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sam.nastase@2b4a9b3e5094dab41e0a4de0b808a2697a3e9860 2020-03-09 18:47:06 +00:00 committed by admin
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[[!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
"""]]