FunctionReporter fails on Rcpp C++Function objects with externalptr in function body #348

Description

pkgnet::FunctionReporter fails when analyzing a package that exposes Rcpp/module-backed functions with class C++Function. In this case, the package is FIMS.

The package report is partly generated, but the function dependency visualization fails with:

Error in as.vector(x, "list") : 
  cannot coerce type 'externalptr' to vector of type 'list'

Expected Behavior

I was trying to build the function dependency network using FunctionReporter. I thought maybe it would skip or parse around Rcpp external pointer objects or produce maybe an error message explaining that C++Function, Rcpp module functions, or externalptr objects listed are unsupported.

I checked the FunctionReporter documentation. It lists limitations for NSE, list-stored functions, R6/reference object methods, and reference class methods, but I did not see Rcpp C++Function / externalptr function bodies mentioned. If these are intentionally outside scope, would it be possible for FunctionReporter to skip them or fail with a more informative message?

Actual behavior

The HTML report renders the Function Network section header, but the visualization fails.

The same failure can be reproduced outside the HTML report:

library(pkgnet)

fr <- pkgnet::FunctionReporter$new()
fr$set_package("FIMS")

fr$nodes
fr$edges
traceback()

Output:

INFO [...] Extracting functions from FIMS as graph nodes...
INFO [...] FIMS ... done extracting functions as nodes.
INFO [...] Extracting dependencies between functions in FIMS as graph edges...
Error in as.vector(x, "list") : 
  cannot coerce type 'externalptr' to vector of type 'list'

The traceback shows the failure occurs inside pkgnet’s recursive function parser:

17: as.list.default(x)
16: as.list(x)
...
6: .parse_function(f)
5: FUN(X[[i]], ...)
4: lapply(X = funs, FUN = .called_by, all_functions = funs, pkg_env = pkg_env)
3: data.table::rbindlist(...)
2: private$extract_edges()
1: fr$edges

Diagnostic Detail

In this package, 22 of 130 function nodes are C++Function objects. Parsing those function bodies with pkgnet’s internal parser produces the same error:

# Example failing objects include:
c(
  "CreateTMBModel",
  "clear",
  "get_fixed",
  "get_log",
  "get_parameter_names",
  "get_random",
  "init_logging",
  "logit",
  "set_fixed",
  "set_random",
  "write_log"
)

Their bodies contain .External(...) calls with pointer objects. Excluding C++Function objects as source functions allows edge extraction for the remaining R functions to succeed:

total_function_nodes = 130
r_function_nodes = 108
cpp_function_nodes = 22
edges_from_r_functions = 141

Environment
OS: Windows 11 x64, build 26200
R version: 4.5.1
pkgnet version: 0.6.0
FIMS version: 0.9.4

I’m happy to provide more diagnostics if helpful. Thank you for your consideration.