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thelovelab / fishpond

Differential expression and allelic analysis, nonparametric statistics
https://thelovelab.github.io/fishpond
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update loadFry function #7

Closed DongzeHE closed 3 years ago

DongzeHE commented 3 years ago

Hi @mikelove,

In alevin-fry 0.4.1, the meta_info.json is called quant.json as discussed at https://github.com/COMBINE-lab/alevin-fry/issues/22#issuecomment-885222997 .

mikelove commented 3 years ago

Thanks, pushing now to Bioc

mikelove commented 3 years ago

Oops with this pull I get a test error when running R CMD check

* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("fishpond")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (5)

  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_loadFry.R:13:3): Reading in Alevin-fry USA count matrix works ───
  Error: argument "txt" is missing, with no default
  Backtrace:
      █
   1. └─fishpond::loadFry(fry.dir) test_loadFry.R:13:2
   2.   └─jsonlite::fromJSON(file = qfile)

  [ FAIL 1 | WARN 0 | SKIP 5 | PASS 18 ]
  Error: Test failures
  Execution halted
mikelove commented 3 years ago

I've removed the loadFry test temporarily, could you take a look and when you get test_file("tests/testthat/test_loadFry.R") and/or R CMD check passing re-PR?

DongzeHE commented 3 years ago

I realized that the error is caused by the discrepancy between rjson and JSONlite packages! It can be easily solved by changing line 55 from meta_info <- fromJSON(file = qfile) to meta_info <- fromJSON(txt = qfile). Sorry about the mistake, I will re-PR.