can't install cyvcf2 using pip

[MeHelmy]

Hi,

I created a Conda environment with python 3.7. I tried to install cuvcf2 as follows pip install cyvcf2 it did not work. error log:

    gcc -pthread -B MY_HOME/conda_dir/envs/cyvcf-test/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ihtslib -Icyvcf2 -IMY_HOME/conda_dir/envs/cyvcf-test/lib/python3.7/site-packages/numpy/core/include -IMY_HOME/conda_dir/envs/cyvcf-test/include/python3.7m -c htslib/cram/cram_io.c -o build/temp.linux-x86_64-3.7/htslib/cram/cram_io.o -Wno-sign-compare -Wno-unused-function -Wno-strict-prototypes -Wno-unused-result -Wno-discarded-qualifiers
    htslib/cram/cram_io.c:53:19: error: bzlib.h: No such file or directory
    htslib/cram/cram_io.c:57:18: error: lzma.h: No such file or directory
    htslib/cram/cram_io.c: In function ‘lzma_mem_deflate’:
    htslib/cram/cram_io.c:722: warning: implicit declaration of function ‘lzma_stream_buffer_bound’
    htslib/cram/cram_io.c:728: error: ‘LZMA_OK’ undeclared (first use in this function)
    htslib/cram/cram_io.c:728: error: (Each undeclared identifier is reported only once
    htslib/cram/cram_io.c:728: error: for each function it appears in.)
    htslib/cram/cram_io.c:728: warning: implicit declaration of function ‘lzma_easy_buffer_encode’
    htslib/cram/cram_io.c:728: error: ‘LZMA_CHECK_CRC32’ undeclared (first use in this function)
    htslib/cram/cram_io.c: In function ‘lzma_mem_inflate’:
    htslib/cram/cram_io.c:738: error: ‘lzma_stream’ undeclared (first use in this function)
    htslib/cram/cram_io.c:738: error: expected ‘;’ before ‘strm’
    htslib/cram/cram_io.c:744: error: ‘LZMA_OK’ undeclared (first use in this function)
    htslib/cram/cram_io.c:744: warning: implicit declaration of function ‘lzma_stream_decoder’
    htslib/cram/cram_io.c:744: error: ‘strm’ undeclared (first use in this function)
    htslib/cram/cram_io.c:744: warning: implicit declaration of function ‘lzma_easy_decoder_memusage’
    htslib/cram/cram_io.c:762: warning: implicit declaration of function ‘lzma_code’
    htslib/cram/cram_io.c:762: error: ‘LZMA_RUN’ undeclared (first use in this function)
    htslib/cram/cram_io.c:763: error: ‘LZMA_STREAM_END’ undeclared (first use in this function)
    htslib/cram/cram_io.c:775: error: ‘LZMA_FINISH’ undeclared (first use in this function)
    htslib/cram/cram_io.c:786: warning: implicit declaration of function ‘lzma_end’
    htslib/cram/cram_io.c: In function ‘cram_uncompress_block’:
    htslib/cram/cram_io.c:1025: error: ‘BZ_OK’ undeclared (first use in this function)
    htslib/cram/cram_io.c:1025: warning: implicit declaration of function ‘BZ2_bzBuffToBuffDecompress’
    htslib/cram/cram_io.c: In function ‘cram_compress_by_method’:
    htslib/cram/cram_io.c:1105: error: ‘BZ_OK’ undeclared (first use in this function)
    htslib/cram/cram_io.c:1105: warning: implicit declaration of function ‘BZ2_bzBuffToBuffCompress’
    At top level:
    cc1: warning: unrecognized command line option "-Wno-discarded-qualifiers"
    cc1: warning: unrecognized command line option "-Wno-unused-result"
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: MY_HOME/conda_dir/envs/cyvcf-test/bin/python3.7 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-avuhvi2w/cyvcf2_051d54e5606842b7a2a77f5e62a7e255/setup.py'"'"'; __file__='"'"'/tmp/pip-install-avuhvi2w/cyvcf2_051d54e5606842b7a2a77f5e62a7e255/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-mti4gson/install-record.txt --single-version-externally-managed --compile --install-headers MY_HOME/conda_dir/envs/cyvcf-test/include/python3.7m/cyvcf2 Check the logs for full command output.

Thanks, Medhat

[ccwang002]

Hi Medhat, since you are using conda, is it possible for you to install cyvcf2 via bioconda?

[MeHelmy]

@ccwang002 Thank you for reaching back. Currently, I'm developing a tool that implicitly uses Cyvcf2. So, I would like to use pip to install all dependencies. Then, I can easily package it. I would appreciate if you have a solution.

Best, Medhat

[CholoTook]

Works fine for me. Is this a conda issue?

[CholoTook]

Close, can't reproduce

[dbolser]

Still close?

[empathy-c]

I use pip install cyvcf2==0.20.0 and use cyvcf2-0.20.0.tar,gz and local install,but both methods are failed and have many errors when installing. But I have to use cyvcf2 0.20.0 to finish my work. Is there anyone install it on python3.8 or python3.10 successfully? Is there anyone meet this problem and solve it?

[CholoTook]

Please post your errors. I'm having trouble installing in a test container too... (works fine with pip on my regular laptop in a .venv): Python 3.10.12, cyvcf2-0.30.22, install-1.3.5

[brentp]

@empathy-c as I mentioned in another issue, you won't be able to use python 3.10 with version 0.20.0, you'll need an older python version.

[CholoTook]

I got v0.22.0 working on 3.8 here: https://github.com/brentp/cyvcf2/pull/283

[CholoTook]

k, plz close as resolved.

On Thu, 5 Oct 2023 at 10:36, Brent Pedersen @.***> wrote:

@empathy-c https://github.com/empathy-c as I mentioned in another issue, you won't be able to use python 3.10 with version 0.20.0, you'll need an older python version.

— Reply to this email directly, view it on GitHub https://github.com/brentp/cyvcf2/issues/220#issuecomment-1748490299, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANKSZTUHNME4TMEO3QQJ53TX5Z5SZAVCNFSM5CPAZWW2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCNZUHA2DSMBSHE4Q . You are receiving this because you commented.Message ID: @.***>