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ablab / VerityMap

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Install problem #1

Closed zhoudreames closed 3 years ago

zhoudreames commented 3 years ago

I run two steps to install TandemMapper2: Step1:conda install --file requirements.txt (this success) Step2:make (present of probem show in blow ) image

zhoudreames commented 3 years ago

@almiheenko could you help me ? thanks

almiheenko commented 3 years ago

@zhoudreames It seems that you use an old compiler and TandemMapper2 is not compatible with it. Do you use Linux system? Could you please check that you have installed gcc-9? You can do the following command: which gcc-9 If it is not installed, you can install it, i.e. through conda, asconda install -c conda-forge gcc_linux-64 (by the way, you may want to do it in a separate conda environment)

Let's assume, you have gcc-9 in /usr/bin/gcc-9. Then you should do: export CC=/usr/bin/gcc-9 export CXX=/usr/bin/g++-9

After that, you can re-run make and it should work. Please let me know if it works for you.

Alla

zhoudreames commented 3 years ago

@zhoudreames It seems that you use an old compiler and TandemMapper2 is not compatible with it. Do you use Linux system? Could you please check that you have installed gcc-9? You can do the following command: which gcc-9 If it is not installed, you can install it, i.e. through conda, asconda install -c conda-forge gcc_linux-64 (by the way, you may want to do it in a separate conda environment)

Let's assume, you have gcc-9 in /usr/bin/gcc-9. Then you should do: export CC=/usr/bin/gcc-9 export CXX=/usr/bin/g++-9

After that, you can re-run make and it should work. Please let me know if it works for you.

Alla

My computer is linux,and i dont install gcc-9. According your reconmend,i install it by using conda: "conda create -c conda-forge gcc_linux-64 -n gcc-9",then conda activate gcc-9, finally,re-run make for tandemMapper2,but it is also install error. Then,I open the bin of gcc-9 in the conda envs,there are many files,i dont know how to add it to my ~/.bashrc,Do you have any suggestions ？ image

zhoudreames commented 3 years ago

@almiheenko I am so sorry again disturb you~

zhoudreames commented 3 years ago

I have installed gcc9.10,and add it to the ~/.bashrc,but again install error when make the tandemmapper2 image

zhoudreames commented 3 years ago

image

zhoudreames commented 3 years ago

installed

yangxiaofeill commented 2 years ago

Dear author, 

   When I installed veritymap there are still errors. Please help me to address them.

Best

[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
seryrzu commented 2 years ago

Hello @yangxiaofeill, let's proceed with a new issue in https://github.com/ablab/VerityMap/issues/22