@@ -133,8 +133,8 @@ jobs:

           ## For textshaping, required by ragg, and required by pkgdown

           brew install harfbuzz fribidi

-          ## Helps compile RCurl from source

-          brew uninstall curl

+          ## For installing usethis's dependency gert

+          brew install libgit2

       - name: Install Windows system dependencies

         if: runner.os == 'Windows'

@@ -153,7 +153,7 @@ jobs:

           BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)

         shell: Rscript {0}

-      - name: Install dependencies

+      - name: Install dependencies pass 1

         run: |

           ## Try installing the package dependencies in steps. First the local

           ## dependencies, then any remaining dependencies to avoid the

@@ -162,22 +162,18 @@ jobs:

           ## https://github.com/r-lib/remotes/issues/296

           ## Ideally, all dependencies should get installed in the first pass.

-          ## Temporary for now due to https://github.com/ropensci/RefManageR/issues/79

-          remotes::install_github("ropensci/bibtex")

-          remotes::install_github("ropensci/RefManageR")

-          remotes::install_github("cboettig/knitcitations")

-          

-          ## install additionall RCurl

-          remotes::install_cran("RCurl")

-          

           ## Pass #1 at installing dependencies

           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))

           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)

+        continue-on-error: true

+        shell: Rscript {0}

+      - name: Install dependencies pass 2

+        run: |

           ## Pass #2 at installing dependencies

           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))

           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)

-

+          

           ## For running the checks

           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))

           remotes::install_cran("rcmdcheck")

@@ -200,7 +196,7 @@ jobs:

       - name: Install pkgdown

         if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'

         run: |

-          remotes::install_github("r-lib/pkgdown")

+          remotes::install_cran("pkgdown")

         shell: Rscript {0}

       - name: Session info