pip install pysam fails with Python 3.8.0 #860
Comments
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Having the exactly same issue on a fresh Ubuntu 19.04 with python 3.8 installed from source |
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What version of Cython are you using? This appears to be cython/cython#2938 and it seems (PR cython/cython#2971) you will need at least cython 0.29.9. |
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Thanks for the suggestions, @jmarshall! I just installed Cython 0.29.14 via In a way, it looks like they were solving the same issue in PR cython/cython#2971, but it does not seem like having the fixed Cython verson installed helps with compiling pysam. |
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The usual reason for that is that your pysam build is using the bundled pre-built libchtslib.c etc (which were likely built with an earlier Cython) rather than re-running Cython. It appears that @myourshaw's build is rebuilding these from libchtslib.pyx etc: Are you certain yours is as well? |
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Yes, confirming that
Running it with no Cython installed fails at during compilation of |
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I, too, have Cython 0.29.14 installed. |
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I see the same error. |
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¯\_(ツ)_/¯ Works for me with Python 3.8.0 (3.8.0-3~18.04 from bionic-updates) and Cython 0.29.14, building pysam from within a tarball with There were some false starts with this |
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I had exactly the same issue when I was running the command |
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I installed Python 3.8.0 from source a few weeks ago on my Ubuntu 19.04. Here is the version information from @jmarshall did you also try to pip install? I still need to check if the tarball works for me |
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/home/myourshaw/.local/include/python3.8/patchlevel.h contains |
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Still have the same issue with Python 3.8.1. |
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Anyone solved the problem. 3.8.0 failed, and upgraded to python 3.8.1 still having the same problem. It is a pain in the neck. I am going to try to change the source code and see that will fix the problem. |
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Looks the latest version of pysam fixed this problem. I used git clone of this project and this problem was gone. I looked at the problem location it was a simple #define directive problem. Someone should close this issue. |
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@kemin711: What exact |
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I did not fix the problem. The crashed line is a C directive #define the function with one extra argument |
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I don't know the exact fix. But it should be some minor mismatch of function signature. |
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Yes. That's |
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I have similarly observed that if I do |
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Of further note: doing However, all is not well for me even after "successfully" installing from source... I guess that installing this way doesn't actually work! |
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This is caused by some .c files in pysam 0.15.3 which were made by Cython 0.29.10. It can be fixed by regenerating them with Cython 0.29.12 or later. I successfully used Cython 0.29.14 together with this addition to setup.cfg: |
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Installing with As @ExplodingCabbage says, the following works. I guess PyPI needs to be updated. |
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Inspired by @pm67nz's post, I tried simply rebuilding with a newer version of Cython (and with my fix from #874) and uploading to PyPI, and everything worked. You can install my version with: and you'll be good to go. @AndreasHeger, if you can spare the time to simply:
then I think everything should be fixed for the official pysam package. |
This is the version @pm67nz indicates is needed for creating a build from source in pysam-developers#860 (comment), so I figure we might as well enforce it everywhere?
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Indeed. The question for the maintainers is whether to make a point release just with regenerated Cython output files, or to do that as part of a larger release updating pysam to htslib/samtools/bcftools 1.10.x. |
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I got it fixed.
Kemin Zhou 858 771-3269
On Tuesday, January 14, 2020, 06:14:07 AM PST, John Marshall <[email protected]> wrote:
Indeed. The question for the maintainers is whether to make a point release just with regenerated Cython output files, or to do that as part of a larger release updating pysam to htslib/samtools/bcftools 1.10.x.
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Thinking about this further, it probably is worthwhile making a point release update just regenerating the Cython outputs. There is a soversion bump between htslib 1.9 and 1.10 and some datatype size changes. So when pysam is updated to include the 1.10.x htslib/samtools/bcftools it would be beneficial to update pysam/* as well to use the htslib 1.10 facilities, including using some new functions. So pysam would then require htslib 1.10. Hence it would be good to have a final htslib-1.9-using pysam release that works nicely with Python 3.8. |
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Makes sense. I have merged some outstanding pull requests and will build a release before moving on to htslib-1.10. |
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@AndreasHeger: Where pysam-0.15.3.tar.gz contained libc*.c files that were generated by a version of Cython that turned out to be a little bit too old, pysam-0.15.4.tar.gz (i.e., the source tarball listed at https://pypi.org/project/pysam/#files) does not contain any Cython-generated *.c files at all. Is this an intended change? |
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Regardless of the point above by @jmarshall (which Andreas may yet want to answer), I can confirm that I can now do |
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Thanks, I will close. |
I get the following error when trying to install pysam with pip in Python 3.8.0 ( I also posted this on the user group):
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