==3996694== Memcheck, a memory error detector
==3996694== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al.
==3996694== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info
==3996694== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R -f testthat.R --restore --save --no-readline --vanilla
==3996694== 

R Under development (unstable) (2026-05-11 r90046) -- "Unsuffered Consequences"
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Platform: x86_64-pc-linux-gnu

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> library(testthat)
> library(harmony)
Loading required package: Rcpp
• This is Harmony2 version 2.0.3
• Read the guide: run vignette()
• Get help: Visit the website at https://korsunskylab.github.io/harmony2/ and
report issues on https://github.com/immunogenomics/harmony/issues
> 
> test_check("harmony")
270exists, retrying for cluster 15 3.29648
115exists, retrying for cluster 25 3.3598
188exists, retrying for cluster 33 3.23944
26exists, retrying for cluster 33 2.8872
249exists, retrying for cluster 33 1.30963
62exists, retrying for cluster 36 1.95639
62exists, retrying for cluster 42 2.65726
9exists, retrying for cluster 45 3.00726
136exists, retrying for cluster 46 1.49259
187exists, retrying for cluster 16 3.09328
69exists, retrying for cluster 19 2.71005
==3996694== Invalid write of size 4
==3996694==    at 0x1EDB9105: partial_sum<__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, __gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, std::plus<unsigned int> > (/usr/include/c++/14/bits/stl_numeric.h:316)
==3996694==    by 0x1EDB9105: harmony::setup(arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool) (packages/tests-vg/harmony/src/harmony.cpp:98)
==3996694==    by 0x1EDEA025: operator() (R-devel/site-library/Rcpp/include/Rcpp/Module.h:385)
==3996694==    by 0x1EDEA025: SEXPREC* Rcpp::internal::call_impl<Rcpp::CppMethodImplN<false, harmony, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>::operator()(harmony*, SEXPREC**)::{lambda(arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool)#1}, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, (void*)0>(Rcpp::CppMethodImplN<false, harmony, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>::operator()(harmony*, SEXPREC**)::{lambda(arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool)#1} const&, SEXPREC**, Rcpp::internal::type_pack<void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>, Rcpp::traits::index_sequence<0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13>) [clone .isra.0] (R-devel/site-library/Rcpp/include/Rcpp/internal/call.h:31)
==3996694==    by 0x1EDEA364: call<Rcpp::CppMethodImplN<false, harmony, void, const arma::Mat<double>&, const arma::SpMat<double>&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, const std::vector<int, std::allocator<int> >&, float, bool>::operator()(harmony*, SEXPREC**)::<lambda(const arma::Mat<double>&, const arma::SpMat<double>&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, const std::vector<int, std::allocator<int> >&, float, bool)>, void, const arma::Mat<double>&, const arma::SpMat<double>&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, const std::vector<int, std::allocator<int> >&, float, bool> (R-devel/site-library/Rcpp/include/Rcpp/internal/call.h:47)
==3996694==    by 0x1EDEA364: Rcpp::CppMethodImplN<false, harmony, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>::operator()(harmony*, SEXPREC**) (R-devel/site-library/Rcpp/include/Rcpp/Module.h:387)
==3996694==    by 0x1EDC6E8A: Rcpp::class_<harmony>::invoke_void(SEXPREC*, SEXPREC*, SEXPREC**, int) (R-devel/site-library/Rcpp/include/Rcpp/module/class.h:219)
==3996694==    by 0x1B2B6F4F: CppMethod__invoke_void(SEXPREC*) (/tmp/Rtmpf3PshP/R.INSTALL3331317aa6f58d/Rcpp/src/module.cpp:200)
==3996694==    by 0x4A73ED: do_External (svn/R-devel/src/main/dotcode.c:576)
==3996694==    by 0x4F4997: Rf_eval (svn/R-devel/src/main/eval.c:1258)
==3996694==    by 0x4F7EE4: do_begin (svn/R-devel/src/main/eval.c:3001)
==3996694==    by 0x4F47B2: Rf_eval (svn/R-devel/src/main/eval.c:1230)
==3996694==    by 0x4F63DD: R_execClosure (svn/R-devel/src/main/eval.c:2398)
==3996694==    by 0x4F709F: applyClosure_core (svn/R-devel/src/main/eval.c:2314)
==3996694==    by 0x4E5B3A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333)
==3996694==    by 0x4E5B3A: bcEval_loop (svn/R-devel/src/main/eval.c:8121)
==3996694==  Address 0xf0c8774 is 0 bytes after a block of size 4 alloc'd
==3996694==    at 0x4843FEC: operator new(unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:487)
==3996694==    by 0x1EDC84A9: allocate (/usr/include/c++/14/bits/new_allocator.h:151)
==3996694==    by 0x1EDC84A9: allocate (/usr/include/c++/14/bits/allocator.h:196)
==3996694==    by 0x1EDC84A9: allocate (/usr/include/c++/14/bits/alloc_traits.h:478)
==3996694==    by 0x1EDC84A9: _M_allocate (/usr/include/c++/14/bits/stl_vector.h:380)
==3996694==    by 0x1EDC84A9: std::vector<int, std::allocator<int> >::_M_default_append(unsigned long) (/usr/include/c++/14/bits/vector.tcc:834)
==3996694==    by 0x1EDB93BF: resize (/usr/include/c++/14/bits/stl_vector.h:1016)
==3996694==    by 0x1EDB93BF: harmony::setup(arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool) (packages/tests-vg/harmony/src/harmony.cpp:97)
==3996694==    by 0x1EDEA025: operator() (R-devel/site-library/Rcpp/include/Rcpp/Module.h:385)
==3996694==    by 0x1EDEA025: SEXPREC* Rcpp::internal::call_impl<Rcpp::CppMethodImplN<false, harmony, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>::operator()(harmony*, SEXPREC**)::{lambda(arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool)#1}, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, (void*)0>(Rcpp::CppMethodImplN<false, harmony, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>::operator()(harmony*, SEXPREC**)::{lambda(arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool)#1} const&, SEXPREC**, Rcpp::internal::type_pack<void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>, Rcpp::traits::index_sequence<0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13>) [clone .isra.0] (R-devel/site-library/Rcpp/include/Rcpp/internal/call.h:31)
==3996694==    by 0x1EDEA364: call<Rcpp::CppMethodImplN<false, harmony, void, const arma::Mat<double>&, const arma::SpMat<double>&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, const std::vector<int, std::allocator<int> >&, float, bool>::operator()(harmony*, SEXPREC**)::<lambda(const arma::Mat<double>&, const arma::SpMat<double>&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, const std::vector<int, std::allocator<int> >&, float, bool)>, void, const arma::Mat<double>&, const arma::SpMat<double>&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, const std::vector<int, std::allocator<int> >&, float, bool> (R-devel/site-library/Rcpp/include/Rcpp/internal/call.h:47)
==3996694==    by 0x1EDEA364: Rcpp::CppMethodImplN<false, harmony, void, arma::Mat<double> const&, arma::SpMat<double> const&, arma::Col<double>, arma::Col<double>, arma::Col<double>, float, int, float, float, int, float, std::vector<int, std::allocator<int> > const&, float, bool>::operator()(harmony*, SEXPREC**) (R-devel/site-library/Rcpp/include/Rcpp/Module.h:387)
==3996694==    by 0x1EDC6E8A: Rcpp::class_<harmony>::invoke_void(SEXPREC*, SEXPREC*, SEXPREC**, int) (R-devel/site-library/Rcpp/include/Rcpp/module/class.h:219)
==3996694==    by 0x1B2B6F4F: CppMethod__invoke_void(SEXPREC*) (/tmp/Rtmpf3PshP/R.INSTALL3331317aa6f58d/Rcpp/src/module.cpp:200)
==3996694==    by 0x4A73ED: do_External (svn/R-devel/src/main/dotcode.c:576)
==3996694==    by 0x4F4997: Rf_eval (svn/R-devel/src/main/eval.c:1258)
==3996694==    by 0x4F7EE4: do_begin (svn/R-devel/src/main/eval.c:3001)
==3996694==    by 0x4F47B2: Rf_eval (svn/R-devel/src/main/eval.c:1230)
==3996694==    by 0x4F63DD: R_execClosure (svn/R-devel/src/main/eval.c:2398)
==3996694== 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 25 ]
> 
> proc.time()
   user  system elapsed 
200.615   2.259 201.761 
==3996694== 
==3996694== HEAP SUMMARY:
==3996694==     in use at exit: 282,986,052 bytes in 55,950 blocks
==3996694==   total heap usage: 486,932 allocs, 430,982 frees, 910,177,202 bytes allocated
==3996694== 
==3996694== LEAK SUMMARY:
==3996694==    definitely lost: 0 bytes in 0 blocks
==3996694==    indirectly lost: 0 bytes in 0 blocks
==3996694==      possibly lost: 0 bytes in 0 blocks
==3996694==    still reachable: 282,985,720 bytes in 55,948 blocks
==3996694==         suppressed: 332 bytes in 2 blocks
==3996694== Reachable blocks (those to which a pointer was found) are not shown.
==3996694== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==3996694== 
==3996694== For lists of detected and suppressed errors, rerun with: -s
==3996694== ERROR SUMMARY: 3 errors from 1 contexts (suppressed: 0 from 0)