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fix: R API — remove outlawed R_UnboundValue #2597

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fix: R API — remove outlawed R_UnboundValue #2597

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a66c43c
fix: R API
maelle Mar 26, 2026
afb5e15
fix older R version error
schochastics Mar 26, 2026
6bf0706
Merge branch 'main' into cran-fix
krlmlr Apr 1, 2026
8497d2f
Update CITATION.cff
github-actions[bot] Apr 1, 2026
169c104
fix: remove use of outlawed R_UnboundValue
Copilot Apr 1, 2026
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3 changes: 1 addition & 2 deletions CITATION.cff
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Original file line number Diff line number Diff line change
Expand Up @@ -642,7 +642,7 @@ references:
title: graph
abstract: 'graph: graph: A package to handle graph data structures'
notes: Enhances
repository: https://bioconductor.org/
repository: https://bioc-release.r-universe.dev
authors:
- family-names: Gentleman
given-names: R
Expand All @@ -657,7 +657,6 @@ references:
- family-names: Shannon
given-names: Paul
year: '2026'
doi: 10.18129/B9.bioc.graph
- type: software
title: cpp11
abstract: 'cpp11: A C++11 Interface for R''s C Interface'
Expand Down
153 changes: 55 additions & 98 deletions src/rinterface_extra.c
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Original file line number Diff line number Diff line change
Expand Up @@ -69,6 +69,22 @@ enum igraph_versions {

#define R_IGRAPH_VERSION_VAR ".__igraph_version__."

#if R_VERSION >= R_Version(4, 5, 0)
# define IGRAPH_R_GET_VAR(sym, env, inherits) \
R_getVar((sym), (env), (inherits))
# define IGRAPH_R_GET_VAR_EX(sym, env, inherits, ifnotfound) \
R_getVarEx((sym), (env), (inherits), (ifnotfound))
#else
static inline SEXP IGRAPH_R_GET_VAR(SEXP sym, SEXP env, Rboolean inherits) {
return inherits ? Rf_findVar(sym, env) : Rf_findVarInFrame(env, sym);
}

static inline SEXP IGRAPH_R_GET_VAR_EX(SEXP sym, SEXP env, Rboolean inherits, SEXP ifnotfound) {
SEXP val = IGRAPH_R_GET_VAR(sym, env, inherits);
return val == R_UnboundValue ? ifnotfound : val;
}
#endif

/* The following three R_check_... functions must only be called from top-level C code,
* i.e. in contexts where igraph_error() does NOT return. */

Expand Down Expand Up @@ -238,14 +254,7 @@ Rx_igraph_safe_eval_result_t Rx_igraph_safe_eval_classify_result(SEXP result) {
SEXP Rx_igraph_safe_eval_in_env(SEXP expr_call, SEXP rho, Rx_igraph_safe_eval_result_t* result) {
/* find `identity` function used to capture errors */
SEXP identity = PROTECT(Rf_install("identity"));
#if R_VERSION >= R_Version(4, 6, 0)
SEXP identity_func = PROTECT(R_getVar(identity, R_BaseNamespace, TRUE));
#else
SEXP identity_func = PROTECT(Rf_findFun(identity, R_BaseNamespace));
if (identity_func == R_UnboundValue) {
Rf_error("Failed to find 'base::identity()'");
}
#endif

/* define the call -- enclose with `tryCatch` so we can record errors */
SEXP try_catch = PROTECT(Rf_install("tryCatch"));
Expand Down Expand Up @@ -2415,55 +2424,39 @@ igraph_error_t Rx_igraph_progress_handler(const char *message, double percent,
void * data) {
SEXP ec;
int ecint;
int px = 0;
SEXP rho;
#if R_VERSION >= R_Version(4, 6, 0)
rho = R_getRegisteredNamespace("igraph");
#else
SEXP l1 = PROTECT(Rf_install("getNamespace")); px++;
SEXP l2 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar("igraph")))); px += 2;
SEXP l3 = PROTECT(Rf_lang2(l1, l2)); px++;
rho = PROTECT(Rf_eval(l3, R_BaseEnv)); px++;
#endif
SEXP l1 = PROTECT(Rf_install("getNamespace"));
SEXP l2 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar("igraph"))));
SEXP l3 = PROTECT(Rf_lang2(l1, l2));
SEXP rho = PROTECT(Rf_eval(l3, R_BaseEnv));

SEXP l4 = PROTECT(Rf_install(".igraph.progress")); px++;
SEXP l5 = PROTECT(Rf_ScalarReal(percent)); px++;
SEXP l6 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar(message)))); px += 2;
SEXP l7 = PROTECT(Rf_lang3(l4, l5, l6)); px++;
PROTECT(ec=Rf_eval(l7, rho)); px++;
SEXP l4 = PROTECT(Rf_install(".igraph.progress"));
SEXP l5 = PROTECT(Rf_ScalarReal(percent));
SEXP l6 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar(message))));
SEXP l7 = PROTECT(Rf_lang3(l4, l5, l6));
PROTECT(ec=Rf_eval(l7, rho));

ecint=INTEGER(ec)[0];
UNPROTECT(px);
UNPROTECT(11);
return ecint;
}

igraph_error_t Rx_igraph_status_handler(const char *message, void *data) {
int px = 0;
SEXP rho;
#if R_VERSION >= R_Version(4, 6, 0)
rho = R_getRegisteredNamespace("igraph");
#else
SEXP l1 = PROTECT(Rf_install("getNamespace")); px++;
SEXP l2 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar("igraph")))); px += 2;
SEXP l3 = PROTECT(Rf_lang2(l1, l2)); px++;
rho = PROTECT(Rf_eval(l3, R_BaseEnv)); px++;
#endif
SEXP l1 = PROTECT(Rf_install("getNamespace"));
SEXP l2 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar("igraph"))));
SEXP l3 = PROTECT(Rf_lang2(l1, l2));
SEXP rho = PROTECT(Rf_eval(l3, R_BaseEnv));

SEXP l4 = PROTECT(Rf_install(".igraph.status")); px++;
SEXP l5 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar(message)))); px += 2;
SEXP l6 = PROTECT(Rf_lang2(l4, l5)); px++;
PROTECT(Rf_eval(l6, rho)); px++;
SEXP l4 = PROTECT(Rf_install(".igraph.status"));
SEXP l5 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar(message))));
SEXP l6 = PROTECT(Rf_lang2(l4, l5));
PROTECT(Rf_eval(l6, rho));

UNPROTECT(px);
UNPROTECT(10);
return 0;
}

static R_xlen_t Rx_igraph_altrep_length(SEXP vec) {
#if R_VERSION >= R_Version(4, 6, 0)
SEXP xp=R_getVar(Rf_install("igraph"), R_altrep_data1(vec), TRUE);
#else
SEXP xp=Rf_findVar(Rf_install("igraph"), R_altrep_data1(vec));
#endif
SEXP xp=IGRAPH_R_GET_VAR(Rf_install("igraph"), R_altrep_data1(vec), TRUE);
igraph_t *g=(igraph_t*)(R_ExternalPtrAddr(xp));
return igraph_ecount(g);
}
Expand All @@ -2472,11 +2465,7 @@ static void *Rx_igraph_altrep_from(SEXP vec, Rboolean writeable) {
SEXP data=R_altrep_data2(vec);
if (data == R_NilValue) {
Rx_igraph_status_handler("Materializing 'from' vector.\n", NULL);
#if R_VERSION >= R_Version(4, 6, 0)
SEXP xp=R_getVar(Rf_install("igraph"), R_altrep_data1(vec), TRUE);
#else
SEXP xp=Rf_findVar(Rf_install("igraph"), R_altrep_data1(vec));
#endif
SEXP xp=IGRAPH_R_GET_VAR(Rf_install("igraph"), R_altrep_data1(vec), TRUE);
igraph_t *g=(igraph_t*)(R_ExternalPtrAddr(xp));

data=Ry_igraph_vector_int_to_SEXP(&g->from);
Expand All @@ -2491,11 +2480,7 @@ static void *Rx_igraph_altrep_to(SEXP vec, Rboolean writeable) {
if (data == R_NilValue) {
Rx_igraph_status_handler("Materializing 'to' vector.\n", NULL);

#if R_VERSION >= R_Version(4, 6, 0)
SEXP xp=R_getVar(Rf_install("igraph"), R_altrep_data1(vec), TRUE);
#else
SEXP xp=Rf_findVar(Rf_install("igraph"), R_altrep_data1(vec));
#endif
SEXP xp=IGRAPH_R_GET_VAR(Rf_install("igraph"), R_altrep_data1(vec), TRUE);
igraph_t *g=(igraph_t*)(R_ExternalPtrAddr(xp));

data=Ry_igraph_vector_int_to_SEXP(&g->to);
Expand Down Expand Up @@ -2542,24 +2527,18 @@ SEXP Rx_igraph_set_verbose(SEXP verbose) {

SEXP R_igraph_finalizer(void) {
IGRAPH_FINALLY_FREE();
int px = 0;
SEXP rho;
#if R_VERSION >= R_Version(4, 6, 0)
rho = R_getRegisteredNamespace("igraph");
#else
SEXP l1 = PROTECT(Rf_install("getNamespace")); px++;
SEXP l2 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar("igraph")))); px += 2;
SEXP l3 = PROTECT(Rf_lang2(l1, l2)); px++;
rho = PROTECT(Rf_eval(l3, R_BaseEnv)); px++;
#endif

SEXP l4 = PROTECT(Rf_install(".igraph.progress")); px++;
SEXP l5 = PROTECT(Rf_ScalarReal(0.0)); px++;
SEXP l6 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar("")))); px += 2;
SEXP l7 = PROTECT(Rf_ScalarLogical(1)); px++;
SEXP l8 = PROTECT(Rf_lang4(l4, l5, l6, l7)); px++;
SEXP l1 = PROTECT(Rf_install("getNamespace"));
SEXP l2 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar("igraph"))));
SEXP l3 = PROTECT(Rf_lang2(l1, l2));
SEXP rho = PROTECT(Rf_eval(l3, R_BaseEnv));

SEXP l4 = PROTECT(Rf_install(".igraph.progress"));
SEXP l5 = PROTECT(Rf_ScalarReal(0.0));
SEXP l6 = PROTECT(Rf_ScalarString(PROTECT(Rf_mkChar(""))));
SEXP l7 = PROTECT(Rf_ScalarLogical(1));
SEXP l8 = PROTECT(Rf_lang4(l4, l5, l6, l7));
Rf_eval(l8, rho);
UNPROTECT(px);
UNPROTECT(11);
return R_NilValue;
}

Expand Down Expand Up @@ -2907,29 +2886,17 @@ igraph_t *Rx_igraph_get_pointer(SEXP graph) {
Rf_error("This graph was created by a now unsupported old igraph version.\n Call upgrade_graph() before using igraph functions on that object.");
}

#if R_VERSION >= R_Version(4, 6, 0)
SEXP xp=R_getVarEx(Rf_install("igraph"), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
SEXP xp=IGRAPH_R_GET_VAR_EX(Rf_install("igraph"), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
if (xp == R_NilValue) {
Rx_igraph_restore_pointer(graph);
xp=R_getVarEx(Rf_install("igraph"), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
}
#else
SEXP xp=Rf_findVar(Rf_install("igraph"), Rx_igraph_graph_env(graph));
if (xp == R_UnboundValue || xp == R_NilValue) {
Rx_igraph_restore_pointer(graph);
xp=Rf_findVar(Rf_install("igraph"), Rx_igraph_graph_env(graph));
xp=IGRAPH_R_GET_VAR_EX(Rf_install("igraph"), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
}
#endif

igraph_t *pgraph=(igraph_t*)(R_ExternalPtrAddr(xp));

if (!pgraph) {
Rx_igraph_restore_pointer(graph);
#if R_VERSION >= R_Version(4, 6, 0)
xp=R_getVarEx(Rf_install("igraph"), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
#else
xp=Rf_findVar(Rf_install("igraph"), Rx_igraph_graph_env(graph));
#endif
xp=IGRAPH_R_GET_VAR_EX(Rf_install("igraph"), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
pgraph=(igraph_t*)(R_ExternalPtrAddr(xp));
}

Expand Down Expand Up @@ -7753,17 +7720,10 @@ SEXP Rx_igraph_graph_version(SEXP graph) {
return Rf_ScalarInteger(ver_0_4);
}

#if R_VERSION >= R_Version(4, 6, 0)
SEXP ver = R_getVarEx(Rf_install(R_IGRAPH_VERSION_VAR), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
SEXP ver = IGRAPH_R_GET_VAR_EX(Rf_install(R_IGRAPH_VERSION_VAR), Rx_igraph_graph_env(graph), TRUE, R_NilValue);
if (ver == R_NilValue) {
return Rf_ScalarInteger(ver_0_7_999);
}
#else
SEXP ver = Rf_findVar(Rf_install(R_IGRAPH_VERSION_VAR), Rx_igraph_graph_env(graph));
if (ver == R_UnboundValue) {
return Rf_ScalarInteger(ver_0_7_999);
}
#endif

if (TYPEOF(ver) == STRSXP) {
return Rf_ScalarInteger(ver_0_8);
Expand Down Expand Up @@ -7797,6 +7757,7 @@ SEXP Rx_igraph_add_version_to_env(SEXP graph) {

SEXP Rx_igraph_add_env(SEXP graph) {
SEXP result = graph;
R_xlen_t i;
uuid_t my_id;
char my_id_chr[40];
int px = 0;
Expand Down Expand Up @@ -7831,11 +7792,7 @@ SEXP Rx_igraph_add_env(SEXP graph) {
}

SEXP Rx_igraph_get_graph_id(SEXP graph) {
#if R_VERSION >= R_Version(4, 6, 0)
return R_getVar(Rf_install("myid"), Rx_igraph_graph_env(graph), TRUE);
#else
return Rf_findVar(Rf_install("myid"), Rx_igraph_graph_env(graph));
#endif
return IGRAPH_R_GET_VAR(Rf_install("myid"), Rx_igraph_graph_env(graph), TRUE);
}

// Wrapper functions for functions not in aaa-auto.R
Expand Down
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