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Fix R and stale ldpaths issue #187

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jfear opened this issue May 28, 2021 · 1 comment · Fixed by #188
Closed

Fix R and stale ldpaths issue #187

jfear opened this issue May 28, 2021 · 1 comment · Fixed by #188
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jfear commented May 28, 2021

In conda-forge/r-base-feedstock#67, they point out that ldpaths is updated each time you activate an R conda environment. This causes issues when activating a shared environment in parallel. I am setting this with grouped calculation of median IDAT leading to stale ldpath handles.
@jfear jfear added the bug Something isn't working label May 28, 2021
@jfear jfear self-assigned this May 28, 2021
@jfear jfear added this to the Phase 1 - Release milestone May 28, 2021
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jfear commented May 28, 2021

I think I am going to try just calling Rscript via absolute path instead of loading the environment.

jfear added a commit that referenced this issue May 28, 2021
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fix(workflow): run rscript directly instead of activating environment
19a4bdc 
Closes #187
@jfear jfear mentioned this issue May 28, 2021
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jfear added a commit that referenced this issue May 28, 2021
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fix(workflow): run rscript directly instead of activating environment
a84772f 
Closes #187
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Fix stale ldpath bug when running illuminaio NCI-CGR/GwasQcPipeline
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