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NatalieZelenka / phenotype_from_genotype

Jupyter book tracking my thesis.
https://nataliezelenka.github.io/phenotype_from_genotype/
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[BUG] GH Pages Action broken #56

Closed NatalieZelenka closed 2 months ago

NatalieZelenka commented 2 years ago

GH Action not updating website :(

Gh-pages peaceiris action is the bit failing:

  [INFO] ForceOrphan: false
  /usr/bin/git clone --depth=1 --single-branch --branch gh-pages ***github.com/NatalieThurlby/phenotype_from_genotype.git /home/runner/actions_github_pages_1639098542290
  Cloning into '/home/runner/actions_github_pages_1639098542290'...
  /usr/bin/git rm -r --ignore-unmatch *
  rm '.buildinfo'
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  [INFO] first deployment, create new branch gh-pages
  ENOENT: no such file or directory, scandir '/home/runner/work/phenotype_from_genotype/phenotype_from_genotype/_build/html'
  /usr/bin/git init
  Reinitialized existing Git repository in /home/runner/actions_github_pages_1639098542290/.git/
  /usr/bin/git checkout --orphan gh-pages
  fatal: A branch named 'gh-pages' already exists.
  Error: Action failed with "The process '/usr/bin/git' failed with exit code 128"
NatalieZelenka commented 2 years ago
NatalieZelenka commented 1 year ago

New similar issue. V1 of the R GitHub action broke. Changed to V2.

Fixed by f08383e0a61a6da8317320a31fd0b084ce542b72

NatalieZelenka commented 1 year ago

New error: jinja2 4.x incompatible with sphinx 3.x Fixed using suggestion (1) from here: https://github.com/executablebooks/jupyter-book/issues/1676 Suggestion (2) doesn't work with this version of jupyter-book.

NatalieZelenka commented 2 months ago

FINALLY fixed!! (having gone through quite a lot of dependency problems) - latest fix was updating to R 4.0.

NatalieZelenka commented 2 months ago

Note - the dependency problems I originally attempted to fix by installing specific versions of R packages, but this turned out to be unnecessary.

Leaving here just in case:


IRkernel = "https://cran.r-project.org/package=IRkernel&version=1.1.1"
glue = "https://cran.r-project.org/package=glue&version=1.2.0"

utils::install.packages(pkgs = glue, repos = NULL)

install.packages('pillar')
install.packages('repr')
install.packages('evaluate')
install.packages('IRdisplay')
install.packages('pbdZMQ')
install.packages('crayon')
install.packages('jsonlite')
install.packages('uuid')
install.packages('digest')

utils::install.packages(pkgs = IRkernel, repos = NULL)