[[!comment format=mdwn
 username="sam.nastase@2b4a9b3e5094dab41e0a4de0b808a2697a3e9860"
 nickname="sam.nastase"
 avatar="http://cdn.libravatar.org/avatar/55c74b521bcb7322069f35bf655f81e0"
 subject="comment 9"
 date="2020-03-09T18:47:06Z"
 content="""
Hmm yeah I may have previously screwed something up with the conda env, because it didn't have git-annex either, which I just manually installed via conda and is now present. This also seems to have installed a new git in the conda env (see conda list below), but for whatever reason, invoking git still reaches outside the conda env (I got the server admin to upgrade to 2.9):

    (datalad) scotty:/jukebox/hasson/snastase/narratives $ git --version
    git version 2.9.3

I'm still hitting a datalad error in trying to save the dataset. 

    (datalad) scotty:/jukebox/hasson/snastase/narratives $ datalad save -m \"Added new 'notthefall' subjects\"
    CommandError: 'git-annex add -c annex.dotfiles=true --json --json-error-messages -- CHANGES README dataset
    _description.json derivatives/fmriprep derivatives/freesurfer derivatives/logs participants.tsv sub-002/su
    b-002_scans.tsv...

and on and on listing many files, then:

    sub-315/sub-315_scans.json sub-315/sub-315_scans.tsv' failed with exitcode 1 under /mnt/bucket/labs/hasson/snastase/narratives
    git-annex: Repository /mnt/bucket/labs/hasson/snastase/narratives is at unsupported version 7. Automatic upgrade exception! derivatives/mriqc: getSymbolicLinkStatus: does not exist (No such file or directory)

I did a `datalad remove` on this derivatives/mriqc directory a few days ago, not sure why that's tripping up.

---

    # packages in environment at /usr/people/snastase/.conda/envs/datalad:
    #
    # Name                    Version                   Build  Channel
    _libgcc_mutex             0.1                        main  
    annexremote               1.3.1                    pypi_0    pypi
    appdirs                   1.4.3                    pypi_0    pypi
    boto                      2.49.0                   pypi_0    pypi
    ca-certificates           2019.11.28           hecc5488_0    conda-forge
    certifi                   2019.11.28               py37_0    conda-forge
    cffi                      1.14.0                   pypi_0    pypi
    chardet                   3.0.4                    pypi_0    pypi
    cryptography              2.8                      pypi_0    pypi
    curl                      7.68.0               hf8cf82a_0    conda-forge
    datalad                   0.12.2                   pypi_0    pypi
    dbus                      1.13.6               he372182_0    conda-forge
    deprecated                1.2.7                    pypi_0    pypi
    expat                     2.2.9                he1b5a44_2    conda-forge
    fasteners                 0.15                     pypi_0    pypi
    future                    0.18.2                   pypi_0    pypi
    gettext                   0.19.8.1          hc5be6a0_1002    conda-forge
    git                       2.23.0          pl526hacde149_0  
    git-annex                 8.20200226         hfc01302_101    conda-forge
    gitdb                     4.0.2                    pypi_0    pypi
    gitpython                 3.1.0                    pypi_0    pypi
    glib                      2.58.3          py37h6f030ca_1002    conda-forge
    gmp                       6.2.0                he1b5a44_2    conda-forge
    humanize                  2.0.0                    pypi_0    pypi
    idna                      2.9                      pypi_0    pypi
    importlib-metadata        1.5.0                    pypi_0    pypi
    iso8601                   0.1.12                   pypi_0    pypi
    jeepney                   0.4.3                    pypi_0    pypi
    jsmin                     2.2.2                    pypi_0    pypi
    keyring                   21.1.1                   pypi_0    pypi
    keyrings-alt              3.4.0                    pypi_0    pypi
    krb5                      1.16.4               h173b8e3_0  
    ld_impl_linux-64          2.33.1               h53a641e_7  
    libcurl                   7.68.0               hda55be3_0    conda-forge
    libedit                   3.1.20181209         hc058e9b_0  
    libffi                    3.2.1                hd88cf55_4  
    libgcc-ng                 9.1.0                hdf63c60_0  
    libiconv                  1.15              h516909a_1005    conda-forge
    libmagic                  5.36                 h516909a_1    conda-forge
    libssh2                   1.8.2                h22169c7_2    conda-forge
    libstdcxx-ng              9.1.0                hdf63c60_0  
    lsof                      4.89                          0    conda-forge
    monotonic                 1.5                      pypi_0    pypi
    msgpack                   1.0.0                    pypi_0    pypi
    ncurses                   6.2                  he6710b0_0  
    openssh                   7.9p1                h0fa992c_1    conda-forge
    openssl                   1.1.1d               h516909a_0    conda-forge
    patool                    1.12                     pypi_0    pypi
    pcre                      8.44                 he1b5a44_0    conda-forge
    perl                      5.26.2            h516909a_1006    conda-forge
    pip                       20.0.2                   py37_1  
    popt                      1.16              h299ea2f_2002    conda-forge
    pycparser                 2.20                     pypi_0    pypi
    pygithub                  1.46                     pypi_0    pypi
    pyjwt                     1.7.1                    pypi_0    pypi
    python                    3.7.6                h0371630_2  
    readline                  7.0                  h7b6447c_5  
    requests                  2.23.0                   pypi_0    pypi
    rsync                     3.1.3             hed695b0_1002    conda-forge
    secretstorage             3.1.2                    pypi_0    pypi
    setuptools                45.2.0                   py37_0  
    simplejson                3.17.0                   pypi_0    pypi
    six                       1.14.0                   pypi_0    pypi
    smmap                     3.0.1                    pypi_0    pypi
    sqlite                    3.31.1               h7b6447c_0  
    tk                        8.6.8                hbc83047_0  
    tqdm                      4.43.0                   pypi_0    pypi
    urllib3                   1.25.8                   pypi_0    pypi
    wheel                     0.34.2                   py37_0  
    whoosh                    2.7.4                    pypi_0    pypi
    wrapt                     1.12.0                   pypi_0    pypi
    xz                        5.2.4                h14c3975_4  
    zipp                      3.1.0                    pypi_0    pypi
    zlib                      1.2.11               h7b6447c_3  

"""]]
