Cant install from Mamba

[blsteven]

Installation fails with mamba with the following error:

nothing provides r 3.2.2* needed by r-magrittr-1.5-r3.2.2_0

[akrinos]

Hi there @blsteven - what version of EUKulele are you trying to install?

[blsteven]

Thanks in advance for the replies and help!

I was able to get the package to install by removing strict channel controls in conda. The mamba installation was successful, but now when I invoke Eukulele I get the following:

File "/Users/blaire/miniconda3/envs/EUKulele/bin/EUKulele", line 6, in
import EUKulele
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/init.py", line 5, in
from EUKulele.EUKulele_main import *
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/EUKulele_main.py", line 12, in
from EUKulele.download_database import downloadDatabase
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/download_database.py", line 12, in
from EUKulele.manage_steps import createAlignmentDatabase
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/manage_steps.py", line 19, in
from EUKulele.visualize_results import visualize_all_results
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/visualize_results.py", line 9, in
import matplotlib.pyplot as plt
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/pyplot.py", line 36, in
import matplotlib.colorbar
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/colorbar.py", line 44, in
import matplotlib.contour as contour
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/contour.py", line 17, in
import matplotlib.text as text
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/text.py", line 16, in
from .textpath import TextPath # Unused, but imported by others.
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/textpath.py", line 11, in
from matplotlib.mathtext import MathTextParser
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/mathtext.py", line 27, in
from PIL import Image
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/PIL/Image.py", line 103, in
from . import _imaging as core
ImportError: dlopen(/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/PIL/_imaging.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libtiff.5.dylib
Referenced from: /Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/PIL/_imaging.cpython-37m-darwin.so
Reason: image not found
(EUKulele) blaire@x86_64-apple-darwin13 ~ % EUKulele
Traceback (most recent call last):
File "/Users/blaire/miniconda3/envs/EUKulele/bin/EUKulele", line 6, in
import EUKulele
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/init.py", line 5, in
from EUKulele.EUKulele_main import *
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/EUKulele_main.py", line 12, in
from EUKulele.download_database import downloadDatabase
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/download_database.py", line 12, in
from EUKulele.manage_steps import createAlignmentDatabase
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/manage_steps.py", line 19, in
from EUKulele.visualize_results import visualize_all_results
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/EUKulele/visualize_results.py", line 9, in
import matplotlib.pyplot as plt
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/pyplot.py", line 36, in
import matplotlib.colorbar
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/colorbar.py", line 44, in
import matplotlib.contour as contour
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/contour.py", line 17, in
import matplotlib.text as text
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/text.py", line 16, in
from .textpath import TextPath # Unused, but imported by others.
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/textpath.py", line 11, in
from matplotlib.mathtext import MathTextParser
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/matplotlib/mathtext.py", line 27, in
from PIL import Image
File "/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/PIL/Image.py", line 103, in
from . import _imaging as core
ImportError: dlopen(/Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/PIL/_imaging.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libtiff.5.dylib
Referenced from: /Users/blaire/miniconda3/envs/EUKulele/lib/python3.7/site-packages/PIL/_imaging.cpython-37m-darwin.so
Reason: image not found

[akrinos]

Hi @blsteven , this is really unusual! Could you send the command you used to install? Never seen this particular error before. I appreciate your patience!

[blsteven]

No problem

I used mamba install -c akrinos -c bioconda -c conda-forge EUKulele. I also tried with omitting the akrinos channel as per another issue, but get the same error.

If it helps I am trying to install on a Mac Pro running OS 10.15.7

Thanks for taking the time!

[akrinos]

Hi @blsteven - leaving off the -c akrinos is the right call - sorry I didn't respond before, the Mac part threw me off a little bit. I've been trying to look into ways to make EUKulele more compatible on Mac systems. I think probably the challenge stems from the OS.