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morris-lab / CellOracle

This is the alpha version of the CellOracle package
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Installation error #47

Closed smorabit closed 3 years ago

smorabit commented 3 years ago

Hi,

I have been trying to install CellOracle using the instructions here. All of the dependencies installed without a problem, but when I tried to run pip install git+https://github.com/morris-lab/CellOracle.git, I got an error message that I do not know how to resolve:

$pip install git+https://github.com/morris-lab/CellOracle.git
Collecting git+https://github.com/morris-lab/CellOracle.git
  Cloning https://github.com/morris-lab/CellOracle.git to /tmp/pip-req-build-drlsr_n9
  Running command git clone -q https://github.com/morris-lab/CellOracle.git /tmp/pip-req-build-drlsr_n9
    ERROR: Command errored out with exit status 1:
     command: /data/homezvol1/smorabit/.conda/envs/celloracle_env/bin/python3.6 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-drlsr_n9/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-drlsr_n9/setup.py'"'"';
f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-19oh25yb
         cwd: /tmp/pip-req-build-drlsr_n9/
    Complete output (21 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-req-build-drlsr_n9/setup.py", line 16, in <module>
        from celloracle import __version__
      File "/tmp/pip-req-build-drlsr_n9/celloracle/__init__.py", line 8, in <module>
        from . import utility, network, network_analysis, go_analysis, data, data_conversion, oracle_utility

      File "/tmp/pip-req-build-drlsr_n9/celloracle/utility/__init__.py", line 18, in <module>
        from .load_hdf5 import load_hdf5
      File "/tmp/pip-req-build-drlsr_n9/celloracle/utility/load_hdf5.py", line 8, in <module>
        from ..motif_analysis.tfinfo_core import load_TFinfo
      File "/tmp/pip-req-build-drlsr_n9/celloracle/motif_analysis/__init__.py", line 11, in <module>
        from .motif_analysis_utility import is_genome_installed
      File "/tmp/pip-req-build-drlsr_n9/celloracle/motif_analysis/motif_analysis_utility.py", line 24, in <module>
        from gimmemotifs.scanner import Scanner
      File "/data/homezvol1/smorabit/.conda/envs/celloracle_env/lib/python3.6/site-packages/gimmemotifs/scanner.py", line 29, in <module>
        from gimmemotifs.utils import parse_cutoff,as_fasta,file_checksum
      File "/data/homezvol1/smorabit/.conda/envs/celloracle_env/lib/python3.6/site-packages/gimmemotifs/utils.py", line 29, in <module>
        from gimmemotifs.plot import plot_histogram
      File "/data/homezvol1/smorabit/.conda/envs/celloracle_env/lib/python3.6/site-packages/gimmemotifs/plot.py", line 19, in <module>
        mpl.use("Agg", warn=False)
    TypeError: use() got an unexpected keyword argument 'warn'
    ----------------------------------------
WARNING: Discarding git+https://github.com/morris-lab/CellOracle.git. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I would greatly appreciate your help in resolving this as I was really interested to use CellOracle!

Thanks, Sam

KenjiKamimoto-ac commented 3 years ago

Hi, Thank you for your feedback!

I guess the error was caused by "gimmemotifs", that is one of the packages used in celloracle because the situation looks similar to this https://github.com/morris-lab/CellOracle/issues/32

Can you please remove gimmemotifs and then, please install it again as follows? pip uninstall gimmemotifs and then conda install gimmemotifs==0.14.4 genomepy==0.8.4

Kenji

smorabit commented 3 years ago

Thanks for the help, I was able to install celloracle by installing those versions of gimmemotifs and genomepy. However, initially I did get another installation error which was resolved using this:

conda install ipyvuetify

rlittman16 commented 3 years ago

I am having issues with the r version that's compatible with these packages. If I let conda choose default after installing celloracle, but before the r packages it chooses 3.2.1, which isn't compatible with later R packages needed. I tried 3.6.1, but am having compatibility issues now when trying "install other python libraries" conda install goatools pyarrow tqdm joblib jupyter gimmemotifs==0.14.4 genomepy==0.8.4

KenjiKamimoto-ac commented 3 years ago

Hi rittman16,

Thank you for your feedback. Could you please post the error messages you got? I need more information to figure out what is going on. Also, could you please tell me information about your environment, such as OS, and other python packages installed in your environment? Please tell me the output of conda list command.

In my understanding, most of the Python packages used by celloracle do not depend on R, so the cause of the error might be something other than the R version. R 3.6 works in my PC.

Also, please let me ask one more question. Are you installing celloracle in a new conda environment? I recommend making a new conda environment for celloracle and start with it to avoid compatibility error.

rlittman16 commented 3 years ago

Hello,

I am following the steps here: https://github.com/morris-lab/CellOracle under the pdf documentation link.

Yes I'm using a new conda environment.

Once I get to 1.1.4 in the documentation I need to install R>=3.5, but conda can't find an R version that satisfies that requirement. It tries to install R 3.2.1 by default. If I try R>=3.5 it says:

Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: / Found conflicts! Looking for incompatible packages.

Here are the results for conda list: _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_gnu conda-forge _py-xgboost-mutex 2.0 cpu_0 conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge abseil-cpp 20200923.3 h9c3ff4c_0 conda-forge alabaster 0.7.12 py_0 conda-forge alsa-lib 1.2.3 h516909a_0 conda-forge anndata 0.7.5 py36h5fab9bb_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argon2-cffi 20.1.0 py36h8f6f2f9_2 conda-forge arpack 3.7.0 hdefa2d7_2 conda-forge arrow-cpp 3.0.0 py36h3d3e26e_10_cpu conda-forge async_generator 1.10 py_0 conda-forge attrs 20.3.0 pyhd3deb0d_0 conda-forge aws-c-cal 0.4.5 h76129ab_8 conda-forge aws-c-common 0.5.2 h7f98852_0 conda-forge aws-c-event-stream 0.2.7 h6bac3ce_1 conda-forge aws-c-io 0.9.1 ha5b09cb_1 conda-forge aws-checksums 0.1.11 h99e32c3_3 conda-forge aws-sdk-cpp 1.8.151 hceb1b1e_1 conda-forge babel 2.9.0 pyhd3deb0d_0 conda-forge backcall 0.2.0 pyh9f0ad1d_0 conda-forge backports 1.0 py_2 conda-forge backports.functools_lru_cache 1.6.3 pyhd8ed1ab_0 conda-forge bedtools 2.30.0 h7d7f7ad_1 bioconda biopython 1.78 py36h8f6f2f9_2 conda-forge bleach 3.3.0 pyh44b312d_0 conda-forge blosc 1.21.0 h9c3ff4c_0 conda-forge boltons 20.2.1 pyh9f0ad1d_0 conda-forge boost-cpp 1.70.0 h8e57a91_2 conda-forge brotli 1.0.9 h9c3ff4c_4 conda-forge brotlipy 0.7.0 py36h8f6f2f9_1001 conda-forge bucketcache 0.12.1 py36h9f0ad1d_2 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.17.1 h7f98852_1 conda-forge ca-certificates 2020.12.5 ha878542_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cairo 1.16.0 hcf35c78_1003 conda-forge celloracle 0.6.5 pypi_0 pypi certifi 2020.12.5 py36h5fab9bb_1 conda-forge cffi 1.14.4 py36h211aa47_0 conda-forge chardet 4.0.0 py36h5fab9bb_1 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge colorama 0.4.4 pyh9f0ad1d_0 conda-forge configparser 5.0.2 pyhd8ed1ab_0 conda-forge cryptography 3.4.7 py36hb60f036_0 conda-forge cycler 0.10.0 py_2 conda-forge cython 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re2 2021.04.01 h9c3ff4c_0 conda-forge readline 8.0 he28a2e2_2 conda-forge represent 1.6.0 py36h8c4c3a4_2 conda-forge requests 2.25.1 pyhd3deb0d_0 conda-forge s2n 1.0.0 h9b69904_0 conda-forge scanpy 1.7.1 py_0 bioconda scikit-learn 0.22.2.post1 py36hcdab131_0 conda-forge scipy 1.5.3 py36h9e8f40b_0 conda-forge seaborn 0.11.1 hd8ed1ab_1 conda-forge seaborn-base 0.11.1 pyhd8ed1ab_1 conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 49.6.0 py36h5fab9bb_3 conda-forge setuptools-scm 6.0.1 pyh44b312d_0 conda-forge setuptools_scm 6.0.1 hd8ed1ab_0 conda-forge sinfo 0.3.1 py_0 conda-forge sip 4.19.8 py36hf484d3e_1000 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sklearn-contrib-lightning 0.6.0 py36h284efc9_0 conda-forge snappy 1.1.8 he1b5a44_3 conda-forge snowballstemmer 2.1.0 pyhd8ed1ab_0 conda-forge sphinx 3.5.3 pyhd8ed1ab_0 conda-forge sphinxcontrib-applehelp 1.0.2 py_0 conda-forge sphinxcontrib-devhelp 1.0.2 py_0 conda-forge sphinxcontrib-htmlhelp 1.0.3 py_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.3 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.4 py_0 conda-forge sqlite 3.35.3 h74cdb3f_0 conda-forge statsmodels 0.12.2 py36h92226af_0 conda-forge stdlib-list 0.7.0 py_2 conda-forge suitesparse 5.7.2 h7a0d4b7_0 conda-forge tabix 0.2.6 ha92aebf_0 bioconda tbb 2020.2 h4bd325d_4 conda-forge terminado 0.9.4 py36h5fab9bb_0 conda-forge testpath 0.4.4 py_0 conda-forge texttable 1.6.3 pyh9f0ad1d_0 conda-forge threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge tk 8.6.10 h21135ba_1 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tornado 6.1 py36h8f6f2f9_1 conda-forge tqdm 4.59.0 pyhd8ed1ab_0 conda-forge traitlets 4.3.3 py36h9f0ad1d_1 conda-forge trawler 2.0 hdfd78af_4 bioconda typing_extensions 3.7.4.3 py_0 conda-forge ucsc-bedtogenepred 377 h0b8a92a_2 bioconda ucsc-bigbedtobed 377 h0b8a92a_2 bioconda ucsc-genepredtobed 377 h0b8a92a_4 bioconda ucsc-genepredtogtf 377 h0b8a92a_4 bioconda ucsc-gff3togenepred 377 h0b8a92a_2 bioconda ucsc-gtftogenepred 377 h0b8a92a_4 bioconda umap-learn 0.5.1 py36h5fab9bb_0 conda-forge unzip 6.0 h7f98852_2 conda-forge urllib3 1.26.4 pyhd8ed1ab_0 conda-forge velocyto 0.17.17 pypi_0 pypi wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge webencodings 0.5.1 py_1 conda-forge weeder 2.0 h7d875b9_5 bioconda wget 1.20.1 h22169c7_0 conda-forge wheel 0.36.2 pyhd3deb0d_0 conda-forge widgetsnbextension 3.5.1 py36h5fab9bb_4 conda-forge xdg 5.0.1 pyhd8ed1ab_0 conda-forge xgboost 1.3.3 py36h5fab9bb_2 conda-forge xlrd 1.2.0 pypi_0 pypi xlsxwriter 1.3.8 pyhd8ed1ab_0 conda-forge xmltodict 0.12.0 py_0 conda-forge xorg-fixesproto 5.0 h14c3975_1002 conda-forge xorg-inputproto 2.3.2 h7f98852_1002 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.6.12 h516909a_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxfixes 5.0.3 h516909a_1004 conda-forge xorg-libxi 1.7.10 h516909a_0 conda-forge xorg-libxpm 3.5.13 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-libxt 1.1.5 h516909a_1003 conda-forge xorg-libxtst 1.2.3 h516909a_1002 conda-forge xorg-recordproto 1.14.2 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xxhash 0.8.0 h7f98852_3 conda-forge xxmotif 1.6 h2d50403_2 bioconda xz 5.2.5 h516909a_1 conda-forge yaml 0.2.5 h516909a_0 conda-forge zeromq 4.3.4 h9c3ff4c_0 conda-forge zipp 3.4.1 pyhd8ed1ab_0 conda-forge zlib 1.2.11 h516909a_1010 conda-forge zstd 1.4.9 ha95c52a_0 conda-forge

KenjiKamimoto-ac commented 3 years ago

Although we recommended using conda for python package installation, it is not the case for R. Please try to install R in another way.

For example, you can download and install R from CRAN. https://cran.r-project.org Also, please make sure to uninstall your R in the celloracle's conda environment.

I'm sorry that this point was not clear in our documentation. We will update our documantation soon.