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renozao / NMF

NMF: A Flexible R package for Nonnegative Matrix Factorization
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Install.extras? #174

Open inofechm opened 1 year ago

inofechm commented 1 year ago

Hi, I was trying to enable shared memory capabilities with install.extras('NMF') , but I cannot seem to understand where the install.extras function can be called from, is there some additional package that has that function? I was able to overcome by manually installing bigmemory and synchronicity, but was wondering where I went wrong. Thanks, Ido

rebeccagj commented 1 year ago

The install.extras() function comes from pkgmaker, I believe. I found this old mailing list posting that shows that NMF used to load pkgmaker by default. From that posting, I also saw that the extra packages installed were bigmemory, synchronicity, and Biobase. I too just manually installed these packages, which does take care of the warning message to install.extra packages.

It would be nice if the install.extras("NMF") registry entry were updated (or instructions given on the proper registry to point to), as I also got this error.

> library(NMF)
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2
> library(pkgmaker)

Attaching package: ‘pkgmaker’

The following objects are masked from ‘package:NMF’:

    isCHECK, isCRANcheck, latex_bibliography, latex_preamble

> install.extras(package = "NMF")
Error in regfetch(regentry$regobj, ..., msg = msg) : 
  extra action - Registry is empty: no matching entry for key “package=NMF”.
yangmean commented 1 year ago

@rebeccagj Hi , I've encountered the same issue. And I'm facing a similar concern about loading the NMF package on the server. The system seems to detect only 2 cores (Cores 2/2), causing the NMF function to operate solely on these 2 cores. even when I allocate more than 2 threads.