8.16.0: Cannot be installed because datrie no longer builds with GCC 14 #2970
Description
Snakemake version
snakemake-8.16.0
Describe the bug
Datrie does not build with GCC 14, and this makes snakemake uninstallable.
Logs
$ python --version
Python 3.11.9
$ gcc --version
gcc (GCC) 14.1.1 20240701 (Red Hat 14.1.1-7)
Copyright (C) 2024 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
$ pip install snakemake
Collecting snakemake
Using cached snakemake-8.16.0-py3-none-any.whl.metadata (2.5 kB)
Requirement already satisfied: appdirs in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from snakemake) (1.4.4)
Collecting immutables (from snakemake)
Using cached immutables-0.20-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.6 kB)
Collecting configargparse (from snakemake)
Using cached ConfigArgParse-1.7-py3-none-any.whl.metadata (23 kB)
Collecting connection-pool>=0.0.3 (from snakemake)
Using cached connection_pool-0.0.3-py3-none-any.whl
Collecting datrie (from snakemake)
Using cached datrie-0.8.2.tar.gz (63 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Collecting docutils (from snakemake)
Using cached docutils-0.21.2-py3-none-any.whl.metadata (2.8 kB)
Collecting gitpython (from snakemake)
Using cached GitPython-3.1.43-py3-none-any.whl.metadata (13 kB)
Collecting humanfriendly (from snakemake)
Using cached humanfriendly-10.0-py2.py3-none-any.whl.metadata (9.2 kB)
Requirement already satisfied: jinja2<4.0,>=3.0 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from snakemake) (3.1.4)
Collecting jsonschema (from snakemake)
Using cached jsonschema-4.23.0-py3-none-any.whl.metadata (7.9 kB)
Collecting nbformat (from snakemake)
Using cached nbformat-5.10.4-py3-none-any.whl.metadata (3.6 kB)
Requirement already satisfied: packaging in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from snakemake) (24.1)
Requirement already satisfied: psutil in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib64/python3.11/site-packages (from snakemake) (6.0.0)
Collecting pulp<2.9,>=2.3.1 (from snakemake)
Using cached PuLP-2.8.0-py3-none-any.whl.metadata (5.4 kB)
Requirement already satisfied: pyyaml in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib64/python3.11/site-packages (from snakemake) (6.0.1)
Requirement already satisfied: requests<3.0,>=2.8.1 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from snakemake) (2.32.3)
Collecting reretry (from snakemake)
Using cached reretry-0.11.8-py2.py3-none-any.whl.metadata (5.5 kB)
Collecting smart-open<8.0,>=4.0 (from snakemake)
Using cached smart_open-7.0.4-py3-none-any.whl.metadata (23 kB)
Collecting snakemake-interface-executor-plugins<10.0,>=9.2.0 (from snakemake)
Using cached snakemake_interface_executor_plugins-9.2.0-py3-none-any.whl.metadata (7.7 kB)
Collecting snakemake-interface-common<2.0,>=1.17.0 (from snakemake)
Using cached snakemake_interface_common-1.17.2-py3-none-any.whl.metadata (760 bytes)
Collecting snakemake-interface-storage-plugins<4.0,>=3.2.3 (from snakemake)
Using cached snakemake_interface_storage_plugins-3.2.3-py3-none-any.whl.metadata (9.4 kB)
Collecting snakemake-interface-report-plugins<2.0.0,>=1.0.0 (from snakemake)
Using cached snakemake_interface_report_plugins-1.0.0-py3-none-any.whl.metadata (3.4 kB)
Collecting stopit (from snakemake)
Using cached stopit-1.1.2-py3-none-any.whl
Requirement already satisfied: tabulate in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from snakemake) (0.9.0)
Collecting throttler (from snakemake)
Using cached throttler-1.2.2-py3-none-any.whl.metadata (7.4 kB)
Collecting toposort<2.0,>=1.10 (from snakemake)
Using cached toposort-1.10-py3-none-any.whl.metadata (4.1 kB)
Collecting wrapt (from snakemake)
Using cached wrapt-1.16.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting yte<2.0,>=1.5.1 (from snakemake)
Using cached yte-1.5.4-py3-none-any.whl.metadata (3.4 kB)
Collecting dpath<3.0.0,>=2.1.6 (from snakemake)
Using cached dpath-2.2.0-py3-none-any.whl.metadata (15 kB)
Collecting conda-inject<2.0,>=1.3.1 (from snakemake)
Using cached conda_inject-1.3.2-py3-none-any.whl.metadata (855 bytes)
Requirement already satisfied: MarkupSafe>=2.0 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib64/python3.11/site-packages (from jinja2<4.0,>=3.0->snakemake) (2.1.5)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib64/python3.11/site-packages (from requests<3.0,>=2.8.1->snakemake) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from requests<3.0,>=2.8.1->snakemake) (3.7)
Requirement already satisfied: urllib3<3,>=1.21.1 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from requests<3.0,>=2.8.1->snakemake) (2.2.2)
Requirement already satisfied: certifi>=2017.4.17 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from requests<3.0,>=2.8.1->snakemake) (2024.7.4)
Collecting argparse-dataclass<3.0.0,>=2.0.0 (from snakemake-interface-common<2.0,>=1.17.0->snakemake)
Using cached argparse_dataclass-2.0.0-py3-none-any.whl.metadata (7.2 kB)
Collecting plac<2.0.0,>=1.3.4 (from yte<2.0,>=1.5.1->snakemake)
Using cached plac-1.4.3-py2.py3-none-any.whl.metadata (5.9 kB)
Collecting gitdb<5,>=4.0.1 (from gitpython->snakemake)
Using cached gitdb-4.0.11-py3-none-any.whl.metadata (1.2 kB)
Requirement already satisfied: attrs>=22.2.0 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from jsonschema->snakemake) (23.2.0)
Collecting jsonschema-specifications>=2023.03.6 (from jsonschema->snakemake)
Using cached jsonschema_specifications-2023.12.1-py3-none-any.whl.metadata (3.0 kB)
Collecting referencing>=0.28.4 (from jsonschema->snakemake)
Using cached referencing-0.35.1-py3-none-any.whl.metadata (2.8 kB)
Collecting rpds-py>=0.7.1 (from jsonschema->snakemake)
Using cached rpds_py-0.19.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB)
Collecting fastjsonschema>=2.15 (from nbformat->snakemake)
Using cached fastjsonschema-2.20.0-py3-none-any.whl.metadata (2.1 kB)
Requirement already satisfied: jupyter-core!=5.0.*,>=4.12 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from nbformat->snakemake) (5.7.2)
Requirement already satisfied: traitlets>=5.1 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from nbformat->snakemake) (5.14.3)
Collecting smmap<6,>=3.0.1 (from gitdb<5,>=4.0.1->gitpython->snakemake)
Using cached smmap-5.0.1-py3-none-any.whl.metadata (4.3 kB)
Requirement already satisfied: platformdirs>=2.5 in /home/asinha/.local/share/virtualenvs/neuroml-cap/lib/python3.11/site-packages (from jupyter-core!=5.0.*,>=4.12->nbformat->snakemake) (4.2.2)
Using cached snakemake-8.16.0-py3-none-any.whl (306 kB)
Using cached conda_inject-1.3.2-py3-none-any.whl (4.1 kB)
Using cached dpath-2.2.0-py3-none-any.whl (17 kB)
Using cached PuLP-2.8.0-py3-none-any.whl (17.7 MB)
Using cached smart_open-7.0.4-py3-none-any.whl (61 kB)
Using cached snakemake_interface_common-1.17.2-py3-none-any.whl (14 kB)
Using cached ConfigArgParse-1.7-py3-none-any.whl (25 kB)
Using cached snakemake_interface_executor_plugins-9.2.0-py3-none-any.whl (22 kB)
Using cached snakemake_interface_report_plugins-1.0.0-py3-none-any.whl (6.9 kB)
Using cached snakemake_interface_storage_plugins-3.2.3-py3-none-any.whl (14 kB)
Using cached reretry-0.11.8-py2.py3-none-any.whl (5.6 kB)
Using cached throttler-1.2.2-py3-none-any.whl (7.6 kB)
Using cached toposort-1.10-py3-none-any.whl (8.5 kB)
Using cached wrapt-1.16.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
Using cached yte-1.5.4-py3-none-any.whl (7.7 kB)
Using cached docutils-0.21.2-py3-none-any.whl (587 kB)
Using cached GitPython-3.1.43-py3-none-any.whl (207 kB)
Using cached humanfriendly-10.0-py2.py3-none-any.whl (86 kB)
Using cached immutables-0.20-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (99 kB)
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Using cached fastjsonschema-2.20.0-py3-none-any.whl (23 kB)
Using cached gitdb-4.0.11-py3-none-any.whl (62 kB)
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Using cached plac-1.4.3-py2.py3-none-any.whl (22 kB)
Using cached referencing-0.35.1-py3-none-any.whl (26 kB)
Using cached rpds_py-0.19.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (355 kB)
Using cached smmap-5.0.1-py3-none-any.whl (24 kB)
Building wheels for collected packages: datrie
Building wheel for datrie (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for datrie (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [95 lines of output]
running bdist_wheel
running build
running build_clib
building 'datrie' library
creating build
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/libdatrie
creating build/temp.linux-x86_64-cpython-311/libdatrie/datrie
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -c libdatrie/datrie/alpha-map.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/alpha-map.o
libdatrie/datrie/alpha-map.c: In function ‘alpha_map_char_to_trie’:
libdatrie/datrie/alpha-map.c:500:21: warning: comparison of integer expressions of different signedness: ‘TrieIndex’ {aka ‘int’} and ‘AlphaChar’ {aka ‘unsigned int’} [-Wsign-compare]
500 | if (alpha_begin <= ac && ac <= alpha_map->alpha_end)
| ^~
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -c libdatrie/datrie/darray.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/darray.o
libdatrie/datrie/darray.c: In function ‘da_fread’:
libdatrie/datrie/darray.c:239:22: warning: comparison of integer expressions of different signedness: ‘TrieIndex’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare]
239 | if (d->num_cells > SIZE_MAX / sizeof (DACell))
| ^
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -c libdatrie/datrie/dstring.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/dstring.o
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -c libdatrie/datrie/fileutils.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/fileutils.o
libdatrie/datrie/fileutils.c: In function ‘file_read_chars’:
libdatrie/datrie/fileutils.c:103:52: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
103 | return (fread (buff, sizeof (char), len, file) == len);
| ^~
libdatrie/datrie/fileutils.c: In function ‘file_write_chars’:
libdatrie/datrie/fileutils.c:109:53: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
109 | return (fwrite (buff, sizeof (char), len, file) == len);
| ^~
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -c libdatrie/datrie/tail.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/tail.o
libdatrie/datrie/tail.c: In function ‘tail_fread’:
libdatrie/datrie/tail.c:144:22: warning: comparison of integer expressions of different signedness: ‘TrieIndex’ {aka ‘int’} and ‘long unsigned int’ [-Wsign-compare]
144 | if (t->num_tails > SIZE_MAX / sizeof (TailBlock))
| ^
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -c libdatrie/datrie/trie-string.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie-string.o
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -c libdatrie/datrie/trie.c -o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie.o
ar rcs build/temp.linux-x86_64-cpython-311/libdatrie.a build/temp.linux-x86_64-cpython-311/libdatrie/datrie/alpha-map.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/darray.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/dstring.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/fileutils.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/tail.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie-string.o build/temp.linux-x86_64-cpython-311/libdatrie/datrie/trie.o
running build_ext
building 'datrie' extension
creating build/temp.linux-x86_64-cpython-311/src
gcc -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -fcf-protection -fexceptions -fcf-protection -fexceptions -fcf-protection -fexceptions -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -Ilibdatrie -I/home/asinha/.local/share/virtualenvs/neuroml-cap/include -I/usr/include/python3.11 -c src/datrie.c -o build/temp.linux-x86_64-cpython-311/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/lib64/ccache/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: Could not build wheels for datrie, which is required to install pyproject.toml-based projects
[notice] A new release of pip is available: 24.0 -> 24.1.2
[notice] To update, run: pip install --upgrade pip
Minimal example
N/A
Additional context
I see that datrie related issues seem to pop up again and again. Given that datrie has not seen a commit for the last 4 years and is unmaintained, perhaps it's time to look at using something else that is actively maintained?
An issue is filed at datrie here:
We're carrying the patch downstream in Fedora to make datrie build, but end users trying to install snakemake via pip etc. cannot be expected to dig up issues, apply PRs and then install software from source.