roll back to master

.github/workflows/check-bioc.yml

@@ -131,7 +131,6 @@ jobs:
           ## Enable installing XML from source if needed
           brew install libxml2
           echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
-          pandoc --version
           ## Required to install magick as noted at
           ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
           brew install imagemagick@6
@@ -158,8 +157,6 @@ jobs:
         run: |
           system("tlmgr --version")
           install.packages("tinytex")
-          tinytex::install_tinytex(version = "2021.03", force = TRUE)
-          tinytex::tlmgr("option repository https://ftp.tu-chemnitz.de/pub/tug/historic/systems/texlive/2020/tlnet-final")
           tinytex::tlmgr_install(pkgs = c("bera", "caption", "changepage", "enumitem", "everysel", "fancyhdr", "footmisc", "grfext", "index", "marginfix", "mathtools", 
                                  "ms", "nowidow", "parnotes", "parskip", "placeins", "preprint", "ragged2e", "side", "soul", "titlesec", "tocbibind", "xstring"))
         shell: Rscript {0}
@@ -214,9 +211,7 @@ jobs:
           ## This pass does not use AnVIL and will thus update any packages
           ## that have seen been updated in Bioconductor
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_version("knitr", "1.45.0")
-          remotes::install_cran("magick")
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = FALSE, force = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
 
       - name: Install BiocGenerics