wtsi-npg / npg_conda

NPG Conda recipes and tools
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Update nettle to 3.7.2 and gnutls to 3.7.1 #236

Closed mksanger closed 3 years ago

mksanger commented 3 years ago

Update of https://github.com/wtsi-npg/npg_conda/pull/170

dkj commented 3 years ago

This looks ok but there's fundamental ABI dependency problem remaining:

CONDA_CHANNELS="https://dnap.cog.sanger.ac.uk/npg/conda/prod/generic/,defaults"  conda create -n testc_gtls33_bbb biobambam2
ldd $(which bamsormadup)  | grep nettle
        libnettle.so.6 => /home/ubuntu/miniconda2/envs/testc_gtls33_bbb/bin/../lib/libnettle.so.6 (0x00007f9f9810b000)

(is without these new packages).

CONDA_CHANNELS="file://$PWD/conda-artefacts,https://dnap.cog.sanger.ac.uk/npg/conda/prod/generic/,defaults"  conda create -n testc_gtls371_bbb biobambam2
ldd $(which bamsormadup)  | grep nettle
        libnettle.so.6 => /usr/lib/x86_64-linux-gnu/libnettle.so.6 (0x00007f0d64611000)
        libnettle.so.8 => /home/ubuntu/miniconda2/envs/testc_gtls371_bbb/bin/../lib/./libnettle.so.8 (0x00007f0d63a00000)

(with these new packages, shows the tool only continues to work as it able to fall back on a system version of libnettle).

mksanger commented 3 years ago

there's fundamental ABI dependency problem remaining

Good spot, I'll add running ldd and checking for non-conda libraries to the integration tests, hopefully that should pick up this type of problem