updating CI (caching of R packages) and proper namespace calling of l…

…me function
kkholst · Dec 20, 2023 · 36d9a98 · 36d9a98
1 parent 9b92b51
commit 36d9a98
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Showing 2 changed files with 19 additions and 10 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -33,20 +33,29 @@ jobs:
  with:
  use-public-rspm: true
 
- - name: Cache R packages
- uses: actions/cache@v3
+ - uses: r-lib/actions/setup-r-dependencies@v2
  with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+ dependencies: '"all"'
+ cache: true
+ extra-packages: |
+ any::rcmdcheck
+ any::pkgdown
+ any::remotes
+ any::covr
+ needs: check
+
+ # - name: Cache R packages
+ # uses: actions/cache@v3
+ # with:
+ # path: ${{ env.R_LIBS_USER }}
+ # key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+ # restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
  - name: Install R dependencies
  run: |
- install.packages("remotes", repos="https://cloud.r-project.org")
  remotes::install_github("kkholst/gof")
  remotes::install_deps(".", dep=T, upgrade=T)
- remotes::install_cran(c("pkgdown","covr","rcmdcheck"))
- remotes::install_bioc("Rgraphviz", upgrade="always")
+ # remotes::install_bioc("Rgraphviz", upgrade="always")
  shell: Rscript {0}
 
  - name: Check

diff --git a/tests/testthat/test-inference.R b/tests/testthat/test-inference.R
@@ -314,7 +314,7 @@ test_that("Random slope model", {
  dd$num <- dd$num+runif(nrow(dd),0,0.2)
  dd0 <- dd[-c(1:2*3),]
  library(lme4)
- l <- lme(y ~ 1+num, random=~1+num|id, data=dd, method="ML")
+ l <- nlme::lme(y ~ 1+num, random=~1+num|id, data=dd, method="ML")
  ##l0 <- lmer(y~ 1+num +(1+num|id),dd,REML=FALSE)
  sl0 <- lava:::varcomp(l)
 
@@ -340,7 +340,7 @@ test_that("Random slope model", {
  testthat::expect_output(e0 <- estimate(m0,d0,missing=TRUE,param="none",control=list(method="NR",constrain=FALSE,start=coef(e),trace=1)),
  "Iter=")
  ## l0 <- lmer(y ~ 1 + num + (1 + num | id), dd0, REML = FALSE)
- l0 <- lme(y~ 1+num, random=~1+num|id, data=dd0, method="ML")
+ l0 <- nlme::lme(y~ 1+num, random=~1+num|id, data=dd0, method="ML")
  testthat::expect_true((logLik(l0)-logLik(e0))^2<1e-5)
 
  m1 <- lvm(c(y1[0:v],y2[0:v],y3[0:v])~1*u)