Fix CRAN NOTE: Replace .attr() with Rf_setAttrib() to avoid non-API ATTRIB calls

[Copilot]

CRAN reported non-API calls to ATTRIB in compiled code. Rcpp's .attr() setter internally uses the non-API ATTRIB function, violating portability requirements.

Changes

Replaced attribute setters with R API calls

• src/hmi.cpp: 5 replacements (var, sd, sem, samples, relativeError)
• src/reduce_tree.cpp: 5 replacements (class, order for phylo/multiPhylo)
• src/spr.cpp: 13 replacements (class, order, dim)

Performance optimization
Cached symbol lookups as static SEXP to avoid repeated Rf_install() calls:

// Before
result.attr("var") = runVar;
result.attr("sd") = runSD;

// After
static SEXP var_sym = Rf_install("var");
static SEXP sd_sym = Rf_install("sd");
Rf_setAttrib(result, var_sym, Rcpp::wrap(runVar));
Rf_setAttrib(result, sd_sym, Rcpp::wrap(runSD));

Note: .attr() getters unchanged—only setters use non-API internals.

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Original prompt

---

This section details on the original issue you should resolve

<issue_title>Cran NOTE</issue_title>
<issue_description>Result: NOTE
File ‘TreeDist/libs/TreeDist.so’:
Found non-API call to R: ‘ATTRIB’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.</issue_description>

<agent_instructions>Please resolve the CRAN note and provide an explanation of the fix.
All tests in the test suite must pass; please take care not to introduce any segementation faults or incompatibilities.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Cran NOTE #169

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[codecov]

Codecov Report

❌ Patch coverage is 75.75758% with 8 lines in your changes missing coverage. Please review.
✅ Project coverage is 99.19%. Comparing base (2cb9ef2) to head (ed0c1fe).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spr.cpp	50.00%	8 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #170      +/-   ##
==========================================
- Coverage   99.31%   99.19%   -0.13%     
==========================================
  Files          43       43              
  Lines        3201     3215      +14     
==========================================
+ Hits         3179     3189      +10     
- Misses         22       26       +4     

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[ms609]

closed by update to Rcpp