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installation problem #176

Open
smurph50 opened this issue May 15, 2023 · 4 comments · May be fixed by #192 or fulcrumgenomics/regtools#1
Open

installation problem #176

smurph50 opened this issue May 15, 2023 · 4 comments · May be fixed by #192 or fulcrumgenomics/regtools#1

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@smurph50
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When I run make after successfully running the previous commands, I get a bunch of errors. Here are the important lines. I am running Monterey 12.5 with an arm M1 Max chip. Any thoughts on how to fix this would be appreciated

/Users/me/build/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id

/Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk/usr/include/c++/v1/__threading_support:457:44: error: use of undeclared identifier '__error'

fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [src/variants/CMakeFiles/variants.dir/variants_main.cc.o] Error 1
make[1]: *** [src/variants/CMakeFiles/variants.dir/all] Error 2
make: *** [all] Error
@kcotto
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Contributor

kcotto commented May 18, 2023

Hi @smurph50, just wanted to let you know that I'm looking into this. I think this relates to the new Mac chips (M1/M2). Are you able to temporarily use the docker image while I troubleshoot this?

@chesi
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chesi commented Jun 21, 2023

I have the same problem. I have the new Mac chips.

@angela-tarantula
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Also can't "make" without those errors, have Mac M1 Pro

@TimD1 TimD1 mentioned this issue Sep 19, 2024
Closed
TimD1 added a commit to fulcrumgenomics/regtools that referenced this issue Sep 19, 2024
@TimD1
fix: CMake build errors on Mac resolved
435e8b8 
 - closes griffithlab#176, CMake was including `src/utils/bedtools/gzstream/version`
   as a C++ source file, when it was a simple text file containing version info
 - I moved this version info into `src/utils/bedtools/gzstream/README`
@TimD1 TimD1 linked a pull request Sep 19, 2024 that will close this issue
Open
@santataRU
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I followed the instructions. However, I failed my installation with similar issues. I am using Mac Sonoma 14.7 with an M3 chip. Error messages attached:

(base) xiaolei@Xiaos-Laptop build % make
[ 1%] Building CXX object src/variants/CMakeFiles/variants.dir/variants_main.cc.o
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:38:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__compare/compare_three_way.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__compare/three_way_comparable.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__compare/common_comparison_category.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:41:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:24:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocation_guard.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocator_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/construct_at.h:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/new:98:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:24:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocation_guard.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocator_traits.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/construct_at.h:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/new:397:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/type_traits:540:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:24:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocation_guard.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocator_traits.h:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/pointer_traits.h:63:27: error: reference to unresolved using declaration
63 | typedef _LIBCPP_NODEBUG ptrdiff_t type;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:24:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocation_guard.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocator_traits.h:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/pointer_traits.h:144:11: error: reference to unresolved using declaration
144 | typedef ptrdiff_t difference_type;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:24:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocation_guard.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocator_traits.h:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/limits:117:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:25:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocator.h:107:11: error: reference to unresolved using declaration
107 | typedef ptrdiff_t difference_type;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:25:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/allocator.h:187:11: error: reference to unresolved using declaration
187 | typedef ptrdiff_t difference_type;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:32:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/uninitialized_algorithms.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__algorithm/copy.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__algorithm/copy_move_common.h:12:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__algorithm/iterator_operations.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__algorithm/ranges_iterator_concept.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__iterator/concepts.h:31:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__iterator/iter_move.h:15:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__iterator/iterator_traits.h:408:11: error: reference to unresolved using declaration
408 | typedef ptrdiff_t difference_type;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/shared_ptr.h:32:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory/uninitialized_algorithms.h:19:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__iterator/reverse_iterator.h:23:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__iterator/iterator.h:22:57: error: reference to unresolved using declaration
22 | template <class _Category, class _Tp, class _Distance = ptrdiff_t, class _Pointer = _Tp*, class _Reference = _Tp&>
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:594:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/tuple:267:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:594:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/tuple:272:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/compare:145:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__compare/partial_order.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__compare/weak_order.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__compare/strong_order.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cmath:317:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:594:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/tuple:272:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/compare:158:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:594:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/tuple:1455:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/exception:86:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:594:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/tuple:1456:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iosfwd:119:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:594:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:20:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/tuple:1460:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/utility:270:
/Users/xiaolei/regtools/src/variants/../utils/bedtools/gzstream/version:1:1: error: expected unqualified-id
1 | 1.5 (08 Jan 2003)
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:600:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__string/char_traits.h:628:9: error: reference to unresolved using declaration
628 | const ptrdiff_t __len2 = __last2 - __first2;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
In file included from /Users/xiaolei/regtools/src/variants/variants_main.cc:25:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/iostream:43:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/ios:223:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__locale:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/string:600:
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/__string/char_traits.h:632:3: error: reference to unresolved using declaration
632 | ptrdiff_t __len1 = __last1 - __first1;
| ^
/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/c++/v1/cstddef:60:1: note: using declaration annotated with 'using_if_exists' here
60 | using ::ptrdiff_t _LIBCPP_USING_IF_EXISTS;
| ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [src/variants/CMakeFiles/variants.dir/variants_main.cc.o] Error 1
make[1]: *** [src/variants/CMakeFiles/variants.dir/all] Error 2
make: *** [all] Error 2

@TimD1 TimD1 linked a pull request Oct 31, 2024 that will close this issue
Open
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@chesi @kcotto @santataRU @angela-tarantula @smurph50