safetyerror: the package for numpy located at /root/anaconda/pkgs/numpy-1.9.3-py27h7e35acb_3 appears

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bala krish

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Feb 12, 2018, 6:37:41 AM2/12/18

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Hi,

I am wondering whether anyone got similar error when try to make a conda environment. I tried to find solution by myself first looking at the forum and try to delete the folder of numpy in the /root/anaconda/"pkgs"/numpy* folder which solved the "Safety error. Numpy files corruped".

"safetyerror: the package for numpy located at /root/anaconda/pkgs/numpy-1.9.3-py27h7e35acb_3 appears to be corrupted. the path 'lib/python2.7/site-packages/numpy/version.pyc' has a sha256 mismatch."

However, when i reconstruct the environment, the functionality is affected and i get some new error which i believe is due to the above process. I tried to search myself about the problem but could not able to get any solutions so far. Any help will be appreciated!

Below is the error:

conda create -n fash16s2 python=2.7 qiime matplotlib=1.4.3 mock nose -c bioconda
Solving environment: done

## Package Plan ##

environment location: /root/anaconda/envs/fash16s2

added / updated specs:
    - matplotlib=1.4.3
    - mock
    - nose
    - python=2.7
    - qiime

The following NEW packages will be INSTALLED:

    backports:

      1.0-py27h63c9359_1
    backports.shutil_get_terminal_size: 1.0.0-py27h5bc021e_2
    biom-format:                        2.1.6-py27_0          bioconda
    burrito:                            0.9.1-py27_0          bioconda
    burrito-fillings:                   0.1.1-py27_0          bioconda
    ca-certificates:                    2017.08.26-h1d4fec5_0
    cairo:                              1.12.18-6
    certifi:                            2018.1.18-py27_0
    click:                              6.7-py27h4225b90_0
    cogent:                             1.5.3-py27_0          bioconda
    decorator:                          4.2.1-py27_0
    emperor:                            0.9.51-py27_0         bioconda
    enum34:                             1.1.6-py27h99a27e9_1
    fontconfig:                         2.11.1-6
    freetype:                           2.5.5-1
    funcsigs:                           1.0.2-py27h83f16ab_0
    future:                             0.16.0-py27_1
    gdata:                              2.0.18-py27_0
    h5py:                               2.7.1-py27h2697762_0
    hdf5:                               1.10.1-h9caa474_1
    icu:                                58.2-h9c2bf20_1
    intel-openmp:                       2018.0.0-hc7b2577_8
    ipython:                            5.4.1-py27_2
    ipython_genutils:                   0.2.0-py27h89fb69b_0
    libedit:                            3.1-heed3624_0
    libffi:                             3.2.1-hd88cf55_4
    libgcc:                             7.2.0-h69d50b8_2
    libgcc-ng:                          7.2.0-h7cc24e2_2
    libgfortran-ng:                     7.2.0-h9f7466a_2
    libpng:                             1.6.17-0
    libstdcxx-ng:                       7.2.0-h7a57d05_2
    libxml2:                            2.9.7-h26e45fe_0
    matplotlib:                         1.4.3-np19py27_2
    mkl:                                2018.0.1-h19d6760_4
    mock:                               2.0.0-py27h0c0c831_0
    mpi4py:                             2.0.0-py27_2
    mpich2:                             1.4.1p1-0
    mysql-python:                       1.2.5-py27_0
    natsort:                            3.5.0-py27_0
    ncurses:                            6.0-h9df7e31_2
    nose:                               1.3.7-py27heec2199_2
    numpy:                              1.9.3-py27h7e35acb_3
    openssl:                            1.0.2n-hb7f436b_0
    pandas:                             0.21.1-py27h38cdd7d_0
    pathlib2:                           2.3.0-py27h6e9d198_0
    pbr:                                3.1.1-py27hf64632f_0
    pexpect:                            4.3.1-py27_0
    pickleshare:                        0.7.4-py27h09770e1_0
    pip:                                9.0.1-py27ha730c48_4
    pixman:                             0.32.6-0
    prompt_toolkit:                     1.0.15-py27h1b593e1_0
    ptyprocess:                         0.5.2-py27h4ccb14c_0
    py2cairo:                           1.10.0-py27_2
    pygments:                           2.2.0-py27h4a8b6f5_0
    pynast:                             1.2.2-py27_0          bioconda
    pyparsing:                          2.0.3-py27_0
    pyqi:                               0.3.2-py27_0          bioconda
    pyqt:                               4.11.4-py27_4
    python:                             2.7.14-h1571d57_29
    python-dateutil:                    2.3-py27_0            bioconda
    pytz:                               2017.3-py27h001bace_0
    qcli:                               0.1.1-py27_0          bioconda
    qiime:                              1.9.1-py27_0          bioconda
    qiime-default-reference:            0.1.3-py27_0          bioconda
    qt:                                 4.8.7-3
    readline:                           7.0-ha6073c6_4
    scandir:                            1.6-py27hf7388dc_0
    scikit-bio:                         0.2.3-py27_0          bioconda
    scipy:                              1.0.0-py27hf5f0f52_0
    setuptools:                         38.4.0-py27_0
    simplegeneric:                      0.8.1-py27_2
    sip:                                4.18-py27_0
    six:                                1.11.0-py27h5f960f1_1
    sqlalchemy:                         1.2.1-py27h14c3975_0
    sqlite:                             3.22.0-h1bed415_0
    tk:                                 8.6.7-hc745277_3
    traitlets:                          4.3.2-py27hd6ce930_0
    wcwidth:                            0.1.7-py27h9e3e1ab_0
    wheel:                              0.30.0-py27h2bc6bb2_1
    xz:                                 5.2.3-h55aa19d_2
    zlib:                               1.2.11-ha838bed_2

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate fash16s2
#
# To deactivate an active environment, use
#
#     $ conda deactivate

root@thl-lnx-d5710:~# source activate fash16s2
(fash16s2) root@thl-lnx-d5710:~# split_libraries_fastq.py -h
Traceback (most recent call last):
File "/root/anaconda/envs/fash16s2/bin/split_libraries_fastq.py", line 4, in <module>
    __import__('pkg_resources').run_script('qiime==1.9.1', 'split_libraries_fastq.py')
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 750, in run_script
    self.require(requires)[0].run_script(script_name, ns)
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1527, in run_script
    exec(code, namespace, namespace)
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/split_libraries_fastq.py", line 15, in <module>
    from skbio.util import safe_md5, create_dir
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/skbio/__init__.py", line 15, in <module>
    import skbio.io
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/skbio/io/__init__.py", line 309, in <module>
    import_module('skbio.io.clustal')
File "/root/anaconda/envs/fash16s2/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/skbio/io/clustal.py", line 123, in <module>
    from skbio.alignment import Alignment
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/skbio/alignment/__init__.py", line 230, in <module>
    from ._alignment import Alignment, SequenceCollection, StockholmAlignment
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/skbio/alignment/_alignment.py", line 21, in <module>
    from skbio.stats.distance import DistanceMatrix
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/skbio/stats/__init__.py", line 45, in <module>
    from ._subsample import subsample, subsample_counts, isubsample
File "/root/anaconda/envs/fash16s2/lib/python2.7/site-packages/skbio/stats/_subsample.py", line 22, in <module>
    from .__subsample import _subsample_counts_without_replacement
File "__init__.pxd", line 155, in init skbio.stats.__subsample (skbio/stats/__subsample.c:3964)
ValueError: numpy.dtype has the wrong size, try recompiling
(fash16s2) root@thl-lnx-d5710:~# conda info

     active environment : fash16s2
    active env location : /root/anaconda/envs/fash16s2
            shell level : 1
       user config file : /root/.condarc
populated config files :
          conda version : 4.4.9
    conda-build version : 3.4.1
         python version : 2.7.14.final.0
       base environment : /root/anaconda (writable)
           channel URLs : https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
          package cache : /root/anaconda/pkgs
                          /root/.conda/pkgs
       envs directories : /root/anaconda/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/4.4.9 requests/2.18.4 CPython/2.7.14 Linux/3.13.0-141-generic ubuntu/14.04 glibc/2.19
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Any help is greatly appreciated!!