datacarpentry/organization-genomics

[zkamvar]

tracking issue for https://github.com/datacarpentry/organization-genomics

• error in build (reason: "source" class block quote does not exist) (addressed in remove unknown "source" class datacarpentry/organization-genomics#149)

Details

── Reading in lesson with pegboard ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error in `purrr::map()`:
ℹ In index: 2.
ℹ With name: /home/zhian/Documents/Carpentries/Git/carpentries/lesson-transition/datacarpentry/organization-genomics/_episodes/02-project-planning.md.
Caused by error in `purrr::map()`:
ℹ In index: 4.
Caused by error in `xml_nodeset()`:
! Expecting an external pointer: [type=NULL]
Backtrace:
     ▆
  1. ├─pegboard::Lesson$new(old, fix_liquid = arguments$fix_liquid)
  2. │ └─pegboard (local) initialize(...)
  3. │   └─pegboard:::read_jekyll_episodes(path, rmd, ...)
  4. │     └─pegboard:::read_markdown_files(md_src, sandpaper = FALSE, ...)
  5. │       └─purrr::map(the_episodes, Episode$new, ...)
  6. │         └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
  7. │           ├─purrr:::with_indexed_errors(...)
  8. │           │ └─base::withCallingHandlers(...)
  9. │           ├─purrr:::call_with_cleanup(...)
 10. │           └─R6 (local) .f(.x[[i]], ...)
 11. │             └─pegboard (local) initialize(...)
 12. │               └─purrr::map(blocks, set_ktag_block)
 13. │                 └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
 14. │                   ├─purrr:::with_indexed_errors(...)
 15. │                   │ └─base::withCallingHandlers(...)
 16. │                   ├─purrr:::call_with_cleanup(...)
 17. │                   └─pegboard (local) .f(.x[[i]], ...)
 18. │                     ├─parents[tag]
 19. │                     └─xml2:::`[.xml_nodeset`(parents, tag)
 20. │                       └─xml2:::xml_nodeset(NextMethod())
 21. └─base::.handleSimpleError(...)
 22.   └─purrr (local) h(simpleError(msg, call))
 23.     └─cli::cli_abort(...)
 24.       └─rlang::abort(...)
Execution halted

• fix github.com links
• fix instructor notes relative link in index
• fix fix jekyll anchor link

episodes/01-tidiness.md:118 [uninformative link text]: [link](https://github.com/datacarpentry/organization-genomics/raw/gh-pages/files/Ecoli_metadata_composite_messy.xlsx)
index.md:51 [missing file]: [Instructor notes](guide/)
instructors/old-ncbi.md:25 [missing file]: [Examining Data on the NCBI SRA Database](03-ncbi-sra/index.html#you-should-now-have-a-file-called-sraruntabletxt)

[zkamvar]

fixed in 83bd8d7