Install issue - optional and variadic templates #22

seryrzu · 2022-07-07T18:46:59Z

Reported in #1 (comment) by @yangxiaofeill

Copied below

[85%] Building CXX object src/projects/veritymap/CMakeFiles/veritymap.dir/veritymap.cpp.o
In file included from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/veritymap.hpp:12,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/veritymap.cpp:5:
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sequences/seqio.hpp:48:33: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
   48 | class SeqIterator : public std::iterator<std::forward_iterator_tag, Sequence, size_t, Sequence *, Sequence &> {
      |                                 ^~~~~~~~
In file included from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_construct.h:61,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/char_traits.h:46,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/string:40,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/stdexcept:39,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/system_error:41,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/std_mutex.h:39,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/atomic_wait.h:49,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/atomic_base.h:41,
                 from /data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/atomic:41,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/tools/common/parallel.h:5,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/veritymap.hpp:7:
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/sketch/common.h:58,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/sketch/update.h:3,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/sketch/ccm.h:6,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/kmer_index/kmer_filter.hpp:9,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/kmer_index/approx_kmer_indexer.hpp:12,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/kmer_index/target_indexer.hpp:12,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/veritymap.hpp:19:
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/sketch/./div.h:150:54: error: expected ')' before '&&' token
  150 |     template<typename...Args>Schismatic<int32_t>(Args &&...args):
      |                                                 ~    ^~~
      |                                                      )
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/sketch/./div.h:154:54: error: expected ')' before '&&' token
  154 |     template<typename...Args>Schismatic<int64_t>(Args &&...args):
      |                                                 ~    ^~~
      |                                                      )
In file included from /data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_vector.hpp:8,
                 from /data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/sketch/ccm.h:8:
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:336:25: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  336 |   typedef typename std::iterator<std::random_access_iterator_tag, IDX>::difference_type difference_type;
      |                         ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp: In member function 'void compact::iterator_imp::common<Derived, IDX, BITS, W, UB>::set_bits(W, unsigned int)':
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:510:25: warning: expected 'template' keyword before dependent template name [-Wmissing-template-keyword]
  510 |     gs<W, BITS, W, UB>::set<TS>(x, self.ptr, bits, self.offset);
      |                         ^~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp: At global scope:
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:676:17: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  676 |     public std::iterator<std::random_access_iterator_tag, IDX>,
      |                 ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:688:16: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  688 |   typedef std::iterator<std::random_access_iterator_tag, IDX> super;
      |                ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:723:15: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  723 |   public std::iterator<std::random_access_iterator_tag, const IDX>,
      |               ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:735:16: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  735 |   typedef std::iterator<std::random_access_iterator_tag, IDX> super;
      |                ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:762:17: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  762 |     public std::iterator<std::random_access_iterator_tag, IDX>,
      |                 ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:773:16: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  773 |   typedef std::iterator<std::random_access_iterator_tag, IDX> super;
      |                ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:810:15: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  810 |   public std::iterator<std::random_access_iterator_tag, const IDX>,
      |               ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/tools/sketch/./include/compact_vector/compact_iterator.hpp:821:16: warning: 'template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator' is deprecated [-Wdeprecated-declarations]
  821 |   typedef std::iterator<std::random_access_iterator_tag, IDX> super;
      |                ^~~~~~~~
/data/home/xfyang/software/miniconda3/envs/gcc-9/x86_64-conda-linux-gnu/include/c++/12.1.0/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/veritymap.hpp:20:
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp:33:22: error: 'optional' in namespace 'std' does not name a template type
   33 |   [[nodiscard]] std::optional<chaining::Chain> MapSingleQuery(const Contig &query,
      |                      ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp:1:1: note: 'std::optional' is defined in header '<optional>'; did you forget to '#include <optional>'?
  +++ |+#include <optional>
    1 | //
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp: In lambda function:
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp:103:12: error: 'optional' is not a member of 'std'
  103 |       std::optional<chaining::Chain> chain = MapSingleQuery(query, indexed_targets);
      |            ^~~~~~~~
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp:103:12: note: 'std::optional' is defined in header '<optional>'; did you forget to '#include <optional>'?
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp:103:36: error: expected primary-expression before '>' token
  103 |       std::optional<chaining::Chain> chain = MapSingleQuery(query, indexed_targets);
      |                                    ^
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp:103:38: error: 'chain' was not declared in this scope; did you mean 'chainer'?
  103 |       std::optional<chaining::Chain> chain = MapSingleQuery(query, indexed_targets);
      |                                      ^~~~~
      |                                      chainer
/data/home/xfyang/software/VerityMap/veritymap/src/projects/veritymap/mapper.hpp:103:46: error: 'MapSingleQuery' was not declared in this scope; did you mean 'MapSingleQueryStrand'?
  103 |       std::optional<chaining::Chain> chain = MapSingleQuery(query, indexed_targets);
      |                                              ^~~~~~~~~~~~~~
      |                                              MapSingleQueryStrand
make[3]: *** [src/projects/veritymap/CMakeFiles/veritymap.dir/veritymap.cpp.o] Error 1
make[3]: Leaving directory `/data/home/xfyang/software/VerityMap/veritymap/build'
make[2]: *** [src/projects/veritymap/CMakeFiles/veritymap.dir/all] Error 2
make[2]: Leaving directory `/data/home/xfyang/software/VerityMap/veritymap/build'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/data/home/xfyang/software/VerityMap/veritymap/build'
make: *** [veritymap] Error 2

The text was updated successfully, but these errors were encountered:

seryrzu · 2022-07-07T18:51:00Z

I committed a change that should be fixing the issue with optional in this branch: https://github.com/ablab/VerityMap/commits/install_bugfix

Not sure what is going on with variadic templates part inside the sketch library. Let me think a bit more about it.

seryrzu · 2022-07-07T18:57:15Z

Which exact version of compiler do you use @yangxiaofeill? I see that it seems to be generally g++-9 which suprises me because we have a github action that checks that the tool compiles and it runs on 9.4.0:

See
https://github.com/ablab/VerityMap/runs/7239623448?check_suite_focus=true

-- The C compiler identification is GNU 9.4.0
-- The CXX compiler identification is GNU 9.4.0

IceFreez3r · 2022-09-20T11:15:49Z

Hey, I ran across almost the same error while building. Your fix branch reduced the error to this

[ 85%] Building CXX object src/projects/veritymap/CMakeFiles/veritymap.dir/veritymap.cpp.o
In file included from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/tools/sketch/./include/sketch/common.h:58,
                 from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/tools/sketch/./include/sketch/update.h:3,
                 from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/tools/sketch/./include/sketch/ccm.h:6,
                 from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/projects/veritymap/kmer_index/kmer_filter.hpp:9,
                 from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/projects/veritymap/kmer_index/approx_kmer_indexer.hpp:12,
                 from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/projects/veritymap/kmer_index/target_indexer.hpp:12,
                 from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/projects/veritymap/veritymap.hpp:19,
                 from /mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/projects/veritymap/veritymap.cpp:5:
/mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/tools/sketch/./include/sketch/./div.h:150:54: error: expected ')' before '&&' token
  150 |     template<typename...Args>Schismatic<int32_t>(Args &&...args):
      |                                                 ~    ^~~
      |                                                      )
/mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/src/tools/sketch/./include/sketch/./div.h:154:54: error: expected ')' before '&&' token
  154 |     template<typename...Args>Schismatic<int64_t>(Args &&...args):
      |                                                 ~    ^~~
      |                                                      )
make[3]: *** [src/projects/veritymap/CMakeFiles/veritymap.dir/build.make:76: src/projects/veritymap/CMakeFiles/veritymap.dir/veritymap.cpp.o] Error 1
make[3]: Leaving directory '/mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/build'
make[2]: *** [CMakeFiles/Makefile2:269: src/projects/veritymap/CMakeFiles/veritymap.dir/all] Error 2
make[2]: Leaving directory '/mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/build'
make[1]: *** [Makefile:91: all] Error 2
make[1]: Leaving directory '/mnt/data/Studium/Forschungspraktikum/code/VerityMap/veritymap/build'
make: *** [Makefile:12: veritymap] Error 2

as 'predicted' by you.
I tested it with both gcc/g++ v9.4 and v11.2 using conda. Same error for both versions.

seryrzu changed the title ~~Install issue~~ Install issue - optional and variadic templates Jul 7, 2022

seryrzu mentioned this issue Jul 7, 2022

Install problem #1

Closed

jeizenga linked a pull request Jun 15, 2023 that will close this issue

Fix compilation on centOS with gcc 11.2.0 #27

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Install issue - optional and variadic templates #22

Install issue - optional and variadic templates #22

seryrzu commented Jul 7, 2022 •

edited

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seryrzu commented Jul 7, 2022

seryrzu commented Jul 7, 2022

IceFreez3r commented Sep 20, 2022

Install issue - optional and variadic templates #22

Install issue - optional and variadic templates #22

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seryrzu commented Jul 7, 2022 • edited Loading

seryrzu commented Jul 7, 2022

seryrzu commented Jul 7, 2022

IceFreez3r commented Sep 20, 2022

seryrzu commented Jul 7, 2022 •

edited

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