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pfmc-assessments / VASTWestCoast

VAST for the NWFSC West Coast data
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INLA remote #21

Closed kellijohnson-NOAA closed 4 years ago

kellijohnson-NOAA commented 4 years ago

Work with remotes in the DESCRIPTION file so that the zzz.R file can be removed. A specific repo that is not housed by github is used to install INLA. I am not sure why we cannot use the CRAN version or even if there is one. I can look to see what FishStatsUtils does. A quick search of INLA in github might also be helpful. Moving the remote to the DESCRIPTION file would make things more transparent for users trying to install things rather than the zzz file that most people don't know about.

kellijohnson-NOAA commented 4 years ago

Removed the zzz file in 474b62c because Description file now has Additional_repositories line in 54fb3697327c6440496f9c0e2252689753e4e4e7

kellijohnson-NOAA commented 4 years ago

I have had good luck with the remote option in the Description file. The only trouble I have had is when I use the development version of R, currently 4.1, which is not yet supported by INLA. They don't build their package for the development version. I foresee a problem with older versions of FishStatsUtils though b/c you wouldn't be able to specify which version of INLA you are installing.

kellijohnson-NOAA commented 4 years ago

INLA suggests two bioconductor packages, where INLA recommends

install.packages("BiocManager")
BiocManager::install(c("graph", "Rgraphviz"), dep=TRUE)

before installing INLA.

I found help regarding how to add bioconductor packages to a Description file. Technically, these should not go in VASTWestCoast, but instead in the INLA Description file. But, I think it might be good to require them here so that users don't get the warning that they are needed.