from ./Lancet.hh:27:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:94:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Lancet.cc:1:
In file included from ./Lancet.hh:27:
In file included from ./Microassembler.hh:32:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:480:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:2194:45: error: static_cast
from 'std::__1::unique_ptr<std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *>,
std::__1::__tree_node_destructor<std::__1::allocator<std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>,
Variant_t>, void *> > > >::pointer' (aka 'std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *>
*') to 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__node_base_pointer' (aka 'std::__1::__tree_node_base<void *> *'), which are not related by inheritance, is not allowed
__insert_node_at(__parent, __child, static_cast<__node_base_pointer>(__h.get()));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1265:16: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_hint_unique_key_args<std::__1::basic_string<char>, const std::__1::pair<const std::__1::basic_string<char>, Variant_t> &>'
requested here
return __emplace_hint_unique_key_args(__p, _NodeTypes::__get_key(__v), __v);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1175:29: note: in instantiation of
member function 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__insert_unique' requested here
{return __tree_.__insert_unique(__p.__i_, __v);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1196:17: note: in instantiation of
member function 'std::__1::map<std::__1::basic_string<char>, Variant_t, std::__1::less<std::__1::basic_string<char> >,
std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> > >::insert' requested here
insert(__e.__i_, *__f);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1009:13: note: in instantiation of
function template specialization 'std::__1::map<std::__1::basic_string<char>, Variant_t, std::__1::less<std::__1::basic_string<char> >,
std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> >
>::insert<std::__1::__map_const_iterator<std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long> > >' requested here
insert(__m.begin(), __m.end());
^
Lancet.cc:562:31: note: in instantiation of member function 'std::__1::map<std::__1::basic_string<char>, Variant_t,
std::__1::less<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> >
>::map' requested here
map<string,Variant_t> db = (assemblers[i]->vDB).DB;
^
In file included from Lancet.cc:1:
In file included from ./Lancet.hh:27:
In file included from ./Microassembler.hh:32:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:480:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:865:62: error: cannot
initialize a member subobject of type 'std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long>::__iter_pointer' (aka
'std::__1::__tree_end_node<std::__1::__tree_node_base<void *> *> *') with an lvalue of type
'std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long>::__node_pointer' (aka
'std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *')
explicit __tree_iterator(__node_pointer __p) _NOEXCEPT : __ptr_(__p) {}
^ ~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:2197:12: note: in instantiation
of member function 'std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long>::__tree_iterator' requested here
return iterator(__r);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1265:16: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_hint_unique_key_args<std::__1::basic_string<char>, const std::__1::pair<const std::__1::basic_string<char>, Variant_t> &>'
requested here
return __emplace_hint_unique_key_args(__p, _NodeTypes::__get_key(__v), __v);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1175:29: note: in instantiation of
member function 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__insert_unique' requested here
{return __tree_.__insert_unique(__p.__i_, __v);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1196:17: note: in instantiation of
member function 'std::__1::map<std::__1::basic_string<char>, Variant_t, std::__1::less<std::__1::basic_string<char> >,
std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> > >::insert' requested here
insert(__e.__i_, *__f);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1009:13: note: in instantiation of
function template specialization 'std::__1::map<std::__1::basic_string<char>, Variant_t, std::__1::less<std::__1::basic_string<char> >,
std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> >
>::insert<std::__1::__map_const_iterator<std::__1::__tree_const_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long> > >' requested here
insert(__m.begin(), __m.end());
^
Lancet.cc:562:31: note: in instantiation of member function 'std::__1::map<std::__1::basic_string<char>, Variant_t,
std::__1::less<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> >
>::map' requested here
map<string,Variant_t> db = (assemblers[i]->vDB).DB;
^
6 errors generated.
In file included from Graph.cc:3:
In file included from ./Graph.hh:47:
./Variant.hh:91:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Graph.cc:3:
In file included from ./Graph.hh:47:
./Variant.hh:92:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Graph.cc:3:
In file included from ./Graph.hh:47:
./Variant.hh:93:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Graph.cc:3:
In file included from ./Graph.hh:47:
./Variant.hh:94:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
Graph.cc:1167:29: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRN = {HP1RN, HP2RN, HP0RN}; // reference HP normal
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
Graph.cc:1168:29: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRT = {HP1RT, HP2RT, HP0RT}; // reference HP tumor
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
Graph.cc:1169:29: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAN = {HP1AN, HP2AN, HP0AN}; // alternative HP normal
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
Graph.cc:1170:29: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAT = {HP1AT, HP2AT, HP0AT}; // alternative HP tumor
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
8 errors generated.
In file included from Microassembler.cc:1:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:91:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Microassembler.cc:1:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:92:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Microassembler.cc:1:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:93:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Microassembler.cc:1:
In file included from ./Microassembler.hh:60:
In file included from ./Graph.hh:47:
./Variant.hh:94:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
4 errors generated.
In file included from VariantDB.cc:3:
In file included from ./VariantDB.hh:32:
./Variant.hh:91:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from VariantDB.cc:3:
In file included from ./VariantDB.hh:32:
./Variant.hh:92:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from VariantDB.cc:3:
In file included from ./VariantDB.hh:32:
./Variant.hh:93:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from VariantDB.cc:3:
In file included from ./VariantDB.hh:32:
./Variant.hh:94:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from VariantDB.cc:3:
In file included from ./VariantDB.hh:26:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:480:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:2161:45: error: static_cast
from 'std::__1::unique_ptr<std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *>,
std::__1::__tree_node_destructor<std::__1::allocator<std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>,
Variant_t>, void *> > > >::pointer' (aka 'std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *>
*') to 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__node_base_pointer' (aka 'std::__1::__tree_node_base<void *> *'), which are not related by inheritance, is not allowed
__insert_node_at(__parent, __child, static_cast<__node_base_pointer>(__h.get()));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1201:14: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_unique_key_args<std::__1::basic_string<char>, std::__1::pair<std::__1::basic_string<char>, Variant_t> >' requested here
return __emplace_unique_key_args(__x.first, _VSTD::forward<_Pp>(__x));
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1163:16: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_unique_extract_key<std::__1::pair<std::__1::basic_string<char>, Variant_t> >' requested here
return __emplace_unique_extract_key(_VSTD::forward<_Pp>(__x),
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1291:16: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_unique<std::__1::pair<std::__1::basic_string<char>, Variant_t> >' requested here
return __emplace_unique(_VSTD::forward<_Vp>(__v));
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1158:29: note: in instantiation of
function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__insert_unique<std::__1::pair<std::__1::basic_string<char>, Variant_t>, void>' requested here
{return __tree_.__insert_unique(_VSTD::forward<_Pp>(__p));}
^
VariantDB.cc:89:6: note: in instantiation of function template specialization 'std::__1::map<std::__1::basic_string<char>, Variant_t,
std::__1::less<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> >
>::insert<std::__1::pair<std::__1::basic_string<char>, Variant_t>, void>' requested here
DB.insert(pair<string,Variant_t>(key,v));
^
In file included from VariantDB.cc:3:
In file included from ./VariantDB.hh:26:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:480:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:865:62: error: cannot
initialize a member subobject of type 'std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long>::__iter_pointer' (aka
'std::__1::__tree_end_node<std::__1::__tree_node_base<void *> *> *') with an lvalue of type
'std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long>::__node_pointer' (aka
'std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *')
explicit __tree_iterator(__node_pointer __p) _NOEXCEPT : __ptr_(__p) {}
^ ~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:2165:33: note: in instantiation
of member function 'std::__1::__tree_iterator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__tree_node<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>, void *> *, long>::__tree_iterator' requested here
return pair<iterator, bool>(iterator(__r), __inserted);
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1201:14: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_unique_key_args<std::__1::basic_string<char>, std::__1::pair<std::__1::basic_string<char>, Variant_t> >' requested here
return __emplace_unique_key_args(__x.first, _VSTD::forward<_Pp>(__x));
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1163:16: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_unique_extract_key<std::__1::pair<std::__1::basic_string<char>, Variant_t> >' requested here
return __emplace_unique_extract_key(_VSTD::forward<_Pp>(__x),
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tree:1291:16: note: in instantiation
of function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__emplace_unique<std::__1::pair<std::__1::basic_string<char>, Variant_t> >' requested here
return __emplace_unique(_VSTD::forward<_Vp>(__v));
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/map:1158:29: note: in instantiation of
function template specialization 'std::__1::__tree<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::__map_value_compare<std::__1::basic_string<char>, std::__1::__value_type<std::__1::basic_string<char>, Variant_t>,
std::__1::less<std::__1::basic_string<char> >, true>, std::__1::allocator<std::__1::__value_type<std::__1::basic_string<char>, Variant_t>
> >::__insert_unique<std::__1::pair<std::__1::basic_string<char>, Variant_t>, void>' requested here
{return __tree_.__insert_unique(_VSTD::forward<_Pp>(__p));}
^
VariantDB.cc:89:6: note: in instantiation of function template specialization 'std::__1::map<std::__1::basic_string<char>, Variant_t,
std::__1::less<std::__1::basic_string<char> >, std::__1::allocator<std::__1::pair<const std::__1::basic_string<char>, Variant_t> >
>::insert<std::__1::pair<std::__1::basic_string<char>, Variant_t>, void>' requested here
DB.insert(pair<string,Variant_t>(key,v));
^
6 errors generated.
In file included from Variant.cc:1:
./Variant.hh:91:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Variant.cc:1:
./Variant.hh:92:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPRT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Variant.cc:1:
./Variant.hh:93:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAN;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
In file included from Variant.cc:1:
./Variant.hh:94:26: error: implicit instantiation of undefined template 'std::__1::array<unsigned short, 3>'
array<unsigned short,3> HPAT;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__tuple:223:64: note: template is
declared here
template <class _Tp, size_t _Size> struct _LIBCPP_TEMPLATE_VIS array;
^
4 errors generated.
make[1]: *** [lancet] Error 1
cp: lancet: No such file or directorygnarzisi commented
Thanks for reporting. I pushed a fix. The problem was due to #include <array> missing in the Variant.hh. Let me know it works now.
jkobject commented
Hello, It seems there might an error with a missing space maybe?
cd src; make; cp lancet ../; cd ../
g++ -std=c++0x -Wno-deprecated -Wall -O3 -fexceptions -g -Wl,-rpath,/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib64/ -I/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/include/bamtools -I/Users/jeremie/Documents/logiciels/lancet/htslib-1.8/ -L/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib/ -L/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib64/ -L/Users/jeremie/Documents/logiciels/lancet/htslib-1.8/ Lancet.cc Edge.cc Node.cc Graph.cc Microassembler.cc Ref.cc Path.cc ContigLink.cc align.cc util.cc sha256.cc VariantDB.cc Variant.cc -o lancet /Users/jeremie/Documents/logiciels/lancet/htslib-1.8/libhts.a -llzma -lbz2 -lz -ldl -lpthread -lcurl -lcrypto -lbamtools
ld: warning: directory not found for option '-L/Users/jeremie/Documents/logiciels/lancet/bamtools-2.5.1/lib64/'
ld: library not found for -lcrypto
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [lancet] Error 1
cp: lancet: No such file or directory
Best,
gnarzisi commented
For some reason the -lcrypto (openssl library) option is not found in your system. Can you try remove that from the Makefile? The code may compile fine also without. The new line would look like:
LDLIBS := -llzma -lbz2 -lz -ldl -lpthread -lcurl -lbamtools
gnarzisi commented
Did it work?
jkobject commented
Sorry I was away for a couple of weeks.
It worked fine!
thanks
gnarzisi commented
Great! Glad it worked. Cheers.