search

tetomonti / CBMRtools

R package with common use scripts for transcriptomics analysis
3 stars 0 forks source link

Devtools doesn't work properly w/ latest version (3.3.1) of R #27

Closed tetomonti closed 7 years ago

tetomonti commented 8 years ago

When running README.CBMRtools.R, installation fails when trying to generate the html pages:

  Error in setwd(wd) : character argument expected
  In addition: There were 18 warnings (use warnings() to see them)

Must be a problem w/ pkgdown (new version of devtools). @lia978 tracked back the error:

  > traceback()
  5: setwd(wd)
  4: rmarkdown::pandoc_convert(input = path, output = tmp, from = "markdown_github-hard_line_breaks", 
         to = "html", options = list("--smart", "--indented-code-classes=R", 
       "--section-divs", ...))
  3: markdown(path = data$path, depth = 0L, index = pkg$topics)
  2: build_home(pkg, path = path)
  1: build_site(pkg = package.dir, path = "docs", examples = TRUE, 
         run_dont_run = FALSE, mathjax = TRUE, preview = FALSE, seed = 1014

For the time being, best to use the old version of the help pages.

tetomonti commented 8 years ago

@gusef has the following suggestion:

you could probably just wrap a pkgdown version into you CBMRtools conda package that works with the R version that is in the package.

Was thinking about that for Hydra. While cran is great for the latest and greatest, we want consistency and for that it’s better to write recipes and wrap them into the conda environment. This is actually quite easy to do, especially since installing a R packages is really straightforward.

However, this is not a solution at the moment, since there's no version that works.

lia978 commented 7 years ago

this issue is resolved by re-downloading staticdoc under R Version 3.3.2, as of 03/14/17

require(devtools) install_github('hadley/staticdocs') require(staticdocs)

see /CBMRtools/inst/package_make/CBMRtools.build.R for script on making documentation

tetomonti commented 7 years ago

Actually, it looks like you have to replace

require(staticdocs) with require(pkgdown)

Otherwise, you get the error:

require(staticdocs) Loading required package: staticdocs Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'staticdocs'

On Mar 14, 2017, at 3:13 PM, lia978 notifications@github.com wrote:

this issue is resolved by re-downloading staticdoc under R Version 3.3.2, as of 03/14/17

require(devtools) install_github('hadley/staticdocs') require(staticdocs)

see /CBMRtools/inst/package_make/CBMRtools.build.R for script on making documentation

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/montilab/CBMRtools/issues/27#issuecomment-286529853, or mute the thread https://github.com/notifications/unsubscribe-auth/AJADHylpNYYZpk3QJ9GeMjP9zINQUSKHks5rlubsgaJpZM4KmPG2.