==2040226== Memcheck, a memory error detector
==2040226== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al.
==2040226== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info
==2040226== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R -f testthat.R --restore --save --no-readline --vanilla
==2040226== 

R Under development (unstable) (2026-03-12 r89611) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(iglm)
Loading required package: RcppProgress
> 
> test_check("iglm")
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
==2040226== Invalid read of size 1
==2040226==    at 0x24865299: get_val (packages/tests-vg/iglm/src/../inst/include/iglm/network_class.h:160)
==2040226==    by 0x24865299: initialize_overlap_counts (packages/tests-vg/iglm/src/../inst/include/iglm/xz_class.h:163)
==2040226==    by 0x24865299: XZ_class::XZ_class(int, bool, arma::Mat<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double) (packages/tests-vg/iglm/src/../inst/include/iglm/xz_class.h:137)
==2040226==    by 0x248655D2: XYZ_class::XYZ_class(int, bool, arma::Col<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/../inst/include/iglm/xyz_class.h:34)
==2040226==    by 0x24838B49: xyz_count_global(arma::Mat<double> const&, arma::Col<double> const&, arma::Col<double> const&, arma::Mat<double> const&, arma::Mat<double> const&, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, int, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/xyz_sampling.cpp:224)
==2040226==    by 0x247FB1E4: _iglm_xyz_count_global (R-devel/site-library/Rcpp/include/Rcpp/as.h:43)
==2040226==    by 0x4A7E79: R_doDotCall (svn/R-devel/src/main/dotcode.c:813)
==2040226==    by 0x4E2103: bcEval_loop (svn/R-devel/src/main/eval.c:8682)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7515)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7500)
==2040226==    by 0x4F258A: Rf_eval (svn/R-devel/src/main/eval.c:1167)
==2040226==    by 0x4F430D: R_execClosure (svn/R-devel/src/main/eval.c:2389)
==2040226==    by 0x4F4FC6: applyClosure_core (svn/R-devel/src/main/eval.c:2302)
==2040226==    by 0x4F2695: Rf_applyClosure (svn/R-devel/src/main/eval.c:2324)
==2040226==    by 0x4F2695: Rf_eval (svn/R-devel/src/main/eval.c:1280)
==2040226==    by 0x4F735C: do_set (svn/R-devel/src/main/eval.c:3581)
==2040226==  Address 0x1547143d is 3 bytes before a block of size 9 alloc'd
==2040226==    at 0x4843FEC: operator new(unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:487)
==2040226==    by 0x24860B92: allocate (/usr/include/c++/14/bits/new_allocator.h:151)
==2040226==    by 0x24860B92: allocate (/usr/include/c++/14/bits/alloc_traits.h:478)
==2040226==    by 0x24860B92: _M_allocate (/usr/include/c++/14/bits/stl_vector.h:380)
==2040226==    by 0x24860B92: _M_create_storage (/usr/include/c++/14/bits/stl_vector.h:398)
==2040226==    by 0x24860B92: _Vector_base (/usr/include/c++/14/bits/stl_vector.h:334)
==2040226==    by 0x24860B92: vector (/usr/include/c++/14/bits/stl_vector.h:571)
==2040226==    by 0x24860B92: std::vector<char, std::allocator<char> >::_M_fill_assign(unsigned long, char const&) (/usr/include/c++/14/bits/vector.tcc:278)
==2040226==    by 0x24864C80: assign (/usr/include/c++/14/bits/stl_vector.h:809)
==2040226==    by 0x24864C80: Network (packages/tests-vg/iglm/src/../inst/include/iglm/network_class.h:46)
==2040226==    by 0x24864C80: XZ_class::XZ_class(int, bool, arma::Mat<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double) (packages/tests-vg/iglm/src/../inst/include/iglm/xz_class.h:117)
==2040226==    by 0x248655D2: XYZ_class::XYZ_class(int, bool, arma::Col<double>, arma::Col<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/../inst/include/iglm/xyz_class.h:34)
==2040226==    by 0x24838B49: xyz_count_global(arma::Mat<double> const&, arma::Col<double> const&, arma::Col<double> const&, arma::Mat<double> const&, arma::Mat<double> const&, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, int, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/xyz_sampling.cpp:224)
==2040226==    by 0x247FB1E4: _iglm_xyz_count_global (R-devel/site-library/Rcpp/include/Rcpp/as.h:43)
==2040226==    by 0x4A7E79: R_doDotCall (svn/R-devel/src/main/dotcode.c:813)
==2040226==    by 0x4E2103: bcEval_loop (svn/R-devel/src/main/eval.c:8682)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7515)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7500)
==2040226==    by 0x4F258A: Rf_eval (svn/R-devel/src/main/eval.c:1167)
==2040226==    by 0x4F430D: R_execClosure (svn/R-devel/src/main/eval.c:2389)
==2040226==    by 0x4F4FC6: applyClosure_core (svn/R-devel/src/main/eval.c:2302)
==2040226== 
==2040226== Invalid read of size 1
==2040226==    at 0x24863198: get_val (packages/tests-vg/iglm/src/../inst/include/iglm/network_class.h:160)
==2040226==    by 0x24863198: initialize_overlap_counts (packages/tests-vg/iglm/src/../inst/include/iglm/xz_class.h:163)
==2040226==    by 0x24863198: XZ_class::XZ_class(int, bool, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double) (packages/tests-vg/iglm/src/../inst/include/iglm/xz_class.h:110)
==2040226==    by 0x24837905: XYZ_class (packages/tests-vg/iglm/src/../inst/include/iglm/xyz_class.h:27)
==2040226==    by 0x24837905: xyz_count_global_statistic(XYZ_class const&, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double (*)(XYZ_class const&, int const&, int const&, arma::Mat<double> const&, double const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool const&), std::allocator<double (*)(XYZ_class const&, int const&, int const&, arma::Mat<double> const&, double const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool const&)> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/xyz_sampling.cpp:118)
==2040226==    by 0x24838EFD: xyz_count_global(arma::Mat<double> const&, arma::Col<double> const&, arma::Col<double> const&, arma::Mat<double> const&, arma::Mat<double> const&, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, int, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/xyz_sampling.cpp:243)
==2040226==    by 0x247FB1E4: _iglm_xyz_count_global (R-devel/site-library/Rcpp/include/Rcpp/as.h:43)
==2040226==    by 0x4A7E79: R_doDotCall (svn/R-devel/src/main/dotcode.c:813)
==2040226==    by 0x4E2103: bcEval_loop (svn/R-devel/src/main/eval.c:8682)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7515)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7500)
==2040226==    by 0x4F258A: Rf_eval (svn/R-devel/src/main/eval.c:1167)
==2040226==    by 0x4F430D: R_execClosure (svn/R-devel/src/main/eval.c:2389)
==2040226==    by 0x4F4FC6: applyClosure_core (svn/R-devel/src/main/eval.c:2302)
==2040226==    by 0x4F2695: Rf_applyClosure (svn/R-devel/src/main/eval.c:2324)
==2040226==    by 0x4F2695: Rf_eval (svn/R-devel/src/main/eval.c:1280)
==2040226==    by 0x4F735C: do_set (svn/R-devel/src/main/eval.c:3581)
==2040226==  Address 0x2405babd is 3 bytes before a block of size 9 alloc'd
==2040226==    at 0x4843FEC: operator new(unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:487)
==2040226==    by 0x24860B92: allocate (/usr/include/c++/14/bits/new_allocator.h:151)
==2040226==    by 0x24860B92: allocate (/usr/include/c++/14/bits/alloc_traits.h:478)
==2040226==    by 0x24860B92: _M_allocate (/usr/include/c++/14/bits/stl_vector.h:380)
==2040226==    by 0x24860B92: _M_create_storage (/usr/include/c++/14/bits/stl_vector.h:398)
==2040226==    by 0x24860B92: _Vector_base (/usr/include/c++/14/bits/stl_vector.h:334)
==2040226==    by 0x24860B92: vector (/usr/include/c++/14/bits/stl_vector.h:571)
==2040226==    by 0x24860B92: std::vector<char, std::allocator<char> >::_M_fill_assign(unsigned long, char const&) (/usr/include/c++/14/bits/vector.tcc:278)
==2040226==    by 0x24862C2D: assign (/usr/include/c++/14/bits/stl_vector.h:809)
==2040226==    by 0x24862C2D: Network (packages/tests-vg/iglm/src/../inst/include/iglm/network_class.h:35)
==2040226==    by 0x24862C2D: XZ_class::XZ_class(int, bool, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >, std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >, arma::Mat<double>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double) (packages/tests-vg/iglm/src/../inst/include/iglm/xz_class.h:81)
==2040226==    by 0x24837905: XYZ_class (packages/tests-vg/iglm/src/../inst/include/iglm/xyz_class.h:27)
==2040226==    by 0x24837905: xyz_count_global_statistic(XYZ_class const&, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::vector<double (*)(XYZ_class const&, int const&, int const&, arma::Mat<double> const&, double const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool const&), std::allocator<double (*)(XYZ_class const&, int const&, int const&, arma::Mat<double> const&, double const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool const&)> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/xyz_sampling.cpp:118)
==2040226==    by 0x24838EFD: xyz_count_global(arma::Mat<double> const&, arma::Col<double> const&, arma::Col<double> const&, arma::Mat<double> const&, arma::Mat<double> const&, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, int, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double) (packages/tests-vg/iglm/src/xyz_sampling.cpp:243)
==2040226==    by 0x247FB1E4: _iglm_xyz_count_global (R-devel/site-library/Rcpp/include/Rcpp/as.h:43)
==2040226==    by 0x4A7E79: R_doDotCall (svn/R-devel/src/main/dotcode.c:813)
==2040226==    by 0x4E2103: bcEval_loop (svn/R-devel/src/main/eval.c:8682)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7515)
==2040226==    by 0x4F2257: bcEval (svn/R-devel/src/main/eval.c:7500)
==2040226==    by 0x4F258A: Rf_eval (svn/R-devel/src/main/eval.c:1167)
==2040226==    by 0x4F430D: R_execClosure (svn/R-devel/src/main/eval.c:2389)
==2040226==    by 0x4F4FC6: applyClosure_core (svn/R-devel/src/main/eval.c:2302)
==2040226== 
iglm object
--------------------------------------------------
Formula:
  xyz_obj_new ~ edges(mode = "local") + attribute_y + attribute_x +     degrees

Observed Sufficient Statistics:
edges(mode = 'local')           attribute_y           attribute_x 
                    0                     0                     0 
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
iglm object
--------------------------------------------------
Formula:
  xyz_obj_new ~ edges(mode = "local") + attribute_y + attribute_x +     degrees

Observed Sufficient Statistics:
edges(mode = 'local')           attribute_y           attribute_x 
                    0                     0                     0 
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 150 ]
> 
> proc.time()
   user  system elapsed 
862.792  20.636 875.325 
==2040226== 
==2040226== HEAP SUMMARY:
==2040226==     in use at exit: 222,546,332 bytes in 46,813 blocks
==2040226==   total heap usage: 21,072,669 allocs, 21,025,856 frees, 3,150,376,238 bytes allocated
==2040226== 
==2040226== 448 bytes in 1 blocks are possibly lost in loss record 207 of 2,998
==2040226==    at 0x484B133: calloc (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:1675)
==2040226==    by 0x4011F63: UnknownInlinedFun (/usr/src/debug/glibc-2.39-38.fc40.x86_64/elf/../include/rtld-malloc.h:44)
==2040226==    by 0x4011F63: allocate_dtv (/usr/src/debug/glibc-2.39-38.fc40.x86_64/elf/../elf/dl-tls.c:395)
==2040226==    by 0x4012A61: _dl_allocate_tls (/usr/src/debug/glibc-2.39-38.fc40.x86_64/elf/../elf/dl-tls.c:673)
==2040226==    by 0x557CC03: allocate_stack (/usr/src/debug/glibc-2.39-38.fc40.x86_64/nptl/allocatestack.c:431)
==2040226==    by 0x557CC03: pthread_create@@GLIBC_2.34 (/usr/src/debug/glibc-2.39-38.fc40.x86_64/nptl/pthread_create.c:660)
==2040226==    by 0x54B0076: gomp_team_start (/usr/src/debug/gcc-14.2.1-3.fc40.x86_64/obj-x86_64-redhat-linux/x86_64-redhat-linux/libgomp/../../../libgomp/team.c:859)
==2040226==    by 0x54A60A0: GOMP_parallel (/usr/src/debug/gcc-14.2.1-3.fc40.x86_64/obj-x86_64-redhat-linux/x86_64-redhat-linux/libgomp/../../../libgomp/parallel.c:176)
==2040226==    by 0x247ED313: min<int> (/usr/include/c++/14/bits/stl_algobase.h:238)
==2040226==    by 0x247ED313: get (R-devel/site-library/RcppArmadillo/include/current/armadillo_bits/mp_misc.hpp:59)
==2040226==    by 0x247ED313: void arma::eop_core<arma::eop_exp>::apply<arma::Mat<double>, arma::Col<double> >(arma::Mat<double>&, arma::eOp<arma::Col<double>, arma::eop_exp> const&) [clone .isra.0] (R-devel/site-library/RcppArmadillo/include/current/armadillo_bits/eop_core_meat.hpp:268)
==2040226==    by 0x24845D73: Mat<arma::Col<double>, arma::eop_exp> (R-devel/site-library/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:5448)
==2040226==    by 0x24845D73: Col<arma::eOp<arma::Col<double>, arma::eop_exp> > (R-devel/site-library/RcppArmadillo/include/current/armadillo_bits/Col_meat.hpp:524)
==2040226==    by 0x24845D73: cond_estimation_nondegrees_pl(arma::Col<double>, arma::Col<unsigned long long>&, arma::Col<unsigned long long>&, arma::Col<unsigned long long>&, bool, std::tuple<arma::Mat<double>, arma::Col<double> >&, int, double, arma::Col<double>&, double, bool&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double, bool) (packages/tests-vg/iglm/src/xyz_sampling.cpp:1669)
==2040226==    by 0x248514DF: outerloop_estimation_pl(arma::Col<double>, arma::Col<double>, arma::Mat<double> const&, arma::Col<double> const&, arma::Col<double> const&, arma::Mat<double> const&, arma::Mat<double> const&, bool, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >, std::vector<arma::Mat<double>, std::allocator<arma::Mat<double> > >&, std::vector<double, std::allocator<double> >&, bool, int, int, int, double, double, bool, bool, bool, bool, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, double, double, bool, int) (packages/tests-vg/iglm/src/xyz_sampling.cpp:2858)
==2040226==    by 0x247FDD08: _iglm_outerloop_estimation_pl (packages/tests-vg/iglm/src/RcppExports.cpp:181)
==2040226==    by 0x4A7B1F: R_doDotCall (svn/R-devel/src/main/dotcode.c:918)
==2040226==    by 0x4A8563: do_dotcall (svn/R-devel/src/main/dotcode.c:1437)
==2040226== 
==2040226== LEAK SUMMARY:
==2040226==    definitely lost: 0 bytes in 0 blocks
==2040226==    indirectly lost: 0 bytes in 0 blocks
==2040226==      possibly lost: 448 bytes in 1 blocks
==2040226==    still reachable: 222,545,736 bytes in 46,811 blocks
==2040226==         suppressed: 148 bytes in 1 blocks
==2040226== Reachable blocks (those to which a pointer was found) are not shown.
==2040226== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==2040226== 
==2040226== For lists of detected and suppressed errors, rerun with: -s
==2040226== ERROR SUMMARY: 17 errors from 3 contexts (suppressed: 0 from 0)