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harvard-ufds / saeczi

Small Area Estimation for Continuous Zero Inflated data
https://harvard-ufds.github.io/saeczi/
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note on actions workflow change #7

Closed joshyam-k closed 9 months ago

joshyam-k commented 11 months ago

Matrix < 1.6-2 and Matrix >= 1.6-2 are binary incompatible. When you change between them, you must re-install from sources packages that link Matrix. Because lme4 depends on Matrix we get the following error: 

Error in `initializePtr()`: function 'cholmod_factor_ldetA' not provided by package 'Matrix'

To fix this inside an R session you can just re-install lme4 from source, but the we have to do a bit more work to get our github actions to run. I set a few new steps in the workflow that set the cran mirror and then install lme4 from source

 - name: Set CRAN mirror
        run: echo "options(repos = c(CRAN='https://cloud.r-project.org/'))" > ~/.Rprofile

 - name: Install problem dependency
        run: |
          install.packages('lme4', type = 'source')
        shell: Rscript {0}

Hopefully we can eventually remove this, but for now the workflow needs these lines to run.

joshyam-k commented 9 months ago

closing