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pytries / datrie

Fast, efficiently stored Trie for Python. Uses libdatrie.
http://pypi.python.org/pypi/datrie/
GNU Lesser General Public License v2.1
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Installing datrie fails with gcc14 #101

Open vandalt opened 4 months ago

vandalt commented 4 months ago

Installation fails with gcc14 on Archlinux, it seems #99 fixes the issue, but I wanted to open an issue just in case others encountered the issue.

  error: subprocess-exited-with-error

  × Building wheel for datrie (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [75 lines of output]
      running bdist_wheel
      running build
      running build_clib
      building 'datrie' library
      creating build
      creating build/temp.linux-x86_64-cpython-312
      creating build/temp.linux-x86_64-cpython-312/libdatrie
      creating build/temp.linux-x86_64-cpython-312/libdatrie/datrie
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -c libdatrie/datrie/alpha-map.c -o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/alpha-map.o
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -c libdatrie/datrie/darray.c -o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/darray.o
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -c libdatrie/datrie/dstring.c -o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/dstring.o
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -c libdatrie/datrie/fileutils.c -o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/fileutils.o
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -c libdatrie/datrie/tail.c -o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/tail.o
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -c libdatrie/datrie/trie-string.c -o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie-string.o
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -c libdatrie/datrie/trie.c -o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie.o
      ar rcs build/temp.linux-x86_64-cpython-312/libdatrie.a build/temp.linux-x86_64-cpython-312/libdatrie/datrie/alpha-map.o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/darray.o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/dstring.o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/fileutils.o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/tail.o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie-string.o build/temp.linux-x86_64-cpython-312/libdatrie/datrie/trie.o
      running build_ext
      building 'datrie' extension
      creating build/temp.linux-x86_64-cpython-312/src
      gcc -fno-strict-overflow -DNDEBUG -g -O3 -Wall -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -ffat-lto-objects -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -march=x86-64 -mtune=generic -O3 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=3 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -g -ffile-prefix-map=/build/python/src=/usr/src/debug/python -flto=auto -fPIC -Ilibdatrie -I/home/vandal/repos/learning/showyourwork-learn/venv/include -I/usr/include/python3.12 -c src/datrie.c -o build/temp.linux-x86_64-cpython-312/src/datrie.o
      src/datrie.c: In function ‘__pyx_pf_6datrie_8BaseTrie___init__’:
      src/datrie.c:5673:53: error: passing argument 1 of ‘trie_new’ from incompatible pointer type [-Wincompatible-pointer-types]
       5673 |   __pyx_v_self->_c_trie = trie_new(__pyx_v_alpha_map->_c_alpha_map);
            |                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                                     |
            |                                                     struct AlphaMap *
      In file included from src/datrie.c:1248:
      src/../libdatrie/datrie/trie.h:120:35: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
        120 | Trie *  trie_new (const AlphaMap *alpha_map);
            |                   ~~~~~~~~~~~~~~~~^~~~~~~~~
      src/datrie.c: In function ‘__pyx_pf_6datrie_8BaseTrie_6clear’:
      src/datrie.c:6351:47: error: passing argument 1 of ‘trie_new’ from incompatible pointer type [-Wincompatible-pointer-types]
       6351 |   __pyx_v__c_trie = trie_new(__pyx_v_alpha_map->_c_alpha_map);
            |                              ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                               |
            |                                               struct AlphaMap *
      src/../libdatrie/datrie/trie.h:120:35: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
        120 | Trie *  trie_new (const AlphaMap *alpha_map);
            |                   ~~~~~~~~~~~~~~~~^~~~~~~~~
      src/datrie.c: In function ‘__pyx_pf_6datrie_8AlphaMap___cinit__’:
      src/datrie.c:27404:30: error: assignment to ‘struct AlphaMap *’ from incompatible pointer type ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} [-Wincompatible-pointer-types]
      27404 |   __pyx_v_self->_c_alpha_map = alpha_map_new();
            |                              ^
      src/datrie.c: In function ‘__pyx_pf_6datrie_8AlphaMap_2__dealloc__’:
      src/datrie.c:27460:32: error: passing argument 1 of ‘alpha_map_free’ from incompatible pointer type [-Wincompatible-pointer-types]
      27460 |     alpha_map_free(__pyx_v_self->_c_alpha_map);
            |                    ~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                |
            |                                struct AlphaMap *
      In file included from src/datrie.c:1247:
      src/../libdatrie/datrie/alpha-map.h:72:39: note: expected ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
         72 | void        alpha_map_free (AlphaMap *alpha_map);
            |                             ~~~~~~~~~~^~~~~~~~~
      src/datrie.c: In function ‘__pyx_f_6datrie_8AlphaMap_copy’:
      src/datrie.c:27875:61: error: passing argument 1 of ‘alpha_map_clone’ from incompatible pointer type [-Wincompatible-pointer-types]
      27875 |   __pyx_v_clone->_c_alpha_map = alpha_map_clone(__pyx_v_self->_c_alpha_map);
            |                                                 ~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                                             |
            |                                                             struct AlphaMap *
      src/../libdatrie/datrie/alpha-map.h:70:46: note: expected ‘const AlphaMap *’ {aka ‘const struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
         70 | AlphaMap *  alpha_map_clone (const AlphaMap *a_map);
            |                              ~~~~~~~~~~~~~~~~^~~~~
      src/datrie.c:27875:31: error: assignment to ‘struct AlphaMap *’ from incompatible pointer type ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} [-Wincompatible-pointer-types]
      27875 |   __pyx_v_clone->_c_alpha_map = alpha_map_clone(__pyx_v_self->_c_alpha_map);
            |                               ^
      src/datrie.c: In function ‘__pyx_f_6datrie_8AlphaMap__add_range’:
      src/datrie.c:28566:50: error: passing argument 1 of ‘alpha_map_add_range’ from incompatible pointer type [-Wincompatible-pointer-types]
      28566 |   __pyx_v_code = alpha_map_add_range(__pyx_v_self->_c_alpha_map, __pyx_v_begin, __pyx_v_end);
            |                                      ~~~~~~~~~~~~^~~~~~~~~~~~~~
            |                                                  |
            |                                                  struct AlphaMap *
      src/../libdatrie/datrie/alpha-map.h:74:45: note: expected ‘AlphaMap *’ {aka ‘struct _AlphaMap *’} but argument is of type ‘struct AlphaMap *’
         74 | int         alpha_map_add_range (AlphaMap  *alpha_map,
            |                                  ~~~~~~~~~~~^~~~~~~~~
      error: command '/usr/bin/gcc' failed with exit code 1
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for datrie
Failed to build datrie
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (datrie)
sanjayankur31 commented 4 months ago

Hello, can someone please merge the notedPR and make a new release? Anything using datrie is now uninstallable on systems with GCC 14 (snakemake is an example).

sanjayankur31 commented 4 months ago

A workaround is to set CFLAGS and CXXFLAGS to downgrade the gcc error:

export CFLAGS="-Wno-error=incompatible-pointer-types" ; export CXXFLAGS="-Wno-error=incompatible-pointer-types" ; pip install datrie
psteinb commented 3 weeks ago

This affects me as well on fedora fc40. Would be cool to merge a fix, as it appears to be available with #99

nylocx commented 6 days ago

With the last commit beeing 4 years old this feels a bit dead. Anyone with a good suggestion for a tri library to switch to?