Pyfftw and scikit-image python package conflict


I am attempting to install cryosparc using the link + licence provided in the email and am running into the following unresolvable python package dependencies.

UnsatisfiableError: The following specifications were found to be in conflict:

  • pyfftw=0.9.2
  • scikit-image=0.12.3

My system is running Linux Mint (uname -a | Linux 4.10.0-42-generic #46~16.04.1-Ubuntu SMP), with nvidia 387.26 drivers (nvidia-smi | NVIDIA-SMI 387.26 Driver Version: 387.26) and CUDA 9 (nvcc --version | cuda compilation tools, release 9.1, V9.1.85).

I have chosen to install anaconda directly into the cryosparc directory as suggested by the installer.

Any information or guidance would be greatly appreciated.


Hi Joey,

I’m running similar configuration, but with Ubuntu 16.04 and I had the same problem. I’m using cuda 8.0 instead of 9 (as suggested by the developer)

In the end, I fixed it by using another pyfftw package and it seems to run smoothly.

To do so replace the line :

conda install -q -y --force -c richli fftw=3.3.4 pyfftw=0.9.2

by the two lines :

conda install -q -y --force -c richli fftw=3.3.4 
conda install -q -y --force -c conda-forge pyfftw 

Note that it’s probably only a temporary fix and a proper installation should probably be done once the problem is fixed.

Hope this help.


Hi Alain,

Something similar ended up working for us as well, and, as you mention, everything seems to be running smoothly so far.


This issue is now fixed in v0.6.5
We did end up switching to conda-forge because the other channel no longer maintains pyfftw binaries.