missing module tifffile
FabianIsensee opened this issue · 4 comments
I installed ilastik as described in the readme. After activating the environment and attempting to run ilastik using run_ilastik.sh I get the following error message:
File "/home/fabian/miniconda/envs/ilastik-devel/ilastik-meta/lazyflow/lazyflow/operators/ioOperators/opTiffReader.py", line 8, in <module>
import tifffile
ImportError: No module named tifffile
Apparently, not all required packages are installed.
My system is a ubuntu 14.04
Cheers,
Fabian
What is the output of conda info --root and conda list? And what if you install tifffile manually via conda install -c ilastik tifffile?
Hi Stuart,
What is the output of conda info --root and conda list?
=> /home/fabian/miniconda
And what if you install tifffile manually via conda install -c
ilastik tifffile?
The following packages will be downloaded:
| package | build |
|---|---|
| numpy-1.10.1 | py27_0 5.9 MB |
The following NEW packages will be INSTALLED:
tifffile: 0.4.1-1
The following packages will be UPDATED:
numpy: 1.9.3-py27_0 --> 1.10.1-py27_0
Proceed ([y]/n)?
It will prompt me to update the numpy version in the evironment. Not sure
whether this will break additional things. Do you think it is safe to do it
anyways?
Cheers,
Fabian
2015-10-22 13:33 GMT+02:00 Stuart Berg notifications@github.com:
What is the output of conda info --root and conda list? And what if you
install tifffile manually via conda install -c ilastik tifffile?—
Reply to this email directly or view it on GitHub
#10 (comment)
.
It will prompt me to update the numpy version in the evironment. Not sure whether this will break additional things.
If it does break something, you can always start over with a fresh environment (it won't need to re-download all the packages again, so starting over will be quick).
Do you think it is safe to do it anyways?
It's hard to know without seeing the output from conda list, but I think it should be fine.
OK, the continuous integration server started having the same problem:
https://circleci.com/gh/ilastik/lazyflow/123
From what I can see conda is making an error in its dependency resolution. Conda is choosing to install the wrong build of our metapackage named ilastik-deps-pc-headless. Instead of choosing the latest build (build-number=2):
linux-64/ilastik-deps-pc-headless-1.1-np19py27_2.tar.bz2,
it is choosing an old build (build-number=0):
linux-64/ilastik-deps-pc-headless-1.1-np19py27_0.tar.bz2
As it turns out, the tifffile dependency is not listed in build 0, so that's why it's missing on your machine.
As a workaround, I've simply removed all old builds of our packages from the main ilastik channel (anaconda.org/ilastik). Now conda has only one choice when installing ilastik-deps-pc-headless.
Long story short: This should be fixed now.