Old Linux distribution import error "GLIBC_2.23' not found"

[cerebis]

Hello, I am on "Red Hat 4.8.5-39" and had the same issue with bzip2, which is gone in the current conda release. However, now pysam has a problem with a different dependency:

ImportError: /lib64/libm.so.6: versionGLIBC_2.23' not found`

Originally posted by @mscharmann in https://github.com/cerebis/qc3C/issues/43#issuecomment-805113006

[cerebis]

From #43

@mscharmann

I haven't tested this as I do not have a RH4.8 environment set up, but there's a possibility that this problem stems from the removal of Python 3.6 support from qc3C.

The removal was in response to an unresolvable (by me) segmentation fault within pytest when run in a conda py36 environment. I have not been able to track down what change within the dependency tree has introduced this problem.

qc3C, however, seems fine. I just cannot run the tests presently, which interrupts the automated build process.

A possible work around which might work for you.

# 1) create a Python 3.6 environment, without qc3C but everything else you'll need.
conda create -y -n qc3c_py36 -c conda-forge -c bioconda -c cerebis samtools jellyfish "python<3.7"
# 2) activate this environment
conda activate qc3c_py36
# 3) install qc3C from github using pip
pip install git+https://github.com/cerebis/qc3C

[cerebis]

Hello Niu,

There is the option to use Docker but if you're on Centos 6 then perhaps that'll also be a problem.

Other than that, my suggested work around was to install qc3C from github, but use Conda to satisfy the remaining dependencies.

1) create a supported Python environment, without qc3C but

everything else you'll need. conda create -y -n qc3c -c conda-forge -c bioconda -c cerebis samtools jellyfish "python>3.6"# 2) activate this environment conda activate qc3c# 3) install qc3C from github using pip pip install git+https://github.com/cerebis/qc3C

On Thu, 20 May 2021 at 17:58, Niu Yiwei @.***> wrote:

Hi, I am using CentOS 6.6 and encountered the same error above. Is there any workaround now?

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[YiweiNiu]

Thank you for your prompt reply! I could install qc3C using the method you provided.

[cerebis]

Great to hear that you were successful

On Fri, 21 May 2021 at 11:15, Niu Yiwei @.***> wrote:

Thank you for your prompt reply! I could install qc3C using the method you provided.

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