'numpy' has no attribute 'typeDict' #310
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@w2wewwww are you a spam bot? |
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If I switch to My conda env: conda env |
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Interesting I’ve never gotten these before. I’ll try to figure it out.
…On Fri, Sep 6, 2024 at 12:33 AM Nick Youngblut ***@***.***> wrote:
If I switch to numpy==1.22.4, the numpy error is fixed, but I instead get:
Traceback (most recent call last):
File "/home/nickyoungblut/miniforge3/envs/ensembl/bin/pyensembl", line 10, in <module>
sys.exit(run())
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/pyensembl/shell.py", line 281, in run
genome.index(overwrite=args.overwrite)
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/pyensembl/genome.py", line 280, in index
self.db.connect_or_create(overwrite=overwrite)
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/pyensembl/database.py", line 286, in connect_or_create
return self.create(overwrite=overwrite)
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/pyensembl/database.py", line 239, in create
self._connection = datacache.db_from_dataframes_with_absolute_path(
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/datacache/database_helpers.py", line 176, in db_from_dataframes_with_absolute_path
tables = build_tables(
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/datacache/database_helpers.py", line 136, in build_tables
table = DatabaseTable.from_dataframe(
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/datacache/database_table.py", line 56, in from_dataframe
column_db_type = db_type(values.dtype)
File "/home/nickyoungblut/miniforge3/envs/ensembl/lib/python3.9/site-packages/datacache/database_types.py", line 96, in db_type
raise ValueError("Failed to find sqlite3 column type for %s" % (
ValueError: Failed to find sqlite3 column type for category
My conda env:
conda env
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
astroid 3.2.4 py39hf3d152e_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
aws-c-auth 0.7.27 hc36b679_0 conda-forge
aws-c-cal 0.7.4 h2abdd08_0 conda-forge
aws-c-common 0.9.27 h4bc722e_0 conda-forge
aws-c-compression 0.2.19 haa50ccc_0 conda-forge
aws-c-event-stream 0.4.3 h570d160_0 conda-forge
aws-c-http 0.8.8 h9b61739_1 conda-forge
aws-c-io 0.14.18 h49c7fd3_7 conda-forge
aws-c-mqtt 0.10.4 h5c8269d_18 conda-forge
aws-c-s3 0.6.5 h9204347_0 conda-forge
aws-c-sdkutils 0.1.19 h038f3f9_2 conda-forge
aws-checksums 0.1.18 h038f3f9_10 conda-forge
aws-crt-cpp 0.28.2 h6552c9e_2 conda-forge
aws-sdk-cpp 1.11.379 hc1bef60_8 conda-forge
azure-core-cpp 1.13.0 h935415a_0 conda-forge
azure-identity-cpp 1.8.0 hd126650_2 conda-forge
azure-storage-blobs-cpp 12.12.0 hd2e3451_0 conda-forge
azure-storage-common-cpp 12.7.0 h10ac4d7_1 conda-forge
azure-storage-files-datalake-cpp 12.11.0 h325d260_1 conda-forge
biopython 1.84 py39hd3abc70_0 conda-forge
brotli-python 1.1.0 py39hf88036b_2 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.33.1 heb4867d_0 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
certifi 2024.8.30 pyhd8ed1ab_0 conda-forge
cffi 1.17.1 py39h15c3d72_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
datacache 1.1.5 py_0 conda-forge
debugpy 1.8.5 py39hf88036b_1 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
dill 0.3.8 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
executing 2.1.0 pyhd8ed1ab_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
glog 0.7.1 hbabe93e_0 conda-forge
gtfparse 2.5.0 pyh7cba7a3_0 bioconda
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 75.1 he02047a_0 conda-forge
idna 3.8 pyhd8ed1ab_0 conda-forge
importlib-metadata 8.4.0 pyha770c72_0 conda-forge
importlib_metadata 8.4.0 hd8ed1ab_0 conda-forge
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 8.18.1 pyh707e725_3 conda-forge
isort 5.13.2 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.2 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py39hf3d152e_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
libabseil 20240116.2 cxx17_he02047a_1 conda-forge
libarrow 17.0.0 h8d2e343_13_cpu conda-forge
libarrow-acero 17.0.0 h5888daf_13_cpu conda-forge
libarrow-dataset 17.0.0 h5888daf_13_cpu conda-forge
libarrow-substrait 17.0.0 hf54134d_13_cpu conda-forge
libblas 3.9.0 23_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hb9d3cd8_2 conda-forge
libbrotlidec 1.1.0 hb9d3cd8_2 conda-forge
libbrotlienc 1.1.0 hb9d3cd8_2 conda-forge
libcblas 3.9.0 23_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.9.1 hdb1bdb2_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.1.0 h77fa898_1 conda-forge
libgcc-ng 14.1.0 h69a702a_1 conda-forge
libgfortran 14.1.0 h69a702a_1 conda-forge
libgfortran-ng 14.1.0 h69a702a_1 conda-forge
libgfortran5 14.1.0 hc5f4f2c_1 conda-forge
libgomp 14.1.0 h77fa898_1 conda-forge
libgoogle-cloud 2.28.0 h26d7fe4_0 conda-forge
libgoogle-cloud-storage 2.28.0 ha262f82_0 conda-forge
libgrpc 1.62.2 h15f2491_0 conda-forge
libiconv 1.17 hd590300_2 conda-forge
liblapack 3.9.0 23_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_hac2b453_1 conda-forge
libparquet 17.0.0 h39682fd_13_cpu conda-forge
libprotobuf 4.25.3 h08a7969_0 conda-forge
libre2-11 2023.09.01 h5a48ba9_2 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.46.1 hadc24fc_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.1.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.1.0 h4852527_1 conda-forge
libthrift 0.20.0 h0e7cc3e_1 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 he7c6b58_4 conda-forge
libzlib 1.3.1 h4ab18f5_1 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mccabe 0.7.0 pyhd8ed1ab_0 conda-forge
memoized-property 1.0.3 py_0 conda-forge
mock 5.1.0 pyhd8ed1ab_0 conda-forge
ncurses 6.5 he02047a_1 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
numpy 1.22.4 py39hc58783e_0 conda-forge
openssl 3.3.2 hb9d3cd8_0 conda-forge
orc 2.0.2 h669347b_0 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 2.2.2 py39hfc16268_1 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pip 24.2 pyh8b19718_1 conda-forge
platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
polars 0.20.31 py39h00d955e_1 conda-forge
progressbar33 2.4 py_0 conda-forge
prompt-toolkit 3.0.47 pyha770c72_0 conda-forge
psutil 6.0.0 py39hd3abc70_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge
pyarrow 17.0.0 py39he8689d4_1 conda-forge
pyarrow-core 17.0.0 py39h4dd629f_1_cpu conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyensembl 2.3.13 pyh7cba7a3_0 bioconda
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pylint 3.2.7 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.9.19 h0755675_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.9 5_cp39 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyzmq 26.2.0 py39h4e4fb57_2 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
s2n 1.5.1 h3400bea_0 conda-forge
serializable 0.2.1 pyhd8ed1ab_0 conda-forge
setuptools 73.0.1 pyhd8ed1ab_0 conda-forge
simplejson 3.19.3 py39h8cd3c5a_1 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.2.1 ha2e4443_0 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
tinytimer 0.0.0 py_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tomlkit 0.13.2 pyha770c72_0 conda-forge
tornado 6.4.1 py39h8cd3c5a_1 conda-forge
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
typechecks 0.1.0 py_0 conda-forge
typing-extensions 4.12.2 hd8ed1ab_0 conda-forge
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024a h8827d51_1 conda-forge
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zeromq 4.3.5 ha4adb4c_5 conda-forge
zipp 3.20.1 pyhd8ed1ab_0 conda-forge
zstandard 0.23.0 py39h08a7858_1 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
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Thanks @iskandr It appears that @w2wewwww was a spammer and deleted their comment. Their comment was instantly added after I created the issue. The content: @iskandr have you ever seen spam posts on GitHub like this before? |
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Don't post it again,it's auto spam virus |
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Unrelated to the topic. GitHub Team is aware of the issue |
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Not sure if you're still having this error. When I created my conda environment, it installed datacache 1.1.5, which is very old, and I see you have installed too. I updated it to the latest version (1.4.1) and managed to successfully create the Ensembl database
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I I have the same error, and |
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The command:
The output:
It might be necessary to explicitly set the numpy versions that actually work in the requirements.txt (e.g.,
numpy<=1.25).My conda env:
conda env
The text was updated successfully, but these errors were encountered: