franciscozorrilla
commented
1 year ago Hello, just wanted to report a different dependency errors when trying to install with pip install --user bio-embeddings[all] in a clean conda environment. It seems like other in the bioembeddings chat have also encountered this issue. I tried conda installing the problematic packages jsonnet & preshed but still no luck.
```
$ conda create -n bioembed
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.7.12
latest version: 23.1.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/fz274/.conda/envs/bioembed
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate bioembed
#
# To deactivate an active environment, use
#
# $ conda deactivate
$ source activate bioembed
$ pip install bio-embeddings[all] --user^C
$ pip install --user bio-embeddings[all]
Collecting bio-embeddings[all]
Downloading bio_embeddings-0.2.2-py3-none-any.whl (105 kB)
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Collecting tqdm<5.0.0,>=4.45.0
Using cached tqdm-4.64.1-py2.py3-none-any.whl (78 kB)
Collecting lock<2019.0.0,>=2018.3.25
Downloading lock-2018.3.25.2110.tar.gz (3.0 kB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: pandas<2.0.0,>=1.2.0 in /home/fz274/.local/lib/python3.7/site-packages (from bio-embeddings[all]) (1.3.5)
Collecting atomicwrites<2.0.0,>=1.4.0
Downloading atomicwrites-1.4.1.tar.gz (14 kB)
Preparing metadata (setup.py) ... done
Collecting biopython<2.0,>=1.79
Downloading biopython-1.80-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB)
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Requirement already satisfied: matplotlib<4.0.0,>=3.2.1 in /home/fz274/.local/lib/python3.7/site-packages (from bio-embeddings[all]) (3.2.1)
Requirement already satisfied: scipy<2.0.0,>=1.4.1 in /home/fz274/.local/lib/python3.7/site-packages (from bio-embeddings[all]) (1.6.3)
Requirement already satisfied: h5py<4.0.0,>=3.2.1 in /home/fz274/.local/lib/python3.7/site-packages (from bio-embeddings[all]) (3.7.0)
Collecting torch<=1.10.0,>=1.8.0
Downloading torch-1.10.0-cp37-cp37m-manylinux1_x86_64.whl (881.9 MB)
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Collecting python-slugify<6.0.0,>=5.0.2
Downloading python_slugify-5.0.2-py2.py3-none-any.whl (6.7 kB)
Collecting humanize<4.0.0,>=3.2.0
Downloading humanize-3.14.0-py3-none-any.whl (98 kB)
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Collecting scikit-learn<0.25.0,>=0.24.0
Using cached scikit_learn-0.24.2-cp37-cp37m-manylinux2010_x86_64.whl (22.3 MB)
Requirement already satisfied: numpy<2.0.0,>=1.18.3 in /home/fz274/.local/lib/python3.7/site-packages (from bio-embeddings[all]) (1.21.6)
Collecting importlib_metadata<5.0.0,>=4.6.1
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Collecting plotly<6.0.0,>=5.1.0
Downloading plotly-5.13.0-py2.py3-none-any.whl (15.2 MB)
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Collecting umap-learn<0.6.0,>=0.5.1
Downloading umap-learn-0.5.3.tar.gz (88 kB)
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Preparing metadata (setup.py) ... done
Collecting gensim<4.0.0,>=3.8.2
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Collecting ruamel.yaml<0.18.0,>=0.17.10
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Collecting fair-esm==0.4.0
Downloading fair_esm-0.4.0-py3-none-any.whl (37 kB)
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Collecting bio-embeddings-tape-proteins==0.5
Downloading bio_embeddings_tape_proteins-0.5-py3-none-any.whl (69 kB)
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Collecting bio-embeddings-bepler==0.0.1
Downloading bio_embeddings_bepler-0.0.1.tar.gz (140 kB)
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Installing build dependencies ... done
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Preparing metadata (pyproject.toml) ... done
Collecting bio-embeddings-plus==0.1.1
Downloading bio_embeddings_PLUS-0.1.1-py3-none-any.whl (43 kB)
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Collecting bio-embeddings-cpcprot==0.0.1
Downloading bio_embeddings_CPCProt-0.0.1-py3-none-any.whl (29 kB)
Collecting transformers<5.0.0,>=4.5.0
Downloading transformers-4.26.0-py3-none-any.whl (6.3 MB)
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Collecting bio-embeddings-deepblast==0.1.0
Downloading bio_embeddings_deepblast-0.1.0-py3-none-any.whl (47.3 MB)
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Collecting bio-embeddings-allennlp==0.9.2
Downloading bio_embeddings_allennlp-0.9.2-py3-none-any.whl (7.6 MB)
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Collecting ftfy
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Collecting pytorch-transformers==1.1.0
Downloading pytorch_transformers-1.1.0-py3-none-any.whl (158 kB)
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Collecting flask-cors>=3.0.7
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Collecting overrides<5,>=4
Downloading overrides-4.1.2-py3-none-any.whl (11 kB)
Collecting parsimonious>=0.8.0
Downloading parsimonious-0.10.0-py3-none-any.whl (48 kB)
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Collecting editdistance
Downloading editdistance-0.6.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (282 kB)
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Collecting spacy<3.0,>=2.1.0
Downloading spacy-2.3.9-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
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Collecting responses>=0.7
Downloading responses-0.22.0-py3-none-any.whl (51 kB)
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Collecting pytorch-pretrained-bert>=0.6.0
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Collecting sqlparse>=0.2.4
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Collecting jsonnet>=0.10.0
Downloading jsonnet-0.19.1.tar.gz (593 kB)
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Collecting lmdb<2.0,>=1.0
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Collecting torch<=1.10.0,>=1.8.0
Downloading torch-1.9.1-cp37-cp37m-manylinux1_x86_64.whl (831.4 MB)
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Building wheels for collected packages: bio-embeddings-bepler, atomicwrites, lock, umap-learn, jax, jsonnet, pynndescent, word2number, alembic
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Created wheel for bio-embeddings-bepler: filename=bio_embeddings_bepler-0.0.1-cp37-cp37m-linux_x86_64.whl size=401794 sha256=22fea4d26ff0ddaebc9fc5f645b8847e742acb850556c187f41bdd4f5a3f601b
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Created wheel for jax: filename=jax-0.1.77-py3-none-any.whl size=516860 sha256=e31550c9f59bae6937879e4e7b86b44277acc85c2b813a390e3d17cc18c9c45b
Stored in directory: /home/fz274/.cache/pip/wheels/56/fa/4f/671e1f56d75e31d33a657975b8aee268877c74bbb99fcdd3a7
Building wheel for jsonnet (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [107 lines of output]
running bdist_wheel
running build
running build_ext
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/desugarer.cpp -o core/desugarer.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/formatter.cpp -o core/formatter.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/libjsonnet.cpp -o core/libjsonnet.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/lexer.cpp -o core/lexer.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/parser.cpp -o core/parser.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/pass.cpp -o core/pass.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/static_analysis.cpp -o core/static_analysis.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/string_utils.cpp -o core/string_utils.o
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/vm.cpp -o core/vm.o
In file included from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/config.hpp:35:0,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/substr.hpp:10,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/std/string.hpp:6,
from third_party/rapidyaml/rapidyaml/src/c4/yml/std/string.hpp:7,
from third_party/rapidyaml/rapidyaml/src/./c4/yml/std/std.hpp:4,
from third_party/rapidyaml/rapidyaml/src/ryml_std.hpp:4,
from core/vm.cpp:29:
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/compiler.hpp:90:13: error: #error "GCC < 5 is not supported"
# error "GCC < 5 is not supported"
^
In file included from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/config.hpp:37:0,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/substr.hpp:10,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/std/string.hpp:6,
from third_party/rapidyaml/rapidyaml/src/c4/yml/std/string.hpp:7,
from third_party/rapidyaml/rapidyaml/src/./c4/yml/std/std.hpp:4,
from third_party/rapidyaml/rapidyaml/src/ryml_std.hpp:4,
from core/vm.cpp:29:
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:19: error: ‘is_trivially_copyable’ is not a member of ‘std’
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:269:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeScalar);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:48: error: expected primary-expression before ‘>’ token
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:269:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeScalar);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:49: error: ‘::value’ has not been declared
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:269:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeScalar);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:19: error: ‘is_trivially_copyable’ is not a member of ‘std’
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:404:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeData);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:48: error: expected primary-expression before ‘>’ token
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:404:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeData);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:49: error: ‘::value’ has not been declared
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:404:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeData);
^
In file included from third_party/rapidyaml/rapidyaml/src/./c4/yml/./parse.hpp:13:0,
from third_party/rapidyaml/rapidyaml/src/./c4/yml/yml.hpp:7,
from third_party/rapidyaml/rapidyaml/src/ryml.hpp:4,
from core/vm.cpp:30:
third_party/rapidyaml/rapidyaml/src/c4/yml/detail/stack.hpp:22:19: error: ‘is_trivially_copyable’ is not a member of ‘std’
static_assert(std::is_trivially_copyable::value, "T must be trivially copyable");
^
third_party/rapidyaml/rapidyaml/src/c4/yml/detail/stack.hpp:22:47: error: expected primary-expression before ‘>’ token
static_assert(std::is_trivially_copyable::value, "T must be trivially copyable");
^
third_party/rapidyaml/rapidyaml/src/c4/yml/detail/stack.hpp:22:48: error: ‘::value’ has not been declared
static_assert(std::is_trivially_copyable::value, "T must be trivially copyable");
^
make: *** [core/vm.o] Error 1
Traceback (most recent call last):
File "", line 36, in
File "", line 34, in
File "/tmp/pip-install-l013a6kh/jsonnet_05895022adeb43d6b170339e4df4edc1/setup.py", line 93, in
test_suite="python._jsonnet_test",
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 192, in run
self.run_command('build')
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-l013a6kh/jsonnet_05895022adeb43d6b170339e4df4edc1/setup.py", line 68, in run
raise Exception('Could not build %s' % (', '.join(LIB_OBJECTS)))
Exception: Could not build core/desugarer.o, core/formatter.o, core/libjsonnet.o, core/lexer.o, core/parser.o, core/pass.o, core/static_analysis.o, core/string_utils.o, core/vm.o, third_party/md5/md5.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/char_traits.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/base64.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/language.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/memory_util.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/format.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/time.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/memory_resource.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/error.o, third_party/rapidyaml/rapidyaml/src/c4/yml/parse.o, third_party/rapidyaml/rapidyaml/src/c4/yml/preprocess.o, third_party/rapidyaml/rapidyaml/src/c4/yml/common.o, third_party/rapidyaml/rapidyaml/src/c4/yml/tree.o
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for jsonnet
Running setup.py clean for jsonnet
Building wheel for pynndescent (setup.py) ... done
Created wheel for pynndescent: filename=pynndescent-0.5.8-py3-none-any.whl size=55497 sha256=db4fdbf6634a4cf2e062e2f626c5668ad0329901c5bd2f6ae0cbbc39957d0031
Stored in directory: /home/fz274/.cache/pip/wheels/19/bc/eb/974072a56a7082a302f8b4be1ad6d21bf5019235c2eff65928
Building wheel for word2number (setup.py) ... done
Created wheel for word2number: filename=word2number-1.1-py3-none-any.whl size=5588 sha256=b13c22c14214102d247e760df05e2485107d25b5532eb14f06711b52dae37c13
Stored in directory: /home/fz274/.cache/pip/wheels/4b/c3/77/a5f48aeb0d3efb7cd5ad61cbd3da30bbf9ffc9662b07c9f879
Building wheel for alembic (pyproject.toml) ... done
Created wheel for alembic: filename=alembic-1.9.3-py3-none-any.whl size=210560 sha256=a07d113b3a10290f9c5567d7a3845fb96f987d081b676c0c878016600dbdb876
Stored in directory: /home/fz274/.cache/pip/wheels/1a/67/b5/a773bac3094b869c04483a1e203db696d29084fd75a85d16a6
Successfully built bio-embeddings-bepler atomicwrites lock umap-learn jax pynndescent word2number alembic
Failed to build jsonnet
Installing collected packages: word2number, wcwidth, wasabi, types-toml, tokenizers, sentencepiece, plac, lock, lmdb, jsonnet, fair-esm, cymem, conllu, bio-embeddings-bepler, unidecode, typing-utils, typing-extensions, tqdm, toml, tensorboardX, tenacity, srsly, sqlparse, ruamel.yaml, regex, pyyaml, python-slugify, murmurhash, multidict, llvmlite, ftfy, fsspec, frozenlist, flaky, editdistance, colorlog, cmaes, blis, biopython, atomicwrites, asynctest, yarl, torch, scikit-learn, responses, preshed, plotly, parsimonious, overrides, jaxlib, jax, importlib_metadata, gensim, catalogue, async-timeout, aiosignal, torchmetrics, thinc, numba, Mako, lightning-utilities, jsonpickle, humanize, huggingface-hub, flask-cors, bio-embeddings-plus, aiohttp, transformers, spacy, pynndescent, alembic, umap-learn, pytorch-transformers, pytorch-pretrained-bert, pytorch-lightning, optuna, bio-embeddings-tape-proteins, jax-unirep, bio-embeddings-deepblast, bio-embeddings-cpcprot, bio-embeddings-allennlp, bio-embeddings
Running setup.py install for jsonnet ... error
error: subprocess-exited-with-error
× Running setup.py install for jsonnet did not run successfully.
│ exit code: 1
╰─> [109 lines of output]
running install
running build
running build_ext
make: `core/desugarer.o' is up to date.
make: `core/formatter.o' is up to date.
make: `core/libjsonnet.o' is up to date.
make: `core/lexer.o' is up to date.
make: `core/parser.o' is up to date.
make: `core/pass.o' is up to date.
make: `core/static_analysis.o' is up to date.
make: `core/string_utils.o' is up to date.
g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json -Ithird_party/rapidyaml/rapidyaml/src/ -Ithird_party/rapidyaml/rapidyaml/ext/c4core/src/ core/vm.cpp -o core/vm.o
In file included from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/config.hpp:35:0,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/substr.hpp:10,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/std/string.hpp:6,
from third_party/rapidyaml/rapidyaml/src/c4/yml/std/string.hpp:7,
from third_party/rapidyaml/rapidyaml/src/./c4/yml/std/std.hpp:4,
from third_party/rapidyaml/rapidyaml/src/ryml_std.hpp:4,
from core/vm.cpp:29:
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/compiler.hpp:90:13: error: #error "GCC < 5 is not supported"
# error "GCC < 5 is not supported"
^
In file included from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/config.hpp:37:0,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/substr.hpp:10,
from third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/std/string.hpp:6,
from third_party/rapidyaml/rapidyaml/src/c4/yml/std/string.hpp:7,
from third_party/rapidyaml/rapidyaml/src/./c4/yml/std/std.hpp:4,
from third_party/rapidyaml/rapidyaml/src/ryml_std.hpp:4,
from core/vm.cpp:29:
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:19: error: ‘is_trivially_copyable’ is not a member of ‘std’
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:269:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeScalar);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:48: error: expected primary-expression before ‘>’ token
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:269:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeScalar);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:49: error: ‘::value’ has not been declared
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:269:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeScalar);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:19: error: ‘is_trivially_copyable’ is not a member of ‘std’
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:404:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeData);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:48: error: expected primary-expression before ‘>’ token
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:404:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeData);
^
third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/types.hpp:221:49: error: ‘::value’ has not been declared
static_assert(std::is_trivially_copyable::value, #ty " must be trivially copyable")
^
third_party/rapidyaml/rapidyaml/src/c4/yml/tree.hpp:404:1: note: in expansion of macro ‘C4_MUST_BE_TRIVIAL_COPY’
C4_MUST_BE_TRIVIAL_COPY(NodeData);
^
In file included from third_party/rapidyaml/rapidyaml/src/./c4/yml/./parse.hpp:13:0,
from third_party/rapidyaml/rapidyaml/src/./c4/yml/yml.hpp:7,
from third_party/rapidyaml/rapidyaml/src/ryml.hpp:4,
from core/vm.cpp:30:
third_party/rapidyaml/rapidyaml/src/c4/yml/detail/stack.hpp:22:19: error: ‘is_trivially_copyable’ is not a member of ‘std’
static_assert(std::is_trivially_copyable::value, "T must be trivially copyable");
^
third_party/rapidyaml/rapidyaml/src/c4/yml/detail/stack.hpp:22:47: error: expected primary-expression before ‘>’ token
static_assert(std::is_trivially_copyable::value, "T must be trivially copyable");
^
third_party/rapidyaml/rapidyaml/src/c4/yml/detail/stack.hpp:22:48: error: ‘::value’ has not been declared
static_assert(std::is_trivially_copyable::value, "T must be trivially copyable");
^
make: *** [core/vm.o] Error 1
Traceback (most recent call last):
File "", line 36, in
File "", line 34, in
File "/tmp/pip-install-l013a6kh/jsonnet_05895022adeb43d6b170339e4df4edc1/setup.py", line 93, in
test_suite="python._jsonnet_test",
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run
return orig.install.run(self)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/command/install.py", line 545, in run
self.run_command('build')
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/software/anaconda/3.2019-10/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-l013a6kh/jsonnet_05895022adeb43d6b170339e4df4edc1/setup.py", line 68, in run
raise Exception('Could not build %s' % (', '.join(LIB_OBJECTS)))
Exception: Could not build core/desugarer.o, core/formatter.o, core/libjsonnet.o, core/lexer.o, core/parser.o, core/pass.o, core/static_analysis.o, core/string_utils.o, core/vm.o, third_party/md5/md5.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/char_traits.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/base64.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/language.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/memory_util.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/format.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/time.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/memory_resource.o, third_party/rapidyaml/rapidyaml/ext/c4core/src/c4/error.o, third_party/rapidyaml/rapidyaml/src/c4/yml/parse.o, third_party/rapidyaml/rapidyaml/src/c4/yml/preprocess.o, third_party/rapidyaml/rapidyaml/src/c4/yml/common.o, third_party/rapidyaml/rapidyaml/src/c4/yml/tree.o
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> jsonnet
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
WARNING: You are using pip version 22.0.4; however, version 23.0 is available.
You should consider upgrading via the '/usr/local/software/anaconda/3.2019-10/bin/python -m pip install --upgrade pip' command.
```
I also tried installing with conda conda install bio-embeddings[all] but then I am not able to import any of the embedders, e.g. from bio_embeddings.embed import SeqVecEmbedder results in an error.
$ python
Python 3.10.9 | packaged by conda-forge | (main, Feb 2 2023, 20:20:04) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import bio_embeddings
from bio_embeddings.embed import SeqVecEmbedder
>>> from bio_embeddings.embed import SeqVecEmbedder
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: cannot import name 'SeqVecEmbedder' from 'bio_embeddings.embed' (/home/fz274/.conda/envs/bioembed/lib/python3.10/site-packages/bio_embeddings/embed/__init__.py)I also tried installing in a clean env from the github repo pip install -U "bio-embeddings[all] @ git+https://github.com/sacdallago/bio_embeddings.git" but I get a different set of errors
$ pip install --user "bio-embeddings[all] @ git+https://github.com/sacdallago/bio_embeddings.git"
Collecting bio-embeddings[all]@ git+https://github.com/sacdallago/bio_embeddings.git
Cloning https://github.com/sacdallago/bio_embeddings.git to /tmp/pip-install-7cq3takv/bio-embeddings_5bc5bd015c164f77bf75251562236a85
Running command git clone --filter=blob:none --quiet https://github.com/sacdallago/bio_embeddings.git /tmp/pip-install-7cq3takv/bio-embeddings_5bc5bd015c164f77bf75251562236a85
Resolved https://github.com/sacdallago/bio_embeddings.git to commit efb9801f0de9b9d51d19b741088763a7d2d0c3a2
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting flask-cors<4.0.0,>=3.0.10
Using cached Flask_Cors-3.0.10-py2.py3-none-any.whl (14 kB)
Collecting plotly<6.0.0,>=5.8.0
Using cached plotly-5.13.0-py2.py3-none-any.whl (15.2 MB)
Collecting ruamel.yaml<0.18.0,>=0.17.10
Using cached ruamel.yaml-0.17.21-py3-none-any.whl (109 kB)
ERROR: Ignored the following versions that require a different python version: 1.4.0 Requires-Python >=3.8; 1.4.0rc0 Requires-Python >=3.8; 1.4.1 Requires-Python >=3.8; 1.4.2 Requires-Python >=3.8; 1.4.3 Requires-Python >=3.8; 1.4.4 Requires-Python >=3.8; 1.5.0 Requires-Python >=3.8; 1.5.0rc0 Requires-Python >=3.8; 1.5.1 Requires-Python >=3.8; 1.5.2 Requires-Python >=3.8; 1.5.3 Requires-Python >=3.8
ERROR: Could not find a version that satisfies the requirement pandas<2.0.0,>=1.4.2 (from bio-embeddings[all]) (from versions: 0.1, 0.2, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.6.0, 0.6.1, 0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.8.0, 0.8.1, 0.9.0, 0.9.1, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 0.19.2, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21.0, 0.21.1, 0.22.0, 0.23.0, 0.23.1, 0.23.2, 0.23.3, 0.23.4, 0.24.0, 0.24.1, 0.24.2, 0.25.0, 0.25.1, 0.25.2, 0.25.3, 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.1.0, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.2.4, 1.2.5, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.3.4, 1.3.5)
ERROR: No matching distribution found for pandas<2.0.0,>=1.4.2Any assistance with these issues would be greatly appreciated. Thanks and best wishes, Francisco
ddofer
Lsz-20
Hello bio_embeddings team,
Thank you for your amazing contribution. It is great to be able to easily use LLMs trained on bio data and perform further research.
I've used the library in the past (approx. 1 year ago) and currently I am trying to re-use it in my research.
The issue is that currently the:
pip install .or thepip install bio-embeddings[all]doesn't work for me, even on a completely new, clean virtual environment.When pip installing bio-embeddings[all] I'm getting the error below:
When pip installing with
pip install .( using poetry)Manually trying to change the package versions to fit the reqs, breaks other things... Is this something you have observed?
Thank you in advance for any help!