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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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'numpy' has no attribute 'typeDict' #310

Open nick-youngblut opened 2 months ago

nick-youngblut commented 2 months ago

The command:

pyensembl install --release 104 --species homo_sapiens

The output:

2024-09-05 20:37:25,680 - pyensembl.shell - INFO - Running 'install' for EnsemblRelease(release=104, species='homo_sapiens')
2024-09-05 20:37:25,680 - pyensembl.download_cache - INFO - Fetching /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.104.gtf.gz from URL https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz
2024-09-05 20:37:25,683 - datacache.download - INFO - Downloading https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz to /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.104.gtf.gz
2024-09-05 20:38:36,538 - pyensembl.download_cache - INFO - Fetching /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.cdna.all.fa.gz from URL https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
2024-09-05 20:38:36,538 - datacache.download - INFO - Downloading https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz to /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.cdna.all.fa.gz
2024-09-05 20:40:21,989 - pyensembl.download_cache - INFO - Fetching /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.ncrna.fa.gz from URL https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz
2024-09-05 20:40:21,990 - datacache.download - INFO - Downloading https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz to /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.ncrna.fa.gz
2024-09-05 20:40:45,914 - pyensembl.download_cache - INFO - Fetching /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.pep.all.fa.gz from URL https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz
2024-09-05 20:40:45,915 - datacache.download - INFO - Downloading https://ftp.ensembl.org/pub/release-104/fasta/homo_sapiens/pep/Homo_sapiens.GRCh38.pep.all.fa.gz to /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.pep.all.fa.gz
2024-09-05 20:41:06,638 - pyensembl.database - INFO - Creating database: /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.104.gtf.db
2024-09-05 20:41:06,638 - pyensembl.database - INFO - Reading GTF from /home/nickyoungblut/.cache/pyensembl/GRCh38/ensembl104/Homo_sapiens.GRCh38.104.gtf.gz
Traceback (most recent call last):
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/bin/pyensembl", line 10, in <module>
    sys.exit(run())
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/pyensembl/shell.py", line 281, in run
    genome.index(overwrite=args.overwrite)
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/pyensembl/genome.py", line 280, in index
    self.db.connect_or_create(overwrite=overwrite)
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/pyensembl/database.py", line 286, in connect_or_create
    return self.create(overwrite=overwrite)
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/pyensembl/database.py", line 239, in create
    self._connection = datacache.db_from_dataframes_with_absolute_path(
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/datacache/database_helpers.py", line 176, in db_from_dataframes_with_absolute_path
    tables = build_tables(
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/datacache/database_helpers.py", line 136, in build_tables
    table = DatabaseTable.from_dataframe(
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/datacache/database_table.py", line 56, in from_dataframe
    column_db_type = db_type(values.dtype)
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/datacache/database_types.py", line 92, in db_type
    for type_name in _candidate_type_names(python_type_representation):
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/datacache/database_types.py", line 64, in _candidate_type_names
    if python_type_representation in np.typeDict:
  File "/home/nickyoungblut/miniforge3/envs/ont_10x/lib/python3.10/site-packages/numpy/__init__.py", line 410, in __getattr__
    raise AttributeError("module {!r} has no attribute "
AttributeError: module 'numpy' has no attribute 'typeDict'. Did you mean: 'sctypeDict'?

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 ``` # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge alsa-lib 1.2.11 hd590300_1 conda-forge anyio 4.3.0 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argcomplete 3.4.0 pyhd8ed1ab_0 conda-forge argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge arrow 1.3.0 pyhd8ed1ab_0 conda-forge astroid 3.2.4 py310hff52083_0 conda-forge asttokens 2.4.1 pyhd8ed1ab_0 conda-forge async-lru 2.0.4 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge aws-c-auth 0.7.22 h96bc93b_2 conda-forge aws-c-cal 0.6.14 h88a6e22_1 conda-forge aws-c-common 0.9.19 h4ab18f5_0 conda-forge aws-c-compression 0.2.18 h83b837d_6 conda-forge aws-c-event-stream 0.4.2 ha47c788_12 conda-forge aws-c-http 0.8.1 h29d6fba_17 conda-forge aws-c-io 0.14.8 h21d4f22_5 conda-forge aws-c-mqtt 0.10.4 h759edc4_4 conda-forge aws-c-s3 0.5.9 h594631b_3 conda-forge aws-c-sdkutils 0.1.16 h83b837d_2 conda-forge aws-checksums 0.1.18 h83b837d_6 conda-forge aws-crt-cpp 0.26.9 he3a8b3b_0 conda-forge aws-sdk-cpp 1.11.329 hba8bd5f_3 conda-forge babel 2.14.0 pyhd8ed1ab_0 conda-forge bash 5.2.21 h7f99829_0 conda-forge bash_kernel 0.9.3 pyh4f82c71_0 conda-forge beautifulsoup4 4.12.3 pyha770c72_0 conda-forge bedtools 2.31.1 hf5e1c6e_1 bioconda binutils_impl_linux-64 2.40 ha885e6a_0 conda-forge bioconductor-annotate 1.80.0 r43hdfd78af_0 bioconda bioconductor-annotationdbi 1.64.1 r43hdfd78af_0 bioconda bioconductor-ballgown 2.34.0 r43hdfd78af_0 bioconda bioconductor-biobase 2.62.0 r43ha9d7317_2 bioconda bioconductor-biocgenerics 0.48.1 r43hdfd78af_2 bioconda bioconductor-biocio 1.12.0 r43hdfd78af_0 bioconda bioconductor-biocparallel 1.36.0 r43hf17093f_2 bioconda bioconductor-biostrings 2.70.1 r43ha9d7317_2 bioconda bioconductor-data-packages 20231203 hdfd78af_0 bioconda bioconductor-delayedarray 0.28.0 r43ha9d7317_2 bioconda bioconductor-edger 4.0.16 r43hf17093f_1 bioconda bioconductor-genefilter 1.84.0 r43ha1e849b_1 bioconda bioconductor-genomeinfodb 1.38.1 r43hdfd78af_1 bioconda bioconductor-genomeinfodbdata 1.2.11 r43hdfd78af_1 bioconda bioconductor-genomicalignments 1.38.0 r43ha9d7317_1 bioconda bioconductor-genomicranges 1.54.1 r43ha9d7317_2 bioconda bioconductor-iranges 2.36.0 r43ha9d7317_2 bioconda bioconductor-keggrest 1.42.0 r43hdfd78af_0 bioconda bioconductor-limma 3.58.1 r43ha9d7317_1 bioconda bioconductor-matrixgenerics 1.14.0 r43hdfd78af_3 bioconda bioconductor-rhtslib 2.4.0 r43ha9d7317_2 bioconda bioconductor-rsamtools 2.18.0 r43hf17093f_2 bioconda bioconductor-rtracklayer 1.62.0 r43ha9d7317_1 bioconda bioconductor-s4arrays 1.2.0 r43ha9d7317_2 bioconda bioconductor-s4vectors 0.40.2 r43ha9d7317_2 bioconda bioconductor-sparsearray 1.2.2 r43ha9d7317_2 bioconda bioconductor-summarizedexperiment 1.32.0 r43hdfd78af_0 bioconda bioconductor-sva 3.50.0 r43ha9d7317_1 bioconda bioconductor-xvector 0.42.0 r43ha9d7317_2 bioconda bioconductor-zlibbioc 1.48.0 r43ha9d7317_2 bioconda biopython 1.84 py310hc51659f_0 conda-forge blast 2.16.0 h6f7f691_0 bioconda bleach 6.1.0 pyhd8ed1ab_0 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.28.1 hd590300_0 conda-forge ca-certificates 2024.8.30 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge certifi 2024.8.30 pyhd8ed1ab_0 conda-forge cffi 1.16.0 py310h2fee648_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 contourpy 1.2.1 py310hd41b1e2_0 conda-forge curl 8.8.0 he654da7_1 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge datacache 1.1.5 py_0 conda-forge debugpy 1.8.1 py310hc6cd4ac_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dill 0.3.8 pyhd8ed1ab_0 conda-forge entrez-direct 22.4 he881be0_0 bioconda entrypoints 0.4 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge executing 2.0.1 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge fonttools 4.53.1 py310h5b4e0ec_0 conda-forge fqdn 1.5.1 pyhd8ed1ab_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge gawk 5.3.0 ha916aea_0 conda-forge gcc_impl_linux-64 13.2.0 h9eb54c0_7 conda-forge gettext 0.22.5 h59595ed_2 conda-forge gettext-tools 0.22.5 h59595ed_2 conda-forge gffread 0.12.7 hdcf5f25_4 bioconda gflags 2.2.2 he1b5a44_1004 conda-forge gfortran_impl_linux-64 13.2.0 h738fc78_7 conda-forge giflib 5.2.2 hd590300_0 conda-forge glog 0.7.1 hbabe93e_0 conda-forge glpk 5.0 h445213a_0 conda-forge gmp 6.3.0 h59595ed_1 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge gtfparse 2.5.0 pyh7cba7a3_0 bioconda gxx_impl_linux-64 13.2.0 h2a599c4_7 conda-forge h11 0.14.0 pyhd8ed1ab_0 conda-forge h2 4.1.0 pyhd8ed1ab_0 conda-forge harfbuzz 8.4.0 h3d44ed6_0 conda-forge hpack 4.0.0 pyh9f0ad1d_0 conda-forge html2text 2024.2.26 pyhd8ed1ab_1 conda-forge htslib 1.20 h81da01d_0 bioconda httpcore 1.0.5 pyhd8ed1ab_0 conda-forge httpx 0.27.0 pyhd8ed1ab_0 conda-forge hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge icu 73.2 h59595ed_0 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge importlib-metadata 7.1.0 pyha770c72_0 conda-forge importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge ipykernel 6.29.3 pyhd33586a_0 conda-forge ipython 8.24.0 pyh707e725_0 conda-forge ipython_genutils 0.2.0 py_1 conda-forge isoduration 20.11.0 pyhd8ed1ab_0 conda-forge isort 5.13.2 pyhd8ed1ab_0 conda-forge jedi 0.19.1 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge jq 1.7.1 hd590300_0 conda-forge json5 0.9.25 pyhd8ed1ab_0 conda-forge jsonpointer 2.4 py310hff52083_3 conda-forge jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jsonschema-with-format-nongpl 4.22.0 pyhd8ed1ab_0 conda-forge jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge jupyter_client 7.4.9 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py310hff52083_0 conda-forge jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge jupyter_server 2.14.0 pyhd8ed1ab_0 conda-forge jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge jupyterlab 4.2.0 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge jupyterlab_server 2.27.1 pyhd8ed1ab_0 conda-forge k8 0.2.5 hdcf5f25_4 bioconda kernel-headers_linux-64 2.6.32 he073ed8_17 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py310hd41b1e2_1 conda-forge krb5 1.21.3 h659f571_0 conda-forge lcms2 2.16 hb7c19ff_0 conda-forge ld_impl_linux-64 2.40 h55db66e_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20240116.2 cxx17_he02047a_1 conda-forge libarrow 16.1.0 hcb6531f_6_cpu conda-forge libarrow-acero 16.1.0 hac33072_6_cpu conda-forge libarrow-dataset 16.1.0 hac33072_6_cpu conda-forge libarrow-substrait 16.1.0 h7e0c224_6_cpu conda-forge libasprintf 0.22.5 h661eb56_2 conda-forge libasprintf-devel 0.22.5 h661eb56_2 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.8.0 hca28451_1 conda-forge libdeflate 1.20 hd590300_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 libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc 14.1.0 h77fa898_1 conda-forge libgcc-devel_linux-64 13.2.0 hceb6213_107 conda-forge libgcc-ng 14.1.0 h69a702a_1 conda-forge libgettextpo 0.22.5 h59595ed_2 conda-forge libgettextpo-devel 0.22.5 h59595ed_2 conda-forge libgfortran-ng 13.2.0 h69a702a_7 conda-forge libgfortran5 13.2.0 hca663fb_7 conda-forge libglib 2.80.2 hf974151_0 conda-forge libgomp 14.1.0 h77fa898_1 conda-forge libgoogle-cloud 2.24.0 h2736e30_0 conda-forge libgoogle-cloud-storage 2.24.0 h3d9a0c8_0 conda-forge libgrpc 1.62.2 h15f2491_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libidn2 2.3.7 hd590300_0 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 22_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_h413a1c8_0 conda-forge libparquet 16.1.0 h6a7eafb_6_cpu conda-forge libpng 1.6.43 h2797004_0 conda-forge libprotobuf 4.25.3 h08a7969_0 conda-forge libre2-11 2023.09.01 h5a48ba9_2 conda-forge libsanitizer 13.2.0 h6ddb7a1_7 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsqlite 3.46.0 hde9e2c9_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-devel_linux-64 13.2.0 hceb6213_107 conda-forge libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge libthrift 0.19.0 hb90f79a_1 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.12.6 h232c23b_2 conda-forge libzlib 1.2.13 hd590300_5 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge mafft 7.526 h4bc722e_0 conda-forge make 4.3 hd18ef5c_1 conda-forge markupsafe 2.1.5 py310h2372a71_0 conda-forge matplotlib-base 3.9.1 py310hf02ac8c_2 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 minimap2 2.28 he4a0461_1 bioconda mistune 3.0.2 pyhd8ed1ab_0 conda-forge mizani 0.11.4 pyhd8ed1ab_0 conda-forge mock 5.1.0 pyhd8ed1ab_0 conda-forge mpfr 4.2.1 h38ae2d0_2 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge mysql-connector-c 6.1.11 h659d440_1008 conda-forge nb_conda 2.2.1 unix_7 conda-forge nb_conda_kernels 2.5.1 pyh707e725_2 conda-forge nbclassic 1.0.0 pyhb4ecaf3_1 conda-forge nbclient 0.10.0 pyhd8ed1ab_0 conda-forge nbconvert 7.16.4 hd8ed1ab_0 conda-forge nbconvert-core 7.16.4 pyhd8ed1ab_0 conda-forge nbconvert-pandoc 7.16.4 hd8ed1ab_0 conda-forge nbformat 5.10.4 pyhd8ed1ab_0 conda-forge ncbi-vdb 3.1.1 h4ac6f70_1 bioconda ncurses 6.5 h59595ed_0 conda-forge nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge notebook 6.5.6 pyha770c72_0 conda-forge notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge numpy 2.0.1 py310hf9f9071_0 conda-forge oniguruma 6.9.9 hd590300_0 conda-forge openjdk 22.0.1 hb622114_0 conda-forge openjpeg 2.5.2 h488ebb8_0 conda-forge openssl 3.3.2 hb9d3cd8_0 conda-forge orc 2.0.1 h17fec99_1 conda-forge overrides 7.7.0 pyhd8ed1ab_0 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py310hf9f9076_1 conda-forge pandoc 3.1.13 ha770c72_0 conda-forge pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge pango 1.52.2 ha41ecd1_0 conda-forge parso 0.8.4 pyhd8ed1ab_0 conda-forge patsy 0.5.6 pyhd8ed1ab_0 conda-forge pcre 8.45 h9c3ff4c_0 conda-forge pcre2 10.43 hcad00b1_0 conda-forge perl 5.32.1 7_hd590300_perl5 conda-forge perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge perl-compress-raw-bzip2 2.201 pl5321h166bdaf_0 conda-forge perl-compress-raw-zlib 2.202 pl5321h166bdaf_0 conda-forge perl-encode 3.21 pl5321hd590300_0 conda-forge perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 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pyhd8ed1ab_0 conda-forge xorg-fixesproto 5.0 h7f98852_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge xorg-libxi 1.7.10 h7f98852_0 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-libxt 1.3.0 hd590300_1 conda-forge xorg-libxtst 1.2.3 h7f98852_1002 conda-forge xorg-recordproto 1.14.2 h7f98852_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yq 3.4.3 pyhd8ed1ab_0 conda-forge zeromq 4.3.5 h75354e8_3 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge ```
nick-youngblut commented 2 months ago

@w2wewwww are you a spam bot?

nick-youngblut commented 2 months ago

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 ```
iskandr commented 2 months ago

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 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

— Reply to this email directly, view it on GitHub https://github.com/openvax/pyensembl/issues/310#issuecomment-2333214720, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAL2OPQ3EHZLPTQRVCI7LTZVEWBLAVCNFSM6AAAAABNXX3U2OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMZTGIYTINZSGA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

nick-youngblut commented 2 months ago

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:

This might help you
https://bit.ly/3yXXzbx
Passcode: d5kp14h1
You must have gcc compiler installed

@iskandr have you ever seen spam posts on GitHub like this before?

w2wewwww commented 2 months ago

Don't post it again,it's auto spam virus

CypherpunkSamurai commented 2 months ago

Unrelated to the topic. GitHub Team is aware of the issue https://github.com/orgs/community/discussions/136836#discussioncomment-10453313

pjlaw commented 3 weeks ago

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

pip install datacache --upgrade

yihuanlin commented 2 days ago

I I have the same error, and pip install datacache --upgrade worked! It turned out that datacache is not up to date in conda