Closed gdevenyi closed 10 years ago
gdevenyi
commented
10 years ago It looks like this software copies stuff to /tmp for execution based on looking at the trace database, I see: 194963|/tmp/best1stepnlreg.pl-cvdoDBku/Sdtig_H001_CAMH_t1_final_masked.mnc|2023434291903437|8|0|5081
From a query of files. Does reprozip use the sql database to build it's pack? I thought it would use the config...
remram44
commented
10 years ago First of all, thanks for trying out ReproZip!
The configuration file is indeed what's used when packing files, but the packer will also get from the trace the list of directories in which files are created or that are used as working directories. I'm guessing that best1stepnlreg.pl-cvdoDBku is a temporary directory that best1stepnlreg.pl creates files in.
ReproZip shouldn't error if these directories don't exist when packing, I will release a fix for that shortly.
remram44
commented
10 years ago @gdevenyi: Can you try with the current v0.3 branch? You should be able to update reprozip with:
$ pip install -e 'git+https://github.com/ViDA-NYU/reprozip.git@master#egg=reprozip&subdirectory=reprozip'If it works I will release 0.3.1 right away.
gdevenyi
commented
10 years ago Obtaining reprozip from git+https://github.com/ViDA-NYU/reprozip.git@master#egg=reprozip&subdirectory=reprozip
Cloning https://github.com/ViDA-NYU/reprozip.git (to master) to ./src/reprozip
Running setup.py egg_info for package reprozip
Traceback (most recent call last):
File "<string>", line 16, in <module>
IOError: [Errno 2] No such file or directory: '/home/m/mchakrav/gdevenyi/myENV/src/reprozip/setup.py'
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 16, in <module>
IOError: [Errno 2] No such file or directory: '/home/m/mchakrav/gdevenyi/myENV/src/reprozip/setup.py'This is a pip bug (which you shouldn't run into with their latest release).
I uploaded a new version of reprozip (0.3.1), so you will be able to update normally (i.e. by running pip install -U reprozip).
0.4 is out the corner anyway, should be released soon (with new easier commands to run experiments, input/output files support, and Docker plugin)
gdevenyi
commented
10 years ago Thanks, packing worked!
fchirigati
commented
10 years ago Hi Gabriel,
Thank you for your interest in ReproZip! We are developing substantial improvements for the unpacking step (reprounzip), so please stay tuned!
I'm experimenting with reprozip as a way to package up software stacks for version quarantine, so I ran it against a test set of data and now I'm trying to pack up the experiment, here's my config file
I've commented a few temp files which I know no longer exist, when I run reprozip pack on this config, it throws the following error:
As you may have seen from the config, there is a file named best1stepnlreg.pl, but not with the extra bits added on the end. I can't tell if this is a reprozip bug or a tarfile bug.