lcdb / lcdb-wf

Robust, tested workflows for RNA-seq, ChIP-seq and other high-throughput sequencing analysis
https://lcdb.github.io/lcdb-wf
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Fix R tests #403

Closed daler closed 4 months ago

daler commented 4 months ago

Turns out that the {testthat} tests for the lcdbwf R package were not exiting with a nonzero exit code upon test failure.

This PR fixes that, and additionally addresses multiple pre-existing and new instances where namespaces were not explicitly used. This now brings the code up to par with the recommendations from Chapter 11 of R Packaging, preferring explicit :: namespacing wherever possible.

It also fixes a couple things from #396 (specifically in f5b8f7839821aad63cc0c23911c716a6b4b6f427, 9828f4690e7bdee50cfabcf4ed46aafa5fd2829b, and 75e62de7f7d250d0a7498f0c4dea84a948888a82) that were then noticeable after making these changes.