* installing *source* package ‘bgns’ ...
** this is package ‘bgns’ version ‘0.4.3’
** package ‘bgns’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C compiler: ‘gcc (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++ compiler: ‘g++ (GCC) 16.2.1 20260819 (Red Hat 16.2.1-2)’
using C++17
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/bgns/src'
g++ -std=gnu++17 -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DBGNS_ENABLE_SIMD=1 -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c bicor.cpp -o bicor.o
bicor.cpp: In function ‘double {anonymous}::mad_raw_tls_from_vec(const std::vector<double>&, double)’:
bicor.cpp:220:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
220 | if(vals.empty()) return NA_REAL; TLS &t=tls(); t.absbuf.resize(vals.size());
| ^~
bicor.cpp:220:38: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
220 | if(vals.empty()) return NA_REAL; TLS &t=tls(); t.absbuf.resize(vals.size());
| ^~~
bicor.cpp: In function ‘{anonymous}::DotStat {anonymous}::gallop_num(const IA*, const double*, int, const IB*, const double*, int)’:
bicor.cpp:296:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
296 | if(jb==nb) break; if((int)bi[jb]==key){ num += av[ia]*bv[jb]; ++ov; }
| ^~
bicor.cpp:296:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
296 | if(jb==nb) break; if((int)bi[jb]==key){ num += av[ia]*bv[jb]; ++ov; }
| ^~
bicor.cpp: In function ‘{anonymous}::DotStat {anonymous}::gallop_inter(const IA*, const double*, int, const IB*, const double*, int)’:
bicor.cpp:305:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
305 | if(jb==nb) break; if((int)bi[jb]==key){ double a=av[ia], b=bv[jb]; num+=a*b; sA+=a*a; sB+=b*b; ++ov; }
| ^~
bicor.cpp:305:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
305 | if(jb==nb) break; if((int)bi[jb]==key){ double a=av[ia], b=bv[jb]; num+=a*b; sA+=a*a; sB+=b*b; ++ov; }
| ^~
bicor.cpp: In function ‘void {anonymous}::dense_panel_sizes(int, int, int, size_t, int&, int&)’:
bicor.cpp:331:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
331 | if(Pa<1)Pa=1; if(Pb<1)Pb=1;
| ^~
bicor.cpp:331:19: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
331 | if(Pa<1)Pa=1; if(Pb<1)Pb=1;
| ^~
bicor.cpp: In function ‘bool {anonymous}::chr_eq(SEXP, SEXP)’:
bicor.cpp:367:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
367 | if(a==b) return true; if(a==NA_STRING && b==NA_STRING) return true; if(a==NA_STRING || b==NA_STRING) return false; return std::strcmp(CHAR(a), CHAR(b))==0;
| ^~
bicor.cpp:367:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
367 | if(a==b) return true; if(a==NA_STRING && b==NA_STRING) return true; if(a==NA_STRING || b==NA_STRING) return false; return std::strcmp(CHAR(a), CHAR(b))==0;
| ^~
bicor.cpp: In function ‘bool {anonymous}::stringvec_identical(SEXP, SEXP)’:
bicor.cpp:370:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
370 | if(!Rf_isString(A) || !Rf_isString(B)) return false; const R_xlen_t n=Rf_xlength(A); if(n!=Rf_xlength(B)) return false;
| ^~
bicor.cpp:370:58: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
370 | if(!Rf_isString(A) || !Rf_isString(B)) return false; const R_xlen_t n=Rf_xlength(A); if(n!=Rf_xlength(B)) return false;
| ^~~~~
bicor.cpp: In function ‘void {anonymous}::build_panel_mixed_from_real(const double*, int, const int*, int, PanelMixed<I>&)’:
bicor.cpp:454:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
454 | for(int q=0;q<m;++q) pm.S.idx[base_off+q]=(I)t.tmpi[q]; pm.S.off.push_back(base_off+(size_t)m);
| ^~~
bicor.cpp:454:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
454 | for(int q=0;q<m;++q) pm.S.idx[base_off+q]=(I)t.tmpi[q]; pm.S.off.push_back(base_off+(size_t)m);
| ^~
bicor.cpp: In function ‘void {anonymous}::build_panel_mixed_from_int(const int*, int, const int*, int, PanelMixed<I>&)’:
bicor.cpp:476:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
476 | for(int q=0;q<m;++q) pm.S.idx[base_off+q]=(I)t.tmpi[q]; pm.S.off.push_back(base_off+(size_t)m);
| ^~~
bicor.cpp:476:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
476 | for(int q=0;q<m;++q) pm.S.idx[base_off+q]=(I)t.tmpi[q]; pm.S.off.push_back(base_off+(size_t)m);
| ^~
bicor.cpp: In function ‘void {anonymous}::build_panel_mixed_from_csc(const int*, const int*, const double*, int, const int*, int, PanelMixed<I>&)’:
bicor.cpp:503:13: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
503 | for(int q=0;q<m;++q) pm.S.idx[base_off+q]=(I)t.tmpi[q]; pm.S.off.push_back(base_off+(size_t)m);
| ^~~
bicor.cpp:503:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
503 | for(int q=0;q<m;++q) pm.S.idx[base_off+q]=(I)t.tmpi[q]; pm.S.off.push_back(base_off+(size_t)m);
| ^~
bicor.cpp: In lambda function:
bicor.cpp:798:21: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
798 | if(!PY.ok_local[tj]) continue; const int gj = PY.local_cols[tj];
| ^~
bicor.cpp:798:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
798 | if(!PY.ok_local[tj]) continue; const int gj = PY.local_cols[tj];
| ^~~~~
bicor.cpp:800:25: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
800 | if(!PX.ok_local[si]) continue; const int gi = PX.local_cols[si];
| ^~
bicor.cpp:800:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
800 | if(!PX.ok_local[si]) continue; const int gi = PX.local_cols[si];
| ^~~~~
bicor.cpp: In function ‘SEXPREC* bicor_knn_impl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, bool, SEXP)’:
bicor.cpp:1581:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
1581 | if (!PY.ok_local[tj]) continue; const int tgt = PY.local_cols[tj];
| ^~
bicor.cpp:1581:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
1581 | if (!PY.ok_local[tj]) continue; const int tgt = PY.local_cols[tj];
| ^~~~~
bicor.cpp:1584:37: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
1584 | if (!PX.ok_local[si]) continue; const int src = PX.local_cols[si]; if (src==tgt) continue;
| ^~
bicor.cpp:1584:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
1584 | if (!PX.ok_local[si]) continue; const int src = PX.local_cols[si]; if (src==tgt) continue;
| ^~~~~
bicor.cpp:1643:33: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
1643 | if (!PY.ok_local[tj]) continue; const int tgt = PY.local_cols[tj];
| ^~
bicor.cpp:1643:65: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
1643 | if (!PY.ok_local[tj]) continue; const int tgt = PY.local_cols[tj];
| ^~~~~
bicor.cpp:1646:37: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
1646 | if (!PX.ok_local[si]) continue; const int src = PX.local_cols[si]; if (src==tgt) continue;
| ^~
bicor.cpp:1646:69: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
1646 | if (!PX.ok_local[si]) continue; const int src = PX.local_cols[si]; if (src==tgt) continue;
| ^~~~~
gcc -I"/data/localhost/ripley/R/R-devel/include" -DNDEBUG -DBGNS_ENABLE_SIMD=1 -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 -c init.c -o init.o
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o bgns.so bicor.o init.o -fopenmp -L/data/localhost/ripley/R/R-devel/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/bgns/src'
make[1]: Entering directory '/data/localhost/ripley/R/packages/tests-devel/bgns/src'
make[1]: Leaving directory '/data/localhost/ripley/R/packages/tests-devel/bgns/src'
installing to /data/localhost/ripley/R/packages/tests-devel/bgns.Rcheck/00LOCK-bgns/00new/bgns/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (bgns)