dysgu Installation Note

I was interested in trying Dysgu, and created a fresh conda environment with python 3.10. When I tried to install dysgu within that fresh env, I got the following error:

(dysgu)$ pip install dysgu
ERROR: Could not find a version that satisfies the requirement dysgu (from versions: none)
ERROR: No matching distribution found for dysgu

This seemed odd to me, and may have something to do with it the new version released 1 day before.

However, when I dropped my python version down to 3.7 it went through (I did have to install numpy first). This is just for your documentation or others' troubleshooting.

Feb 07 '22 10:02 nickhsmith

Hi, thanks for pointing this out, python 3.10 is not yet supported on pypi. I will add this to the documentation. Im not sure why you needed to install numpy first though, I will have to investigate that

Feb 07 '22 10:02 kcleal

Thanks! I look forward to trying the tool. For recreating my error this was my process

conda create -n dysgu_env python==3.7
pip install dysgu

Collecting dysgu
  Downloading dysgu-1.3.5-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (70.5 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 70.5/70.5 MB 18.4 MB/s eta 0:00:00
Collecting scikit-learn
  Downloading scikit_learn-1.0.2-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (24.8 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 24.8/24.8 MB 33.5 MB/s eta 0:00:00
Collecting ncls
  Downloading ncls-0.0.63.tar.gz (467 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 467.0/467.0 KB 14.7 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Collecting cython
  Downloading Cython-0.29.27-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 39.3 MB/s eta 0:00:00
Collecting numpy>=1.16.5
  Downloading numpy-1.21.5-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 43.1 MB/s eta 0:00:00
Requirement already satisfied: sortedcontainers in PATH/lib/python3.7/site-packages (from dysgu) (2.2.2)
Collecting scipy
  Downloading scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 38.1/38.1 MB 28.4 MB/s eta 0:00:00
Collecting networkx>=2.4
  Downloading networkx-2.6.3-py3-none-any.whl (1.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.9/1.9 MB 30.1 MB/s eta 0:00:00
Collecting scikit-bio
  Downloading scikit-bio-0.5.6.tar.gz (8.4 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.4/8.4 MB 46.8 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [6 lines of output]
      Traceback (most recent call last):
        File "<string>", line 36, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/scratch/tmp/smith/pip-install-r915jx9v/scikit-bio_7e74df2fd52d43e5965fb82e566ef36b/setup.py", line 20, in <module>
          import numpy as np
      ModuleNotFoundError: No module named 'numpy'
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

install numpy pip install numpy
pip install dysgu

Then it seemed to have worked

Feb 07 '22 10:02 nickhsmith

Hi, I have the same installation issue. I tried the above solution (create a conda new env with python==3.7 and install numpy first), but I still got this error:

$ pip install dysgu
ERROR: Could not find a version that satisfies the requirement dysgu (from versions: none)
ERROR: No matching distribution found for dysgu

I have also tried to install all required packages listed here in conda env first and then use pip install dysgu. No matter under python 3.6.7, 3.7.11 or 3.8.1 env, it didn't work.

I use MacOS 10.15.7.

Any suggestion? Thank you

Feb 09 '22 16:02 YYeah

Hi, I have the same issue with YYeah's comment, and I also tried each step in the INSTALL.sh file, and the python3 setup.py install is the specific step that failed. I am under Mac 11.6.1. Thank you.

Feb 09 '22 17:02 Bingbing19

Thanks for raising this. Could you try pip install dysgu==1.3.4? Im not sure what is causing this yet, but looking in to it. Would you be able to post the error message from python setup.py install, thanks

Feb 09 '22 19:02 kcleal

pip install dysgu==1.3.4 does not work for me with ERROR: Could not find a version that satisfies the requirement dysgu==1.3.4 (from versions: none) ERROR: No matching distribution found for dysgu==1.3.4

python setup.py install error is as following. And I am using Python 3.8.12. gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/opt/anaconda3/envs/test/include -arch x86_64 -I/opt/anaconda3/envs/test/include -arch x86_64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/opt/anaconda3/envs/test/lib/python3.8/site-packages/numpy/core/include -I/Users/name/dysgu -I/Users/name/dysgu/dysgu/htslib/htslib -I/Users/name/dysgu/dysgu/htslib/cram -I/opt/anaconda3/envs/test/lib/python3.8/site-packages/pysam -I/opt/anaconda3/envs/test/lib/python3.8/site-packages/pysam/include/htslib -I/opt/anaconda3/envs/test/lib/python3.8/site-packages/pysam/include/samtools -I/opt/anaconda3/envs/test/include/python3.8 -c dysgu/sv2bam.cpp -o build/temp.macosx-10.9-x86_64-3.8/dysgu/sv2bam.o -std=c++11 -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile 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

Feb 09 '22 20:02 Bingbing19

pip install dysgu==1.3.4 doesn't work for me as well.

Feb 09 '22 20:02 YYeah

Earlier today pip install dysgu==1.3.4 would not work as generated this error ERROR: No matching distribution found for dysgu==1.3.4 but pip install dysgu==1.3.7 did install, but it still wouldn't run. Now, there is no version that appears to be available through pip install dysgu. All approaches that allowed an install (pip install dysgu==1.3.7 or via git) still failed to run (python 3.7 or 3.9.6)

Feb 10 '22 03:02 kaplancd

The latest version on pypi is only 1.3.5 https://pypi.org/search/?q=dysgu. I'm wondering if this is a problem with xcode? See this post: https://apple.stackexchange.com/questions/254380/why-am-i-getting-an-invalid-active-developer-path-when-attempting-to-use-git-a

Feb 10 '22 09:02 kcleal

For the manual install on the mac it seems like issue could be the c++ compiler as was reading that mac uses clang and clang++ and not g++. However, it is still not clear why pip install returns ``` ERROR: Could not find a version that satisfies the requirement dysgu (from versions: none) ERROR: No matching distribution found for dysgu

Feb 10 '22 17:02 kaplancd

It is confusing. I have not problems building with clang, so not sure what is going. The other option would be to try docker. I will get try and get a docker image published asap

Feb 10 '22 18:02 kcleal

Hi! this neither worked for me! (base) gerardo@Gerardos-MacBook-Pro / % pip install dysgu==1.3.4 ERROR: Could not find a version that satisfies the requirement dysgu==1.3.4 (from versions: none) ERROR: No matching distribution found for dysgu==1.3.4

Feb 07 '23 17:02 Gedofs

@Gedofs, are you using an M1 chip by any chance?

Feb 07 '23 21:02 kcleal

Yes, I am. However, I am considering to use docker or to first install the requirements (in fact, none of them working for me)

Feb 07 '23 21:02 Gedofs

Have you tried building dysgu from source? I can try a build on M1 tomorrow...

Feb 07 '23 21:02 kcleal

Yes, im working on that but I havent succeeded yet. It would be awesome if you try a build on M1

Feb 07 '23 21:02 Gedofs

Seems like there other issues related to the installation. Here is an example...

bash-3.2$ sudo pip3 install -r cython click>=8.0 numpy scipy pandas pysam networkx>=2.4 scikit-learn>=0.22 edlib sortedcontainers lightgbm
Password: WARNING: The directory '/Users/gerardo/Library/Caches/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag.

ERROR: Could not open requirements file: [Errno 2] No such file or directory: 'cython' bash-3.2$ sudo -H pip3 install -r cython click>=8.0 numpy scipy pandas pysam networkx>=2.4 scikit-learn>=0.22 edlib sortedcontainers lightgbm

ERROR: Could not open requirements file: [Errno 2] No such file or directory: 'cython'

Feb 07 '23 21:02 Gedofs

Are you using the system default python? If so I recommend installing miniconda instead. It should make installing the dependencies easy at least

Feb 07 '23 22:02 kcleal

yes, im using default python. Thanks for comment, Ill try with miniconda

Feb 07 '23 22:02 Gedofs

Hi @Gedofs, did you manage to build? I tested the build on an Apple M1 and it worked, although some of the dependencies did not install using pip (lightgbm and pysam). To get those dependencies I used conda to install them, then dysgu build worked. I first downloaded dysgu from the releases page, then used bash INSTALL.sh, then after fixing dependencies, used python setup.py install. Hope that helps

Feb 08 '23 13:02 kcleal

Hi @kcleal , I´m working on onstallation, however I will better follow your suggestion! Ill let you know how it goes!

Feb 08 '23 15:02 Gedofs

*I still have problems... Is there an other way to install pysam? Is it ok if I install lightgbm using homebrew?

PackagesNotFoundError: The following packages are not available from current channels:

pysam Current channels:
https://conda.anaconda.org/bioconda/osx-arm64
https://conda.anaconda.org/bioconda/noarch
https://conda.anaconda.org/r/osx-arm64
https://conda.anaconda.org/r/noarch
https://conda.anaconda.org/conda-forge/osx-arm64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/osx-arm64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-arm64
https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

Feb 08 '23 16:02 Gedofs

Seems that I already have installed pysam

(base) gerardo@Gerardos-MacBook-Pro / % pip install pysam

Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (0.19.1)

*** Here is the problem: error: legacy-install-failure

Feb 08 '23 16:02 Gedofs

Seems like it is already installed but not sure how ir works.

By the way, Can I analyze SV from pacbio HiFi CCS long reads and illumina exome short read sequencing?

Feb 08 '23 17:02 Gedofs

Could you share the full error output. Thanks

Sent from Outlook for Androidhttps://aka.ms/AAb9ysg

From: Gerardo Fabián @.> Sent: Wednesday, February 8, 2023 5:42:52 PM To: kcleal/dysgu @.> Cc: Kez Cleal @.>; Mention @.> Subject: Re: [kcleal/dysgu] Installation Note (Issue #21)

External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

[Screenshot 2023-02-08 at 11 42 30]https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F94254364%2F217609668-d293ff93-05c8-4b1a-9015-96665d96e9c0.png&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C9433c92ab80145fe74dc08db09fbe7d9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114749747227484%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yLYOMn8R8oWOgxshoRkVrMQKsN9yP1iil%2FgcNMMWBIQ%3D&reserved=0

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkcleal%2Fdysgu%2Fissues%2F21%23issuecomment-1423003884&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C9433c92ab80145fe74dc08db09fbe7d9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114749747227484%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GHxb%2BIU5HVKZzk8SZn3ncqnYmmS8atu4XY3WZPsgFJ0%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAKIBQHPTFHZCAIIZIXGDQPLWWPLJZANCNFSM5NXA26IA&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C9433c92ab80145fe74dc08db09fbe7d9%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114749747227484%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Gm7ACw1pPqKAvio15hyGxdZTc79GyrJSifhG%2Bznl0Zg%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

Feb 08 '23 18:02 kcleal

(base) gerardo@Gerardos-MacBook-Pro htslib % make cd ../../ pip install -r requirements.txt pip install . make: *** No targets specified and no makefile found. Stop. Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (8.1.3) Requirement already satisfied: numpy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.1.1) Collecting edlib Downloading edlib-1.3.9.tar.gz (91 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.4/91.4 kB 1.2 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (2.4.0) Collecting lightgbm Using cached lightgbm-3.3.5.tar.gz (1.5 MB) Preparing metadata (setup.py) ... done Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2022.1) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (1.1.0) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (3.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->-r requirements.txt (line 11)) (0.38.4) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->-r requirements.txt (line 5)) (1.16.0) Building wheels for collected packages: edlib, lightgbm Building wheel for edlib (setup.py) ... done Created wheel for edlib: filename=edlib-1.3.9-cp39-cp39-macosx_11_0_arm64.whl size=57270 sha256=6f7cfa225f1fe51dd9a258ba3c9e338bc02b42d5967096d4af20847f76a444fc Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/29/51/4b/4a8f1b2f4d3027d7940f11e0c4a914c54afe512f625c8f5bd9 Building wheel for lightgbm (setup.py) ... done Created wheel for lightgbm: filename=lightgbm-3.3.5-py3-none-any.whl size=1085139 sha256=cfeaa68b786f3597334d4829e9145569df551565e64bb88f07e2d6c1b5c6676b Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/f8/4b/7b/f32d3b4a00a2992aa795a722a50dea28613869d453dc280b8c Successfully built edlib lightgbm Installing collected packages: edlib, lightgbm Successfully installed edlib-1.3.9 lightgbm-3.3.5 Processing /Users/gerardo/LightGBM/build/dysgu Preparing metadata (setup.py) ... done Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (8.1.3) Requirement already satisfied: numpy>=1.18 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.1.1) Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.4.0) Requirement already satisfied: lightgbm in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (3.3.5) Requirement already satisfied: edlib in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.3.9) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (3.1.0) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (1.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->dysgu==1.3.14) (0.38.4) Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2022.1) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->dysgu==1.3.14) (1.16.0) Building wheels for collected packages: dysgu Building wheel for dysgu (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running bdist_wheel running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info creating dysgu.egg-info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt writing manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960: /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with "
^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for dysgu Running setup.py clean for dysgu Failed to build dysgu Installing collected packages: dysgu Running setup.py install for dysgu ... error error: subprocess-exited-with-error

× Running setup.py install for dysgu did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running install /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960: /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with "
^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 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. ╰─> dysgu

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

Feb 08 '23 18:02 Gedofs

Ah ok, it looks like htslib is not installing properly. It looks like the rest of the dependencies installed though.

Can you try getting dysgu from the releases page:

wget https://github.com/kcleal/dysgu/releases/download/v1.3.12/dysgu.tar.bz2 tar -xvf dysgu.tar.bz2 && cd dysgu

bash INSTALL.sh

Kez

On 8 Feb 2023, at 18:43, Gerardo Fabián @.@.>> wrote:

External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

(base) @.*** htslib % make cd ../../ pip install -r requirements.txt pip install . make: *** No targets specified and no makefile found. Stop. Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (8.1.3) Requirement already satisfied: numpy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.1.1) Collecting edlib Downloading edlib-1.3.9.tar.gz (91 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.4/91.4 kB 1.2 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (2.4.0) Collecting lightgbm Using cached lightgbm-3.3.5.tar.gz (1.5 MB) Preparing metadata (setup.py) ... done Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2022.1) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (1.1.0) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (3.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->-r requirements.txt (line 11)) (0.38.4) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->-r requirements.txt (line 5)) (1.16.0) Building wheels for collected packages: edlib, lightgbm Building wheel for edlib (setup.py) ... done Created wheel for edlib: filename=edlib-1.3.9-cp39-cp39-macosx_11_0_arm64.whl size=57270 sha256=6f7cfa225f1fe51dd9a258ba3c9e338bc02b42d5967096d4af20847f76a444fc Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/29/51/4b/4a8f1b2f4d3027d7940f11e0c4a914c54afe512f625c8f5bd9 Building wheel for lightgbm (setup.py) ... done Created wheel for lightgbm: filename=lightgbm-3.3.5-py3-none-any.whl size=1085139 sha256=cfeaa68b786f3597334d4829e9145569df551565e64bb88f07e2d6c1b5c6676b Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/f8/4b/7b/f32d3b4a00a2992aa795a722a50dea28613869d453dc280b8c Successfully built edlib lightgbm Installing collected packages: edlib, lightgbm Successfully installed edlib-1.3.9 lightgbm-3.3.5 Processing /Users/gerardo/LightGBM/build/dysgu Preparing metadata (setup.py) ... done Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (8.1.3) Requirement already satisfied: numpy>=1.18 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.1.1) Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.4.0) Requirement already satisfied: lightgbm in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (3.3.5) Requirement already satisfied: edlib in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.3.9) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (3.1.0) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (1.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->dysgu==1.3.14) (0.38.4) Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2022.1) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->dysgu==1.3.14) (1.16.0) Building wheels for collected packages: dysgu Building wheel for dysgu (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running bdist_wheel running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info creating dysgu.egg-info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt writing manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960: /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for dysgu Running setup.py clean for dysgu Failed to build dysgu Installing collected packages: dysgu Running setup.py install for dysgu ... error error: subprocess-exited-with-error

× Running setup.py install for dysgu did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools'] Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running install /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960: /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 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. ╰─> dysgu

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkcleal%2Fdysgu%2Fissues%2F21%23issuecomment-1423078240&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7CePRDhG624YgASXQvKDV6FZpjRgO6m5X6cdqZpFu2k%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAKIBQHKKBXDC46MLYYFZZM3WWPSLNANCNFSM5NXA26IA&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C8CTRhPr%2F2bsFay%2BGiil75VS2y%2FiD7mhakcUQzXb9q0%3D&reserved=0. You are receiving this because you were mentioned.Message ID: @.***>

Feb 08 '23 19:02 kcleal

thanks, i will

El mié, 8 feb 2023 a la(s) 13:11, Kez Cleal @.***) escribió:

Ah ok, it looks like htslib is not installing properly. It looks like the rest of the dependencies installed though.

Can you try getting dysgu from the releases page:

wget https://github.com/kcleal/dysgu/releases/download/v1.3.12/dysgu.tar.bz2 tar -xvf dysgu.tar.bz2 && cd dysgu

bash INSTALL.sh

Kez

On 8 Feb 2023, at 18:43, Gerardo Fabián @.@.>> wrote:

External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

(base) @.*** htslib % make cd ../../ pip install -r requirements.txt pip install . make: *** No targets specified and no makefile found. Stop. Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (8.1.3) Requirement already satisfied: numpy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.1.1) Collecting edlib Downloading edlib-1.3.9.tar.gz (91 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.4/91.4 kB 1.2 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (2.4.0) Collecting lightgbm Using cached lightgbm-3.3.5.tar.gz (1.5 MB) Preparing metadata (setup.py) ... done Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2022.1) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (1.1.0) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (3.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->-r requirements.txt (line 11)) (0.38.4) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->-r requirements.txt (line 5)) (1.16.0) Building wheels for collected packages: edlib, lightgbm Building wheel for edlib (setup.py) ... done Created wheel for edlib: filename=edlib-1.3.9-cp39-cp39-macosx_11_0_arm64.whl size=57270 sha256=6f7cfa225f1fe51dd9a258ba3c9e338bc02b42d5967096d4af20847f76a444fc Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/29/51/4b/4a8f1b2f4d3027d7940f11e0c4a914c54afe512f625c8f5bd9

Building wheel for lightgbm (setup.py) ... done Created wheel for lightgbm: filename=lightgbm-3.3.5-py3-none-any.whl size=1085139 sha256=cfeaa68b786f3597334d4829e9145569df551565e64bb88f07e2d6c1b5c6676b Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/f8/4b/7b/f32d3b4a00a2992aa795a722a50dea28613869d453dc280b8c

Successfully built edlib lightgbm Installing collected packages: edlib, lightgbm Successfully installed edlib-1.3.9 lightgbm-3.3.5 Processing /Users/gerardo/LightGBM/build/dysgu Preparing metadata (setup.py) ... done Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (8.1.3) Requirement already satisfied: numpy>=1.18 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.1.1) Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.4.0) Requirement already satisfied: lightgbm in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (3.3.5) Requirement already satisfied: edlib in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.3.9) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (3.1.0) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (1.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->dysgu==1.3.14) (0.38.4) Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2022.1) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->dysgu==1.3.14) (1.16.0) Building wheels for collected packages: dysgu Building wheel for dysgu (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running bdist_wheel running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info creating dysgu.egg-info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt writing manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:

/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for dysgu Running setup.py clean for dysgu Failed to build dysgu Installing collected packages: dysgu Running setup.py install for dysgu ... error error: subprocess-exited-with-error

× Running setup.py install for dysgu did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running install /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:

/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 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. ╰─> dysgu

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

— Reply to this email directly, view it on GitHub< https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkcleal%2Fdysgu%2Fissues%2F21%23issuecomment-1423078240&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7CePRDhG624YgASXQvKDV6FZpjRgO6m5X6cdqZpFu2k%3D&reserved=0>, or unsubscribe< https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAKIBQHKKBXDC46MLYYFZZM3WWPSLNANCNFSM5NXA26IA&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C8CTRhPr%2F2bsFay%2BGiil75VS2y%2FiD7mhakcUQzXb9q0%3D&reserved=0>.

You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/kcleal/dysgu/issues/21#issuecomment-1423109682, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWPDKHFXCS2OCFJS3YR3RJDWWPVUZANCNFSM5NXA26IA . You are receiving this because you were mentioned.Message ID: @.***>

Feb 08 '23 19:02 Gedofs

Installing dysgu script to /Users/gerardo/opt/anaconda3/bin

Installed /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg

Processing dependencies for dysgu==1.3.12

Searching for dysgu==1.3.12

Reading https://pypi.org/simple/dysgu/

No local packages or working download links found for dysgu==1.3.12

error: Could not find suitable distribution for Requirement.parse('dysgu==1.3.12')

Traceback (most recent call last):

File "/Users/gerardo/opt/anaconda3/bin/dysgu", line 33, in

sys.exit(load_entry_point('dysgu==1.3.12', 'console_scripts',

'dysgu')())

File "/Users/gerardo/opt/anaconda3/bin/dysgu", line 25, in importlib_load_entry_point

return next(matches).load()

File "/Users/gerardo/opt/anaconda3/lib/python3.9/importlib/metadata.py", line 86, in load

module = import_module(match.group('module'))

File "/Users/gerardo/opt/anaconda3/lib/python3.9/importlib/init.py", line 127, in import_module

return _bootstrap._gcd_import(name[level:], package, level)

File "", line 1030, in _gcd_import

File "", line 1007, in _find_and_load

File "", line 972, in _find_and_load_unlocked

File "", line 228, in _call_with_frames_removed

File "", line 1030, in _gcd_import

File "", line 1007, in _find_and_load

File "", line 986, in _find_and_load_unlocked

File "", line 680, in _load_unlocked

File "", line 850, in exec_module

File "", line 228, in _call_with_frames_removed

File "/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/init.py", line 2, in

from dysgu.python_api import DysguSV,\

File "/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/python_api.py", line 9, in

from dysgu.cluster import pipe1, merge_events

ImportError: dlopen(/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/ cluster.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/lib/libhts.3.dylib

Referenced from: <3C2C31C3-E4EB-34FF-891E-427C38D4A92D> /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/ cluster.cpython-39-darwin.so

Reason: tried: '/usr/local/lib/libhts.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libhts.3.dylib' (no such file), '/usr/local/lib/libhts.3.dylib' (no such file), '/usr/lib/libhts.3.dylib' (no such file, not in dyld cache)

Done

El mié, 8 feb 2023 a la(s) 13:49, Gerardo Fabián @.***) escribió:

thanks, i will

El mié, 8 feb 2023 a la(s) 13:11, Kez Cleal @.***) escribió:

Ah ok, it looks like htslib is not installing properly. It looks like the rest of the dependencies installed though.

Can you try getting dysgu from the releases page:

wget https://github.com/kcleal/dysgu/releases/download/v1.3.12/dysgu.tar.bz2 tar -xvf dysgu.tar.bz2 && cd dysgu

bash INSTALL.sh

Kez

On 8 Feb 2023, at 18:43, Gerardo Fabián @.@.>> wrote:

External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

(base) @.*** htslib % make cd ../../ pip install -r requirements.txt pip install . make: *** No targets specified and no makefile found. Stop. Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (8.1.3) Requirement already satisfied: numpy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.1.1) Collecting edlib Downloading edlib-1.3.9.tar.gz (91 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.4/91.4 kB 1.2 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (2.4.0) Collecting lightgbm Using cached lightgbm-3.3.5.tar.gz (1.5 MB) Preparing metadata (setup.py) ... done Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2022.1) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (1.1.0) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (3.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->-r requirements.txt (line 11)) (0.38.4) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->-r requirements.txt (line 5)) (1.16.0) Building wheels for collected packages: edlib, lightgbm Building wheel for edlib (setup.py) ... done Created wheel for edlib: filename=edlib-1.3.9-cp39-cp39-macosx_11_0_arm64.whl size=57270 sha256=6f7cfa225f1fe51dd9a258ba3c9e338bc02b42d5967096d4af20847f76a444fc Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/29/51/4b/4a8f1b2f4d3027d7940f11e0c4a914c54afe512f625c8f5bd9

Building wheel for lightgbm (setup.py) ... done Created wheel for lightgbm: filename=lightgbm-3.3.5-py3-none-any.whl size=1085139 sha256=cfeaa68b786f3597334d4829e9145569df551565e64bb88f07e2d6c1b5c6676b Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/f8/4b/7b/f32d3b4a00a2992aa795a722a50dea28613869d453dc280b8c

Successfully built edlib lightgbm Installing collected packages: edlib, lightgbm Successfully installed edlib-1.3.9 lightgbm-3.3.5 Processing /Users/gerardo/LightGBM/build/dysgu Preparing metadata (setup.py) ... done Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (8.1.3) Requirement already satisfied: numpy>=1.18 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.1.1) Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.4.0) Requirement already satisfied: lightgbm in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (3.3.5) Requirement already satisfied: edlib in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.3.9) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (3.1.0) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (1.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->dysgu==1.3.14) (0.38.4) Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2022.1) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->dysgu==1.3.14) (1.16.0) Building wheels for collected packages: dysgu Building wheel for dysgu (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running bdist_wheel running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info creating dysgu.egg-info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt writing manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:

/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for dysgu Running setup.py clean for dysgu Failed to build dysgu Installing collected packages: dysgu Running setup.py install for dysgu ... error error: subprocess-exited-with-error

× Running setup.py install for dysgu did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running install /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:

/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 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. ╰─> dysgu

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

— Reply to this email directly, view it on GitHub< https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkcleal%2Fdysgu%2Fissues%2F21%23issuecomment-1423078240&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7CePRDhG624YgASXQvKDV6FZpjRgO6m5X6cdqZpFu2k%3D&reserved=0>, or unsubscribe< https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAKIBQHKKBXDC46MLYYFZZM3WWPSLNANCNFSM5NXA26IA&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C8CTRhPr%2F2bsFay%2BGiil75VS2y%2FiD7mhakcUQzXb9q0%3D&reserved=0>.

You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/kcleal/dysgu/issues/21#issuecomment-1423109682, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWPDKHFXCS2OCFJS3YR3RJDWWPVUZANCNFSM5NXA26IA . You are receiving this because you were mentioned.Message ID: @.***>

Feb 08 '23 19:02 Gedofs

seems like libhts.3.dylib is not installed.

El mié, 8 feb 2023 a la(s) 13:56, Gerardo Fabián @.***) escribió:

Installing dysgu script to /Users/gerardo/opt/anaconda3/bin

Installed /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg

Processing dependencies for dysgu==1.3.12

Searching for dysgu==1.3.12

Reading https://pypi.org/simple/dysgu/

No local packages or working download links found for dysgu==1.3.12

error: Could not find suitable distribution for Requirement.parse('dysgu==1.3.12')

Traceback (most recent call last):

File "/Users/gerardo/opt/anaconda3/bin/dysgu", line 33, in
sys.exit(load_entry_point('dysgu==1.3.12', 'console_scripts',
'dysgu')())

File "/Users/gerardo/opt/anaconda3/bin/dysgu", line 25, in importlib_load_entry_point
return next(matches).load()
File "/Users/gerardo/opt/anaconda3/lib/python3.9/importlib/metadata.py", line 86, in load
module = import_module(match.group('module'))
File "/Users/gerardo/opt/anaconda3/lib/python3.9/importlib/init.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import

File "", line 1007, in _find_and_load

File "", line 972, in _find_and_load_unlocked

File "", line 228, in _call_with_frames_removed

File "", line 1030, in _gcd_import

File "", line 1007, in _find_and_load

File "", line 986, in _find_and_load_unlocked

File "", line 680, in _load_unlocked

File "", line 850, in exec_module

File "", line 228, in _call_with_frames_removed

File "/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/init.py", line 2, in
from dysgu.python_api import DysguSV,\
File "/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/python_api.py", line 9, in
from dysgu.cluster import pipe1, merge_events
ImportError: dlopen(/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/ cluster.cpython-39-darwin.so, 0x0002): Library not loaded: /usr/local/lib/libhts.3.dylib

Referenced from: <3C2C31C3-E4EB-34FF-891E-427C38D4A92D> /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/dysgu-1.3.12-py3.9-macosx-11.0-arm64.egg/dysgu/ cluster.cpython-39-darwin.so

Reason: tried: '/usr/local/lib/libhts.3.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/usr/local/lib/libhts.3.dylib' (no such file), '/usr/local/lib/libhts.3.dylib' (no such file), '/usr/lib/libhts.3.dylib' (no such file, not in dyld cache)

Done

El mié, 8 feb 2023 a la(s) 13:49, Gerardo Fabián @.***) escribió:

thanks, i will

El mié, 8 feb 2023 a la(s) 13:11, Kez Cleal @.***) escribió:

Ah ok, it looks like htslib is not installing properly. It looks like the rest of the dependencies installed though.

Can you try getting dysgu from the releases page:

wget https://github.com/kcleal/dysgu/releases/download/v1.3.12/dysgu.tar.bz2 tar -xvf dysgu.tar.bz2 && cd dysgu

bash INSTALL.sh

Kez

On 8 Feb 2023, at 18:43, Gerardo Fabián @.@.>> wrote:

External email to Cardiff University - Take care when replying/opening attachments or links. Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth ateb/agor atodiadau neu ddolenni.

(base) @.*** htslib % make cd ../../ pip install -r requirements.txt pip install . make: *** No targets specified and no makefile found. Stop. Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 1)) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 2)) (8.1.3) Requirement already satisfied: numpy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 3)) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 4)) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 5)) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 6)) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 7)) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 8)) (1.1.1) Collecting edlib Downloading edlib-1.3.9.tar.gz (91 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 91.4/91.4 kB 1.2 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from -r requirements.txt (line 10)) (2.4.0) Collecting lightgbm Using cached lightgbm-3.3.5.tar.gz (1.5 MB) Preparing metadata (setup.py) ... done Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->-r requirements.txt (line 5)) (2022.1) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (1.1.0) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->-r requirements.txt (line 8)) (3.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->-r requirements.txt (line 11)) (0.38.4) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->-r requirements.txt (line 5)) (1.16.0) Building wheels for collected packages: edlib, lightgbm Building wheel for edlib (setup.py) ... done Created wheel for edlib: filename=edlib-1.3.9-cp39-cp39-macosx_11_0_arm64.whl size=57270 sha256=6f7cfa225f1fe51dd9a258ba3c9e338bc02b42d5967096d4af20847f76a444fc Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/29/51/4b/4a8f1b2f4d3027d7940f11e0c4a914c54afe512f625c8f5bd9

Building wheel for lightgbm (setup.py) ... done Created wheel for lightgbm: filename=lightgbm-3.3.5-py3-none-any.whl size=1085139 sha256=cfeaa68b786f3597334d4829e9145569df551565e64bb88f07e2d6c1b5c6676b Stored in directory: /Users/gerardo/Library/Caches/pip/wheels/f8/4b/7b/f32d3b4a00a2992aa795a722a50dea28613869d453dc280b8c

Successfully built edlib lightgbm Installing collected packages: edlib, lightgbm Successfully installed edlib-1.3.9 lightgbm-3.3.5 Processing /Users/gerardo/LightGBM/build/dysgu Preparing metadata (setup.py) ... done Requirement already satisfied: cython in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.29.30) Requirement already satisfied: click>=8.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (8.1.3) Requirement already satisfied: numpy>=1.18 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.22.3) Requirement already satisfied: scipy in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.8.1) Requirement already satisfied: pandas in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.4.3) Requirement already satisfied: pysam in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (0.19.1) Requirement already satisfied: networkx>=2.4 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.8.4) Requirement already satisfied: scikit-learn>=0.22 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.1.1) Requirement already satisfied: sortedcontainers in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (2.4.0) Requirement already satisfied: lightgbm in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (3.3.5) Requirement already satisfied: edlib in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from dysgu==1.3.14) (1.3.9) Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (3.1.0) Requirement already satisfied: joblib>=1.0.0 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn>=0.22->dysgu==1.3.14) (1.1.0) Requirement already satisfied: wheel in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from lightgbm->dysgu==1.3.14) (0.38.4) Requirement already satisfied: python-dateutil>=2.8.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2.8.2) Requirement already satisfied: pytz>=2020.1 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from pandas->dysgu==1.3.14) (2022.1) Requirement already satisfied: six>=1.5 in /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.8.1->pandas->dysgu==1.3.14) (1.16.0) Building wheels for collected packages: dysgu Building wheel for dysgu (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running bdist_wheel running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info creating dysgu.egg-info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt writing manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:

/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for dysgu Running setup.py clean for dysgu Failed to build dysgu Installing collected packages: dysgu Running setup.py install for dysgu ... error error: subprocess-exited-with-error

× Running setup.py install for dysgu did not run successfully. │ exit code: 1 ╰─> [127 lines of output] Using packaged htslib Libs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/hts'] Library dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Include dirs ['/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include', '/Users/gerardo/LightGBM/build/dysgu', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib', '/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib', '/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools']

Runtime dirs ['/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib'] Extras compiler args ['-std=c++17', '-stdlib=libc++', '-Wno-sign-compare', '-Wno-unused-function', '-Wno-unused-result', '-Wno-ignored-qualifiers', '-Wno-deprecated-declarations', '-Wno-volatile'] Found packages ['scripts', 'dysgu', 'dysgu.tests', 'dysgu.scikitbio'] running install /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py creating build creating build/lib.macosx-11.0-arm64-cpython-39 creating build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/python_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/view.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/re_map.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sites_utils.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/main.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/test_api.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests creating build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/init.py -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running egg_info writing dysgu.egg-info/PKG-INFO writing dependency_links to dysgu.egg-info/dependency_links.txt writing entry points to dysgu.egg-info/entry_points.txt writing requirements to dysgu.egg-info/requires.txt writing top-level names to dysgu.egg-info/top_level.txt reading manifest file 'dysgu.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'dysgu/htslib/.o' warning: no files found matching 'dysgu/htslib/.c' warning: no files found matching 'dysgu/htslib/.h' warning: no files found matching 'dysgu/htslib/htslib/.h' warning: no files found matching 'dysgu/htslib/cram/.c' warning: no files found matching 'dysgu/htslib/cram/.h' warning: no directories found matching 'dysgu/htslib/os' warning: no directories found matching 'dysgu/htslib/m4' warning: no directories found matching 'dysgu/htslib/htscodecs/htscodecs' warning: no directories found matching 'dysgu/htslib/htscodecs/m4' no previously-included directories found matching 'dysgu/htslib/test' no previously-included directories found matching 'dysgu/htslib/htscodecs/test' warning: no previously-included files found matching 'dysgu/htslib/.' warning: no previously-included files found matching 'dysgu/scikitbio/.' adding license file 'LICENSE.md' writing manifest file 'dysgu.egg-info/SOURCES.txt' copying dysgu/IITreeBFS.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/assembler.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/call_component.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/cluster.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/coverage.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/dysgu_model.1.pkl.gz -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/find_reads.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/graph.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/io_funcs.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/map_set_utils.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/post_call_metrics.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/robin_hood.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv2bam.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.cpp -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pxd -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/sv_category.pyx -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/wrap_map_set2.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/xxhash64.h -> build/lib.macosx-11.0-arm64-cpython-39/dysgu copying dysgu/tests/ref.fa -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/ref.fa.fai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.bam.bai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.cram.crai -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/small.dysgu.sam -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/tests/targets.bed -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/tests copying dysgu/scikitbio/_ssw_wrapper.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio copying dysgu/scikitbio/ssw.c -> build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio running build_ext building 'dysgu.scikitbio._ssw_wrapper' extension creating build/temp.macosx-11.0-arm64-cpython-39 creating build/temp.macosx-11.0-arm64-cpython-39/dysgu creating build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/_ssw_wrapper.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/_ssw_wrapper.o -Wno-deprecated-declarations -std=c99 -I. In file included from dysgu/scikitbio/_ssw_wrapper.c:731: In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:5:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:

In file included from /Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1960:

/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings] #warning "Using deprecated NumPy API, disable it with " ^ dysgu/scikitbio/_ssw_wrapper.c:11708:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ dysgu/scikitbio/_ssw_wrapper.c:11719:21: warning: fallthrough annotation in unreachable code [-Wunreachable-code-fallthrough] CYTHON_FALLTHROUGH; ^ dysgu/scikitbio/_ssw_wrapper.c:325:34: note: expanded from macro 'CYTHON_FALLTHROUGH' #define CYTHON_FALLTHROUGH attribute((fallthrough)) ^ 3 warnings generated. clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -Idysgu/scikitbio -I/Users/gerardo/LightGBM/build/dysgu/dysgu/scikitbio -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/scikitbio/ssw.c -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -Wno-deprecated-declarations -std=c99 -I. clang -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib -Wl,-rpath,/Users/gerardo/opt/anaconda3/lib -L/Users/gerardo/opt/anaconda3/lib build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw_wrapper.o build/temp.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ssw.o -o build/lib.macosx-11.0-arm64-cpython-39/dysgu/scikitbio/ ssw_wrapper.cpython-39-darwin.so building 'dysgu.sv2bam' extension clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -fPIC -O2 -isystem /Users/gerardo/opt/anaconda3/include -arch arm64 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -Idysgu -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/gerardo/LightGBM/build/dysgu -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/htslib -I/Users/gerardo/LightGBM/build/dysgu/dysgu/htslib/cram -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/htslib -I/Users/gerardo/opt/anaconda3/lib/python3.9/site-packages/pysam/include/samtools -I/Users/gerardo/opt/anaconda3/include/python3.9 -c dysgu/sv2bam.cpp -o build/temp.macosx-11.0-arm64-cpython-39/dysgu/sv2bam.o -std=c++17 -stdlib=libc++ -Wno-sign-compare -Wno-unused-function -Wno-unused-result -Wno-ignored-qualifiers -Wno-deprecated-declarations -Wno-volatile warning: unknown warning option '-Wno-volatile' [-Wunknown-warning-option] In file included from dysgu/sv2bam.cpp:767: dysgu/find_reads.h:12:10: fatal error: 'htslib/htslib/sam.h' file not found #include "htslib/htslib/sam.h" ^~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command '/usr/bin/clang' failed with exit code 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. ╰─> dysgu

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

— Reply to this email directly, view it on GitHub< https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkcleal%2Fdysgu%2Fissues%2F21%23issuecomment-1423078240&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7CePRDhG624YgASXQvKDV6FZpjRgO6m5X6cdqZpFu2k%3D&reserved=0>, or unsubscribe< https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAKIBQHKKBXDC46MLYYFZZM3WWPSLNANCNFSM5NXA26IA&data=05%7C01%7Cclealk%40cardiff.ac.uk%7C92c1f8b6bffb4d415d8708db0a044fc0%7Cbdb74b3095684856bdbf06759778fcbc%7C1%7C0%7C638114785863615414%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=C8CTRhPr%2F2bsFay%2BGiil75VS2y%2FiD7mhakcUQzXb9q0%3D&reserved=0>.

You are receiving this because you were mentioned.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/kcleal/dysgu/issues/21#issuecomment-1423109682, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWPDKHFXCS2OCFJS3YR3RJDWWPVUZANCNFSM5NXA26IA . You are receiving this because you were mentioned.Message ID: @.***>

Feb 09 '23 00:02 Gedofs