Thanks to visit codestin.com
Credit goes to github.com

Skip to content

fix: local search c errors #307

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 5 commits into
base: main
Choose a base branch
from
Open

fix: local search c errors #307

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
99977ed
fix: local search c errors
be-marc Oct 13, 2025
6a1b7c0
...
be-marc Oct 14, 2025
3505d29
...
be-marc Oct 14, 2025
65a79d5
...
be-marc Oct 14, 2025
88e8ae9
...
be-marc Oct 14, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
224 changes: 224 additions & 0 deletions attic/issues.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,224 @@
* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/bbotk.Rcheck’
* using R Under development (unstable) (2025-10-10 r88914)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘bbotk/DESCRIPTION’ ... OK
* this is package ‘bbotk’ version ‘1.7.0’
* package encoding: UTF-8
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package ‘bbotk’ can be installed ... [161s/519s] WARNING
Found the following significant warnings:
test_local_search.h:8:6: warning: type of ‘c_test_toposort_params’ does not match original declaration [-Wlto-type-mismatch]
See ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/bbotk.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
* checking package directory ... OK
* checking whether the package can be loaded ... [5s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/10s] OK
* checking whether the package can be unloaded cleanly ... [4s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/16s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/18s] OK
* checking loading without being on the library search path ... [4s/16s] OK
* checking compiled code ... OK
* checking examples ... [87s/273s] OK
* checking tests ... [26m/32m] OK
Running ‘testthat.R’ [26m/32m]
* DONE
Status: 1 WARNING






* installing *source* package ‘bbotk’ ...
** this is package ‘bbotk’ version ‘1.7.0’
** package ‘bbotk’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[2]: Entering directory '/data/gannet/ripley/R/packages/tests-LTO/bbotk/src'
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -c init.c -o init.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -c is_dominated.c -o is_dominated.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -c local_search.c -o local_search.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -c rc_helpers.c -o rc_helpers.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -c test_local_search.c -o test_local_search.o
gcc -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -flto=10 -fpic -L/usr/local/lib64 -o bbotk.so init.o is_dominated.o local_search.o rc_helpers.o test_local_search.o
test_local_search.h:8:6: warning: type of ‘c_test_toposort_params’ does not match original declaration [-Wlto-type-mismatch]
8 | SEXP c_test_toposort_params(SEXP s_ss, SEXP s_ctrl);
| ^
test_local_search.c:170:6: note: type mismatch in parameter 3
170 | SEXP c_test_toposort_params(SEXP s_ss, SEXP s_expected_param_sort, SEXP s_expected_cond_sort) {
| ^
test_local_search.c:170:6: note: type ‘struct SEXPREC *’ should match type ‘void’
test_local_search.c:170:6: note: ‘c_test_toposort_params’ was previously declared here
make[2]: Leaving directory '/data/gannet/ripley/R/packages/tests-LTO/bbotk/src'
installing to /data/gannet/ripley/R/packages/tests-LTO/Libs/bbotk-lib/00LOCK-bbotk/00new/bbotk/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bbotk)
Time 1:09.29, 35.17 + 1.23







Package bbotk version 1.7.0
Package built using 88914/R 4.6.0; x86_64-pc-linux-gnu; 2025-10-12 18:49:48 UTC; unix
Checked with rchk version 35618ebbccf3cd0b45a3530e6303970a22a9056b LLVM version 14.0.6
More information at https://github.com/kalibera/cran-checks/blob/master/rchk/PROTECT.md
For rchk in docker image see https://github.com/kalibera/rchk/blob/master/doc/DOCKER.md

Function RC_named_list_create_PROTECT
[PB] has possible protection stack imbalance bbotk/src/rc_helpers.c:24

Function RC_named_list_create_emptynames_PROTECT
[PB] has possible protection stack imbalance bbotk/src/rc_helpers.c:13

Function catch_condition
[UP] calling allocating function Rf_eval with a fresh pointer (stop_call <arg 1>) bbotk/src/local_search.c:287

Function dt_generate_PROTECT
[PB] has possible protection stack imbalance bbotk/src/local_search.c:187





Whats the issuue? Fix R Under development (unstable) (2025-10-10 r88914) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin25.0.0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace("testthat", quietly = TRUE)) {
+ library("testthat")
+ library("checkmate")
+ test_check("bbotk")
+ }
Loading required package: bbotk
Loading required package: paradox
local_search.c:333:27: runtime error: inf is outside the range of representable values of type 'int'
#0 0x00010e89a388 in extract_ss_info_PROTECT local_search.c:333
#1 0x00010e8a1c34 in c_local_search local_search.c:775
#2 0x0001064fb268 in R_doDotCall dotcode.c:763
#3 0x000106598858 in do_dotcall dotcode.c:1437
#4 0x000106736fb0 in bcEval_loop eval.c:8114
#5 0x0001066e94e8 in bcEval eval.c:7497
#6 0x0001066e767c in Rf_eval eval.c:1167
#7 0x0001066f2174 in R_execClosure eval.c:2389
#8 0x0001066edad4 in applyClosure_core eval.c:2302
#9 0x0001066e7fa4 in Rf_eval eval.c:1280
#10 0x0001066f2174 in R_execClosure eval.c:2389
#11 0x0001066edad4 in applyClosure_core eval.c:2302
#12 0x000106741b24 in bcEval_loop eval.c:8085
#13 0x0001066e94e8 in bcEval eval.c:7497
#14 0x0001066e767c in Rf_eval eval.c:1167
#15 0x0001066f2174 in R_execClosure eval.c:2389
#16 0x0001066edad4 in applyClosure_core eval.c:2302
#17 0x0001066e7fa4 in Rf_eval eval.c:1280
#18 0x0001066f2174 in R_execClosure eval.c:2389
#19 0x0001066edad4 in applyClosure_core eval.c:2302
#20 0x0001066e7fa4 in Rf_eval eval.c:1280
#21 0x0001066fc2b8 in do_begin eval.c:2992
#22 0x0001066e7a70 in Rf_eval eval.c:1232
#23 0x000106704ecc in do_eval eval.c:3937
#24 0x000106736fb0 in bcEval_loop eval.c:8114
#25 0x0001066e94e8 in bcEval eval.c:7497
#26 0x0001066e767c in Rf_eval eval.c:1167
#27 0x0001066f2174 in R_execClosure eval.c:2389
#28 0x0001066edad4 in applyClosure_core eval.c:2302
#29 0x0001066e7fa4 in Rf_eval eval.c:1280
#30 0x000106705304 in do_eval eval.c:3955
#31 0x000106736fb0 in bcEval_loop eval.c:8114
#32 0x0001066e94e8 in bcEval eval.c:7497
#33 0x0001066e767c in Rf_eval eval.c:1167
#34 0x0001066f2174 in R_execClosure eval.c:2389
#35 0x0001066edad4 in applyClosure_core eval.c:2302
#36 0x0001066ef544 in R_forceAndCall eval.c:2456
#37 0x00010631d3c4 in do_lapply apply.c:75
#38 0x0001068b4b24 in do_internal names.c:1411
#39 0x000106727558 in bcEval_loop eval.c:8134
#40 0x0001066e94e8 in bcEval eval.c:7497
#41 0x0001066e767c in Rf_eval eval.c:1167
#42 0x0001066f2174 in R_execClosure eval.c:2389
#43 0x0001066edad4 in applyClosure_core eval.c:2302
#44 0x0001066e7fa4 in Rf_eval eval.c:1280
#45 0x0001066fc2b8 in do_begin eval.c:2992
#46 0x0001066e7a70 in Rf_eval eval.c:1232
#47 0x0001066e7a70 in Rf_eval eval.c:1232
#48 0x000106838f68 in Rf_ReplIteration main.c:264
#49 0x00010683cfcc in R_ReplConsole main.c:317
#50 0x00010683cdc8 in run_Rmainloop main.c:1235
#51 0x00010683d0e8 in Rf_mainloop main.c:1242
#52 0x000104d355ec in main Rmain.c:29
#53 0x0001810b9d50 in start+0x1c0c (dyld:arm64e+0x3d50)

SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior local_search.c:333:27
[ FAIL 0 | WARN 0 | SKIP 52 | PASS 962 ]

══ Skipped tests (52) ══════════════════════════════════════════════════════════
• On CRAN (51): 'test_ArchiveAsync.R:2:3', 'test_ArchiveAsync.R:61:3',
'test_ArchiveAsyncFrozen.R:2:3', 'test_ArchiveBatch.R:3:3',
'test_CallbackAsync.R:4:3', 'test_CallbackAsync.R:31:3',
'test_CallbackAsync.R:59:3', 'test_CallbackAsync.R:88:3',
'test_CallbackAsync.R:118:3', 'test_CallbackAsync.R:154:3',
'test_CallbackAsync.R:183:3', 'test_CallbackAsync.R:210:3',
'test_CallbackAsync.R:239:3', 'test_CallbackAsync.R:269:3',
'test_CallbackAsync.R:297:3', 'test_Objective.R:9:3',
'test_OptimInstanceAsyncSingleCrit.R:2:3',
'test_OptimInstanceAsyncSingleCrit.R:26:3',
'test_OptimInstanceAsyncSingleCrit.R:45:3',
'test_OptimInstanceAsyncSingleCrit.R:65:3',
'test_OptimInstanceAsyncSingleCrit.R:82:3',
'test_OptimInstanceAsyncSingleCrit.R:109:3',
'test_OptimInstanceBatchMultiCrit.R:3:3',
'test_OptimInstanceBatchSingleCrit.R:8:3',
'test_OptimizerAsynDesignPoints.R:2:3', 'test_OptimizerAsynGridSearch.R:2:3',
'test_OptimizerAsync.R:2:3', 'test_OptimizerAsync.R:26:3',
'test_OptimizerAsync.R:50:3', 'test_OptimizerAsync.R:73:3',
'test_OptimizerAsync.R:95:3', 'test_OptimizerAsync.R:124:3',
'test_OptimizerAsync.R:155:3', 'test_OptimizerAsyncRandomSearch.R:2:3',
'test_OptimizerBatchCmaes.R:28:3', 'test_OptimizerBatchDesignPoints.R:5:3',
'test_OptimizerBatchFocusSearch.R:4:3', 'test_OptimizerBatchGenSA.R:6:3',
'test_OptimizerBatchGridSearch.R:4:3', 'test_OptimizerBatchNLoptr.R:9:3',
'test_OptimizerBatchRandomSearch.R:4:3', 'test_TerminatorClockTime.R:5:3',
'test_TerminatorCombo.R:6:3', 'test_TerminatorEvals.R:5:3',
'test_TerminatorNone.R:5:3', 'test_TerminatorPerfReached.R:4:3',
'test_TerminatorRunTime.R:2:5', 'test_TerminatorStagnation.R:5:3',
'test_TerminatorStagnationBatch.R:5:3',
'test_TerminatorStagnationBatch.R:19:3', 'test_mlr_callbacks.R:58:3'
• TRUE is TRUE (1): 'test_mlr_callbacks.R:19:3'

[ FAIL 0 | WARN 0 | SKIP 52 | PASS 962 ]
>
> proc.time()
user system elapsed
43 changes: 20 additions & 23 deletions src/local_search.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -141,8 +141,8 @@ void dt_set_na(SEXP s_dt, int row_i, int param_j) {
}

// Create an uninitialized data.table with col types from SearchSpace
// Return DT is PROTECTed and must be unprotected by the caller
SEXP dt_generate_PROTECT(int n, SearchSpace* ss) {
// Return DT must be protected by the caller
SEXP dt_generate(int n, SearchSpace* ss) {
SEXP s_dt = PROTECT(allocVector(VECSXP, ss->n_params));
for (int j = 0; j < ss->n_params; j++) {
int param_class = ss->param_classes[j];
Expand All @@ -161,10 +161,11 @@ SEXP dt_generate_PROTECT(int n, SearchSpace* ss) {
}
// Set column names
SEXP s_colnames = PROTECT(allocVector(STRSXP, ss->n_params));
for (int j = 0; j < ss->n_params; j++) {
for (int j = 0; j < ss->n_params; j++) {
SET_STRING_ELT(s_colnames, j, mkChar(ss->param_names[j]));
}
setAttrib(s_dt, R_NamesSymbol, s_colnames);

// Set class to data.table
SEXP class_attr = PROTECT(allocVector(STRSXP, 2));
SET_STRING_ELT(class_attr, 0, mkChar("data.table"));
Expand All @@ -182,8 +183,7 @@ SEXP dt_generate_PROTECT(int n, SearchSpace* ss) {
SEXP selfref = PROTECT(allocVector(INTSXP, 1));
INTEGER(selfref)[0] = NA_INTEGER;
setAttrib(s_dt, Rf_install(".internal.selfref"), selfref);

UNPROTECT(4); // colnames, rownames, class_attr, selfref
UNPROTECT(5); // s_colnames class_attr s_rownames selfref s_dt
return s_dt;
}

Expand Down Expand Up @@ -263,13 +263,6 @@ void dt_set_random(SEXP s_dt, int row_i, int param_j, const SearchSpace* ss) {
}





/************ General functions for R data types *********** */



/************ try-eval-catch *********** */

// internal function to evaluate an expression in the global environment
Expand All @@ -283,8 +276,9 @@ SEXP catch_condition(SEXP s_condition, void *data) {
DEBUG_PRINT("Caught R condition of class: %s\n",
CHAR(STRING_ELT(Rf_getAttrib(s_condition, R_ClassSymbol), 0)));
if (!Rf_inherits(s_condition, "terminator_exception")) {
SEXP stop_call = Rf_lang2(Rf_install("stop"), s_condition);
SEXP stop_call = PROTECT(Rf_lang2(Rf_install("stop"), s_condition));
Rf_eval(stop_call, R_GlobalEnv);
UNPROTECT(1); // stop_call
}
return R_NilValue;
}
Expand Down Expand Up @@ -325,12 +319,15 @@ void extract_ss_info_PROTECT(SEXP s_ss, SearchSpace* ss) {
}

// copy nlevels
// paradox stores nlevels as double because for ParamDbl nlevels is Inf
// The code below only works because we never access the nlevels of ParamDbl
ss->n_levels = (int*) R_alloc(ss->n_params, sizeof(int));
double* nlevels = REAL(RC_get_dt_col_by_name(s_data, "nlevels"));
for (int i = 0; i < ss->n_params; i++) {
ss->n_levels[i] = (int)nlevels[i];
if (!R_FINITE(nlevels[i])) {
// For ParamDbl, nlevels is Inf - set to 0 since we never access it
ss->n_levels[i] = 0;
} else {
ss->n_levels[i] = (int)nlevels[i];
}
}

// copy param_classes
Expand Down Expand Up @@ -664,7 +661,7 @@ int eval_obj(int n, SEXP s_x, SEXP s_obj, double* y, const Control* ctrl) {
}


SEXP get_best_pop_element_PROTECT(SEXP s_pop_x, const double* pop_y, const SearchSpace* ss, const Control* ctrl) {
SEXP get_best_pop_element(SEXP s_pop_x, const double* pop_y, const SearchSpace* ss, const Control* ctrl) {
// find the best point in the population
double best_y = pop_y[0];
int best_i = 0;
Expand All @@ -675,8 +672,8 @@ SEXP get_best_pop_element_PROTECT(SEXP s_pop_x, const double* pop_y, const Searc
}
}
best_y *= ctrl->obj_mult; // convert to original scale
SEXP s_res = RC_named_list_create_PROTECT(2, (const char*[]){"x", "y"});
SEXP s_res_x = RC_named_list_create_PROTECT(ss->n_params, ss->param_names);
SEXP s_res = PROTECT(RC_named_list_create(2, (const char*[]){"x", "y"}));
SEXP s_res_x = PROTECT(RC_named_list_create(ss->n_params, ss->param_names));


for (int j = 0; j < ss->n_params; j++) {
Expand All @@ -695,7 +692,7 @@ SEXP get_best_pop_element_PROTECT(SEXP s_pop_x, const double* pop_y, const Searc
}
SET_VECTOR_ELT(s_res, 0, s_res_x);
SET_VECTOR_ELT(s_res, 1, ScalarReal(best_y));
UNPROTECT(1); // s_res_x
UNPROTECT(2); // s_res_x, s_res
return s_res;
}

Expand Down Expand Up @@ -784,7 +781,7 @@ SEXP c_local_search(SEXP s_obj, SEXP s_ss, SEXP s_ctrl, SEXP s_initial_x) {
SEXP s_pop_x = PROTECT(duplicate(s_initial_x));
dt_print(s_pop_x, 10);

SEXP s_neighs_x = dt_generate_PROTECT(ctrl.n_searches * ctrl.n_neighs, &ss);
SEXP s_neighs_x = PROTECT(dt_generate(ctrl.n_searches * ctrl.n_neighs, &ss));

// y-values for pop. we wil later write into this array
double *pop_y = (double*) R_alloc(ctrl.n_searches, sizeof(double));
Expand All @@ -805,7 +802,7 @@ SEXP c_local_search(SEXP s_obj, SEXP s_ss, SEXP s_ctrl, SEXP s_initial_x) {
}
}
}
SEXP s_global_best_x = RC_named_list_create_PROTECT(ss.n_params, ss.param_names);
SEXP s_global_best_x = PROTECT(RC_named_list_create(ss.n_params, ss.param_names));
if (global_best_i >= 0) {
for (int j = 0; j < ss.n_params; j++) {
int param_class = ss.param_classes[j];
Expand Down Expand Up @@ -846,7 +843,7 @@ SEXP c_local_search(SEXP s_obj, SEXP s_ss, SEXP s_ctrl, SEXP s_initial_x) {
PutRNGstate();
// Build result from global best (convert y back to original scale)
double best_y_out = global_best_y * ctrl.obj_mult;
SEXP s_res = RC_named_list_create_PROTECT(2, (const char*[]){"x", "y"});
SEXP s_res = PROTECT(RC_named_list_create(2, (const char*[]){"x", "y"}));
SET_VECTOR_ELT(s_res, 0, s_global_best_x);
SET_VECTOR_ELT(s_res, 1, ScalarReal(best_y_out));
UNPROTECT(4 + ss.n_conds); // s_pop_x, s_neighs_x, s_global_best_x, s_res, and cond rhs
Expand Down
4 changes: 2 additions & 2 deletions src/local_search.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,7 @@ typedef struct {
int random_int(int a, int b);
double random_normal(double mean, double sd);

SEXP dt_generate_PROTECT(int n, SearchSpace *ss);
SEXP dt_generate(int n, SearchSpace *ss);
void dt_set_na(SEXP s_dt, int row_i, int param_j);
int dt_is_na(SEXP s_dt, int row_i, int param_j);
void dt_set_random(SEXP s_dt, int row_i, int param_j, const SearchSpace *ss);
Expand All @@ -93,6 +93,6 @@ void generate_neighs(SEXP s_pop_x, SEXP s_neighs_x, const SearchSpace* ss, const
void copy_best_neighs_to_pop(SEXP s_neighs_x, double* neighs_y, SEXP s_pop_x, double *pop_y,
int* stagnate_count, double *global_best_y, SEXP s_global_best_x, const SearchSpace* ss, const Control* ctrl);
SEXP c_local_search(SEXP s_obj, SEXP s_ss, SEXP s_ctrl, SEXP s_initial_x);
SEXP get_best_pop_element_PROTECT(SEXP s_pop_x, const double* pop_y, const SearchSpace* ss, const Control* ctrl);
SEXP get_best_pop_element(SEXP s_pop_x, const double* pop_y, const SearchSpace* ss, const Control* ctrl);

#endif // LOCAL_SEARCH_H
Loading