Refactor/fixes

[timcadman]

Background

Fixes found in a full review of the v7.0 refactor (batches 1–10): a data leak, behaviour that changed relative to 6.3.5, and small doc and code errors.

What's changed

• ds.asList data leak: asListDS returned the converted object to the client. It is now an assign function. It was an aggregate only to work around an old repository quirk with lists; tests confirm lists now assign correctly on Opal and Armadillo.
• NULL objects: .loadServersideObject now errors on a NULL object ("is NULL") for every function, including ds.class, which used to return "NULL". Deliberate breaking change: NULL objects only arise from mistakes such as a typo in ds.make.
• Class rules restored to 6.3.5 behaviour:
  • meanDS/varDS accept logical, so an all-NA column no longer breaks the call.
  • corDS/covDS accept factors again (correlated on level codes).
  • glm/glmSLMA/glmer/lmer/gamlss accept data.frame or list, not matrix, matching what the model functions accept.
  • lengthDS/dimDS accept any class.
  • meanSdGpDS accepts a numeric grouping variable.
• Behaviour restored:
  • ds.cor/ds.cov ignore y (with a warning) when x is a matrix or data.frame.
  • ds.changeRefGroup treats a numeric ref as a level name again.
  • BooleDS accepts "TRUE"/"FALSE"/"NA" as V2.
  • levelsDS checks the privacy level first.
• ds.mdPattern combine: pools columns by variable name, not position. md.pattern orders columns by missingness, which differs between studies, so variables could be mixed.
• seqDS: from/to/by/length.out are converted with as.numeric instead of being looked up as object names.
• glmChecks, ds.table: restore the user's warn option on exit. This fix was on 6.3.x but never ported to v7.

[github-actions]

⏳ 4 of 5 checks reported so far

Check	Result
Devtools checks	✅ passed
Code quality	✅ 0 new findings (package total: 2016)
Armadillo unit tests	✅ [ FAIL 0 | WARN 0 | SKIP 27 | PASS 12397 ]
Opal unit tests	✅ [ FAIL 0 | WARN 0 | SKIP 27 | PASS 11960 ]
Test coverage	ℹ️ no coverable lines changed (project: 68.9%)

Tested against dsBase versions:
Armadillo: 7.0.0.9000
Opal: 7.0.0.9000

Logs: Devtools checks · Code quality · Armadillo unit tests · Opal unit tests · Codecov

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 68.93%. Comparing base (52c57bf) to head (00b02f6).

Additional details and impacted files

@@             Coverage Diff              @@
##           v7.0-dev     #710      +/-   ##
============================================
+ Coverage     68.64%   68.93%   +0.29%     
============================================
  Files           142      142              
  Lines          5785     5788       +3     
============================================
+ Hits           3971     3990      +19     
+ Misses         1814     1798      -16     

Flag	Coverage Δ
armadillo-arg	21.02% <ø> (+0.26%)	⬆️
armadillo-misc	15.65% <ø> (+<0.01%)	⬆️
armadillo-perf-1	9.29% <ø> (+0.01%)	⬆️
armadillo-perf-2	17.82% <ø> (-0.01%)	⬇️
armadillo-perf-3	16.15% <ø> (+0.06%)	⬆️
armadillo-smk-1	35.03% <ø> (+0.03%)	⬆️
armadillo-smk-2	39.72% <ø> (+0.30%)	⬆️

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[StuartWheater]

• Changes appear consistent
  • The CRAN were very particular about error/warning production and required changes around suppressing error messages. I don't think there changes will be a problem.