Problem installing pentads with conda #11
Comments
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Dear @rlisenhart, I believe you have some issues with CommandLineTools on your machine. These are the lines describing the error:
Quick googling gives some hints:
Can you try to solve this issue and let me know if it works? Best, |
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Thanks so much @magnitov. I think it was a problem setting up a new computer. I have now installed and I can run the test data, but I am still having a problem running my own data. I'm wondering if the issue is coming from the smaller chromosome segments included in the cool file? I've included two errors below. After getting the first one, I tried to remove the small chromosome segments from the bedGraph compartment signal file since I only care about the main chromosome arms. That seemed to run a bit further and resulted in the second error below. Any advice you have would be greatly appreciated!! Error 1: Error 2 (after filtering the BedGraph file for only the main chromosomes (X, 2L, 2R, 3L, 3R, Y, 4)). |
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Hi @rlisenhart, Good to know that it works. I assume this is Drosophila data. From my experience, you probably do not have any bins with compartments for all these unplaced scaffolds. For Drosophila data I would restrict the analysis to chr2L, chr2R, chr3L, chr3R, and chrX. That is what most people do. For now, Pentad only has Best, |
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Hi @rlisenhart , I added parameter Best, |
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Hi @magnitov, Thanks so much! The addition of the --incl_chrms parameter greatly helps! The cis analysis works nicely, as does the distance cutoff! The trans analysis is still not running for me. It prints: Running trans pentad calculation for [cool_file] with [compartment_file] but then nothing else happens. I left it overnight just to see if it was going slowly, but it doesn't seem to be doing anything. Since there is no error message its hard to figure out what is happening. Also I have a quick question. Is there a way to directly export the values for each compartment analyzed rather than the average for the whole chromosome? I'd like to look at a distribution of the compartment A strengths in control vs in treatment. I was wondering if that was what you plotted in your box plots of your paper next to the pentads schematics. -Randi |
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Hi @rlisenhart, Great news, I'm glad it works! Did you get the message "'Trans-expected values calculated!'" ? If not, the calculation of in-trans observed-over-expected is not done. I guess that's where the script gets stuck. Since cooltools does it for the whole matrix, it means all chromosomes are included in this step, despite the specified parameter What I plotted in the paper is actually a boxplot of average compartment strength per chromosome. However, for Drosophila it might indeed be not optimal. If you want to have a distribution of compartment A strengths, I think it's best to save all the sub-matrices and then calculate these values manually. I can add a flag that will allow one to dump all sub-matrices into a file. You would have to then make an average AB compartment and use it as denominator for each compartment A area extracted. Does this makes sense to you? Best, |
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Hi @magnitov, I do not get the message "Trans-expected values calculated!", so I think it is stuck before that. That makes sense that the cooltools would operate on the whole matrix. I see, yes plotting per chromosome makes sense for organisms with quite a few, but my similar plot looks a bit strange coming from 5 data points. If it is not too much trouble to add the flag to dump the individual matrices, that sounds like it would be ideal. Thanks again, |
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Hi @rlisenhart, I am really sorry that it took way longer that you could have expected. I have added flag If you still plan to use it, I would appreciate your feedback. Best, |
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Hi @magnitov , Thanks so much for building in that feature. I'd love to try it. I don't mean to be going back in time here, but I'm actually having trouble just using the tool again. The computer I was running it on before died so I'm using a new machine to try to run it on a computing cluster. I can follow your installation prompts, but when I run the test I get many errors involving the package cv2 (output included below). I had this problem when I set it up before, but with the help of a lab mate we were able to solve the problem by re-installing the opencv package. This is not solving the problem now. I've gone down some rabbit holes in the past week of uninstalling and re-installing variations of opencv (opencv-python, opencv-python-headless, etc) but nothing seems to work. I don't know if there is a version issue or something, but I can't run anything. I'm not sure if you have any advice. Other Hi-C packages seem to be running on this computing cluster fine (hicexplorer, pygenometracks, etc) so I don't think its a problem there. It all seems to boil down to this opencv package. -Randi |
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I forgot to include the error. I won't include the whole thing because its long. Basically the wget of the files works, but from there I get this: compartment_signal.txt.gz 100%[=========================================================================>] 1.38M 3.47MB/s in 0.4s 2022-11-10 12:08:14 (3.47 MB/s) - ‘compartment_signal.txt.gz’ saved [1451622/1451622] Traceback (most recent call last): This error keeps repeating for each command trying to run in the test file |
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@rlisenhart Have you created conda environment for Pentad using the YML file from the repository, or you are setting it up by yourself? |
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Dear @magnitov, Thank you a lot for the interesting tool, it's very useful for my project. But I met a problem that I can't get right results I think. This is installing info blow. Successfully installed PyWavelets-1.3.0 asciitree-0.3.3 bioframe-0.3.3 charset-normalizer-3.0.1 click-8.1.3 cooler-0.9.1 cooltools-0.5.1 cytoolz-0.12.1 dill-0.3.6 h5py-3.8.0 idna-3.4 imageio-2.26.0 importlib-metadata-6.0.0 joblib-1.2.0 llvmlite-0.39.1 multiprocess-0.70.14 networkx-2.6.3 numba-0.56.4 pyyaml-6.0 requests-2.28.2 scikit-image-0.19.3 scikit-learn-1.0.2 simplejson-3.18.3 threadpoolctl-3.1.0 tifffile-2021.11.2 toolz-0.12.0 urllib3-1.26.14 zipp-3.15.0 To activate this environment, use And next I ran test script and got results, please find the attached errors txt and results what I got. Could you please help me find what happened? Thank you! |
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Hi @hanshanmengqi, I believe this is cause by a new version of cooler being released recently. You got v0.9 installed, while I was using v0.8 while developing the tool. I have updated YML file to install correct versions. Can you remove your current pentad-env environment and try creating it with a new YML file? Best, |
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Hello @magnitov , Thank you for your swift reply. I tried new YML file but got same problem. Installing info I got: Successfully built cytoolz pypairix And error txt file: Thank you for your help. |
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Do you still get NaNs instead of matrices in json file? Because that is the main problem - the script does not generate the expected data for plotting. I also did not see the logs printed that are supposed to accompany the execution of the tool. I initially thought that it is caused by a new version of cooler, but it seems to be not the case. Mikhail |
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Yes, the json files still got NaNs. Need I check version of each tool/package? Han |
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@hanshanmengqi, I tried it as well on a different machine and I can reproduce the issue. I will dive a bit deeper. I'll let you know when I fix it. |
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@magnitov , Thank you very much. |
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@hanshanmengqi, should be fixed now. I had to pull one of the earlier versions and make some changes though. If you were expecting to select specific chromosomes for the analysis, this subset is now not working. I will fix it, but can take a while. Let me know if the tools finally works for you. |
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@magnitov , It's worked! I ran test data and got normal heatmap! Thank you a lot. Best, |
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@magnitov Dear Mikhail, I tried my data but got error which .json contain NaNs. Do you mind I sent you my data and check what I should fix? Thank you in advance. Best, |
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Dear Han @hanshanmengqi , Sure, let's try that. You can send me a link by email: m.magnitov@nki.nl. Best, |
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@magnitov , Han |
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@magnitov |
Hello, I am having trouble installing pentads. I followed the install instructions, but when building the conda environment I get a series of errors. The first one appears to be:
Failed to build cooltools cytoolz pypairix
Which then cause a downstream series of errors. I'm wondering if you have any advice to solve this issue? I've included the entire error below.
Best,
Randi
Collecting package metadata (repodata.json): done
Solving environment: done
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: - Ran pip subprocess with arguments:
['/Users/isenhart/opt/anaconda3/envs/pentads/bin/python', '-m', 'pip', 'install', '-U', '-r', '/Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt']
Pip subprocess output:
Collecting cooler>=0.8.5
Using cached cooler-0.8.11-py2.py3-none-any.whl (100 kB)
Collecting cooltools>=0.5.0
Using cached cooltools-0.5.1.tar.gz (8.0 MB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting multiprocess
Using cached multiprocess-0.70.13-py37-none-any.whl (115 kB)
Requirement already satisfied: pandas in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.3.5)
Collecting h5py>=2.5
Using cached h5py-3.7.0-cp37-cp37m-macosx_10_9_x86_64.whl (3.1 MB)
Collecting click>=7
Using cached click-8.1.3-py3-none-any.whl (96 kB)
Collecting cytoolz<0.11
Using cached cytoolz-0.10.1.tar.gz (475 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: scipy>=0.16 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.7.3)
Collecting pyfaidx
Using cached pyfaidx-0.7.1-py3-none-any.whl
Collecting asciitree
Using cached asciitree-0.3.3-py3-none-any.whl
Collecting pyyaml
Using cached PyYAML-6.0-cp37-cp37m-macosx_10_9_x86_64.whl (189 kB)
Collecting simplejson
Using cached simplejson-3.17.6-cp37-cp37m-macosx_10_9_x86_64.whl (74 kB)
Collecting pypairix
Using cached pypairix-0.3.7.tar.gz (65 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Requirement already satisfied: six in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.16.0)
Requirement already satisfied: numpy>=1.9 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (1.21.6)
Collecting bioframe>=0.3.3
Using cached bioframe-0.3.3-py2.py3-none-any.whl (112 kB)
Requirement already satisfied: cython in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (0.29.32)
Collecting joblib
Using cached joblib-1.2.0-py3-none-any.whl (297 kB)
Requirement already satisfied: matplotlib in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (3.5.3)
Collecting numba
Using cached numba-0.56.2-cp37-cp37m-macosx_10_14_x86_64.whl (2.4 MB)
Collecting scikit-learn
Using cached scikit_learn-1.0.2-cp37-cp37m-macosx_10_13_x86_64.whl (7.8 MB)
Collecting scikit-image
Using cached scikit_image-0.19.3-cp37-cp37m-macosx_10_13_x86_64.whl (13.2 MB)
Collecting requests
Using cached requests-2.28.1-py3-none-any.whl (62 kB)
Collecting importlib-metadata
Using cached importlib_metadata-4.12.0-py3-none-any.whl (21 kB)
Collecting toolz>=0.8.0
Using cached toolz-0.12.0-py3-none-any.whl (55 kB)
Requirement already satisfied: python-dateutil>=2.7.3 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from pandas->cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (2.8.2)
Requirement already satisfied: pytz>=2017.3 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from pandas->cooler>=0.8.5->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 1)) (2022.2.1)
Requirement already satisfied: packaging>=20.0 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (21.3)
Requirement already satisfied: cycler>=0.10 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (4.37.3)
Requirement already satisfied: pyparsing>=2.2.1 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (3.0.9)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (1.4.4)
Requirement already satisfied: pillow>=6.2.0 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (9.2.0)
Collecting dill>=0.3.5.1
Using cached dill-0.3.5.1-py2.py3-none-any.whl (95 kB)
Collecting llvmlite<0.40,>=0.39.0dev0
Using cached llvmlite-0.39.1-cp37-cp37m-macosx_10_9_x86_64.whl (25.5 MB)
Requirement already satisfied: setuptools<60 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from numba->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (59.8.0)
Collecting networkx>=2.2
Using cached networkx-2.6.3-py3-none-any.whl (1.9 MB)
Collecting imageio>=2.4.1
Using cached imageio-2.22.0-py3-none-any.whl (3.4 MB)
Collecting tifffile>=2019.7.26
Using cached tifffile-2021.11.2-py3-none-any.whl (178 kB)
Collecting PyWavelets>=1.1.1
Using cached PyWavelets-1.3.0-cp37-cp37m-macosx_10_13_x86_64.whl (4.3 MB)
Collecting threadpoolctl>=2.0.0
Using cached threadpoolctl-3.1.0-py3-none-any.whl (14 kB)
Requirement already satisfied: typing-extensions in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from kiwisolver>=1.0.1->matplotlib->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (4.3.0)
Collecting zipp>=0.5
Using cached zipp-3.8.1-py3-none-any.whl (5.6 kB)
Requirement already satisfied: certifi>=2017.4.17 in /Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages (from requests->bioframe>=0.3.3->cooltools>=0.5.0->-r /Users/isenhart/pentads/condaenv.c7jpgos3.requirements.txt (line 2)) (2022.9.14)
Collecting urllib3<1.27,>=1.21.1
Using cached urllib3-1.26.12-py2.py3-none-any.whl (140 kB)
Collecting charset-normalizer<3,>=2
Using cached charset_normalizer-2.1.1-py3-none-any.whl (39 kB)
Collecting idna<4,>=2.5
Using cached idna-3.4-py3-none-any.whl (61 kB)
Building wheels for collected packages: cooltools, cytoolz, pypairix
Building wheel for cooltools (setup.py): started
Building wheel for cooltools (setup.py): finished with status 'error'
Running setup.py clean for cooltools
Building wheel for cytoolz (setup.py): started
Building wheel for cytoolz (setup.py): finished with status 'error'
Running setup.py clean for cytoolz
Building wheel for pypairix (setup.py): started
Building wheel for pypairix (setup.py): finished with status 'error'
Running setup.py clean for pypairix
Failed to build cooltools cytoolz pypairix
Installing collected packages: pypairix, asciitree, zipp, urllib3, toolz, tifffile, threadpoolctl, simplejson, pyyaml, PyWavelets, pyfaidx, networkx, llvmlite, joblib, imageio, idna, h5py, dill, charset-normalizer, scikit-learn, scikit-image, requests, multiprocess, importlib-metadata, cytoolz, numba, click, bioframe, cooler, cooltools
Running setup.py install for pypairix: started
Running setup.py install for pypairix: finished with status 'error'
Pip subprocess error:
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [59 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/cooltools
copying cooltools/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools
copying cooltools/main.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/saddle.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/eigs_cis.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/util.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/eigs_trans.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/dots.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/insulation.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/pileup.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/expected_cis.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/sample.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/logbin_expected.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/expected_trans.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
copying cooltools/cli/genome.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/cli
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/expected_smoothing.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/cool2cworld.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/pairs_scaling_functions.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/balance.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
copying cooltools/sandbox/contrast.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/sandbox
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/peaks.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/checks.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/numutils.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/plotting.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/_query.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/io.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/schemas.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/common.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
copying cooltools/lib/runlength.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/lib
creating build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/saddle.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/directionality.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/init.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/coverage.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/insulation.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/expected.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/sample.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/eigdecomp.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/dotfinder.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
copying cooltools/api/snipping.py -> build/lib.macosx-10.9-x86_64-3.7/cooltools/api
running build_ext
building 'cooltools.lib._numutils' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/cooltools
creating build/temp.macosx-10.9-x86_64-3.7/cooltools/lib
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/numpy/core/include -I/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/numpy/core/include -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c cooltools/lib/_numutils.c -o build/temp.macosx-10.9-x86_64-3.7/cooltools/lib/_numutils.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for cooltools
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [58 lines of output]
[1/5] Cythonizing cytoolz/utils.pyx
[2/5] Cythonizing cytoolz/dicttoolz.pyx
[3/5] Cythonizing cytoolz/functoolz.pyx
[4/5] Cythonizing cytoolz/itertoolz.pyx
[5/5] Cythonizing cytoolz/recipes.pyx
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-3.7
creating build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/compatibility.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/utils_test.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/_version.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/init.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/_signatures.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
creating build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/curried/operator.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/curried/init.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/curried/exceptions.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/curried
copying cytoolz/itertoolz.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/dicttoolz.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/functoolz.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/recipes.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/utils.pyx -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/utils.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/init.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/recipes.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/functoolz.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/dicttoolz.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/cpython.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
copying cytoolz/itertoolz.pxd -> build/lib.macosx-10.9-x86_64-3.7/cytoolz
creating build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_none_safe.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_utils.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_curried.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_compatibility.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_embedded_sigs.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_functoolz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_inspect_args.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_doctests.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_tlz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_signatures.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/dev_skip_test.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_recipes.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_docstrings.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_dev_skip_test.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_dicttoolz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_serialization.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_curried_toolzlike.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
copying cytoolz/tests/test_itertoolz.py -> build/lib.macosx-10.9-x86_64-3.7/cytoolz/tests
running build_ext
building 'cytoolz.dicttoolz' extension
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/cytoolz
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c cytoolz/dicttoolz.c -o build/temp.macosx-10.9-x86_64-3.7/cytoolz/dicttoolz.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for cytoolz
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [12 lines of output]
/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/setuptools/dist.py:726: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
% (opt, underscore_opt)
running bdist_wheel
running build
running build_ext
building 'pypairix' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c src/bgzf.c -o build/temp.macosx-10.9-x86_64-3.7/src/bgzf.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pypairix
error: subprocess-exited-with-error
× Running setup.py install for pypairix did not run successfully.
│ exit code: 1
╰─> [14 lines of output]
/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/setuptools/dist.py:726: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
% (opt, underscore_opt)
running install
/Users/isenhart/opt/anaconda3/envs/pentads/lib/python3.7/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
setuptools.SetuptoolsDeprecationWarning,
running build
running build_ext
building 'pypairix' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.7
creating build/temp.macosx-10.9-x86_64-3.7/src
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -I/Users/isenhart/opt/anaconda3/envs/pentads/include -arch x86_64 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE=1 -Isrc -I/Users/isenhart/opt/anaconda3/envs/pentads/include/python3.7m -c src/bgzf.c -o build/temp.macosx-10.9-x86_64-3.7/src/bgzf.o
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
error: command 'gcc' failed with exit status 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> pypairix
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
failed
CondaEnvException: Pip failed
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