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FertigLab / CoGAPS

Bayesian MCMC matrix factorization algorithm
https://www.bioconductor.org/packages/release/bioc/html/CoGAPS.html
BSD 3-Clause "New" or "Revised" License
66 stars 17 forks source link

Enable the Checkpoints #101

Open dimalvovs opened 7 months ago

dimalvovs commented 7 months ago

Can we get saving and starting from Checkpoints reinitialized for CoGAPS? Otherwise given the execution speed the results are lost if runtime is longer than the time limit for some of compute clusters.

dimalvovs commented 7 months ago

The checkpoints are disabled by default:

> 
> library("CoGAPS")
> packageVersion("CoGAPS")
[1] ‘3.24.0’
> CoGAPS::checkpointsEnabled()
[1] FALSE

It looks like these are disabled in https://github.com/FertigLab/CoGAPS/blob/cc8c42cd2a9dc9c99e63e22dba076fabfdb8461e/configure#L3241

Potentially could be enabled by removing the -DGAPS_DISABLE_CHECKPOINTS flag.

dimalvovs commented 5 months ago

Related to #49