[FIX] CircleCI supports R 3.6 as it is a popular R version

[zhao-cy]

[zhao-cy]

Also need to change ModelArray requirement in the DESCRIPTION file

[zhao-cy]

Working on R 3.6.3. There are also issues as R 4.1.0: when installing the ModelArray package, the R did not install the versions required in DESCRIPTION -> "Imports"... e.g. package "rlang" installed was 0.4.5; I have to ssh into CircleCI to uninstall and manually install with:
install.packages("https://cran.r-project.org/src/contrib/Archive/rlang/rlang_0.4.6.tar.gz", repo=NULL, type="source")

[zhao-cy]

If these specified packages are installed by "install.packages()", I'm thinking about why it did not install the most up-to-date version?

[zhao-cy]

Trying: install R packages in docker image, before running devtools::install_deps(dep = TRUE):

• installed the specific version if: R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/vctrs/vctrs_0.3.0.tar.gz', repo=NULL, type='source')"
• still installing vctrs_0.2.4 if: R -e "packageVersion('vctrs')"

Also tried: R -e "devtools::install_deps(dep = TRUE, upgrade = 'always')"
This step passed without error, but the next step of "R CMD build ." failed - those R packages are still not up-to-date, e.g. rlang is still 0.4.5...

Also tried update.packages("packageName") or just update.packages(), but rlang, vctrs are not updated...

[zhao-cy]

• build a docker image:
  • from rocker 3.6 (for example, for any r version for testing)
  • add commands from circle ci first several lines:
  • • run:
      name: Install libraries
      command: apt-get update && apt-get install -y --no-install-recommends libhdf5-dev
    • run:
      name: Install libraries for latex
      command: apt-get update && apt-get install -y --no-install-recommends texlive-fonts-recommended
    • run:
      name: Install package dependencies (hdf5r)
      command: R -e "require(hdf5r)" # "lapply(c('hdf5r','HDF5Array','DelayedArray'), require, character.only=TRUE)"
  • skip: devtools::install_deps
• Then use this docker image, enter the R session, then debug the installation of ModelArray there

[zhao-cy]

rocker/verse:3.6.3 already has several packages installed, including those packages with version we don't want:

packageVersion("vctrs")
[1] '0.2.4'
packageVersion("rlang")
[1] '0.4.5'
packageVersion("tidyselect")
[1] '1.0.0'
packageVersion("tidyr")
[1] '1.0.2'

rocker/r-ver:3.6.3 does not have those packages installed. However when installing devtools (which is required anyway to install ModelArray), there are two problems:

1. It installs the vctrs and rlang with the version that we don't want....

2. There are some errors:

• ERROR: dependencies ‘curl’, ‘gh’ are not available for package ‘usethis’
  • removing ‘/usr/local/lib/R/site-library/usethis’
• ERROR: dependencies ‘usethis’, ‘covr’, ‘httr’, ‘roxygen2’, ‘rversions’ are not available for package ‘devtools’
  • removing ‘/usr/local/lib/R/site-library/devtools’

Although I could try installing a specific rlang and vctrs for circle ci testing, I'm not sure if circle ci serves its purpose of testing the general case (that probably people installed old version of rlang and vctrs)....

The key is still: why those packages aren't updated with update.packages(ask = FALSE) ?

[zhao-cy]

see issue #48