R Under development (unstable) (2024-06-18 r86779) -- "Unsuffered Consequences"
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> pkgname <- "pedmod"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('pedmod')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("biconnected_components")
> ### * biconnected_components
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: biconnected_components
> ### Title: Finds the Biconnected Components
> ### Aliases: biconnected_components biconnected_components_pedigree
> 
> ### ** Examples
> 
> # example of a data set in pedigree and graph form
> library(pedmod)
> dat_pedigree <- data.frame(
+   id = 1:48,
+   mom = c(
+     NA, NA, 2L, 2L, 2L, NA, NA, 7L, 7L, 7L, 3L, 3L, 3L, 3L, NA, 15L, 15L, 43L,
+     18L, NA, NA, 21L, 21L, 9L, 9L, 9L, 9L, NA, NA, 29L, 29L, 29L, 30L, 30L, NA,
+     NA, 36L, 36L, 36L, 38L, 38L, NA, NA, 43L, 43L, 43L, 32L, 32L),
+   dad = c(NA, NA, 1L, 1L, 1L, NA, NA, 6L, 6L, 6L, 8L, 8L, 8L, 8L, NA, 4L, 4L,
+           42L, 5L, NA, NA, 20L, 20L, 22L, 22L, 22L, 22L, NA, NA, 28L, 28L, 28L,
+           23L, 23L, NA, NA, 35L, 35L, 35L, 31L, 31L, NA, NA, 42L, 42L, 42L,
+           45L, 45L),
+   sex = c(1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,
+           2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L,
+           1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L))
> 
> dat <- list(
+   to = c(
+     3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L, 22L, 23L,
+     24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L, 39L, 40L, 41L, 44L,
+     45L, 46L, 47L, 48L, 3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L,
+     18L, 19L, 22L, 23L, 24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L,
+     39L, 40L, 41L, 44L, 45L, 46L, 47L, 48L),
+   from = c(
+     1L, 1L, 1L, 6L, 6L, 6L, 8L, 8L, 8L, 8L, 4L, 4L, 42L, 5L, 20L, 20L, 22L, 22L,
+     22L, 22L, 28L, 28L, 28L, 23L, 23L, 35L, 35L, 35L, 31L, 31L, 42L, 42L, 42L,
+     45L, 45L, 2L, 2L, 2L, 7L, 7L, 7L, 3L, 3L, 3L, 3L, 15L, 15L, 43L, 18L, 21L,
+     21L, 9L, 9L, 9L, 9L, 29L, 29L, 29L, 30L, 30L, 36L, 36L, 36L, 38L, 38L, 43L,
+     43L, 43L, 32L, 32L))
> 
> # they give the same
> out_pedigree <- biconnected_components_pedigree(
+   id = dat_pedigree$id, father.id = dat_pedigree$dad,
+   mother.id = dat_pedigree$mom)
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c1384210 in Rcpp::traits::r_vector_cache<14, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c1384210 in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c1384210 in get_biconnected_components(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1719
    #3 0x7f70c1050a74 in _pedmod_get_biconnected_components /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:24
    #4 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c13841fc in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c13841fc in get_biconnected_components(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1719
    #2 0x7f70c1050a74 in _pedmod_get_biconnected_components /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:24
    #3 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c1384141 in Rcpp::traits::r_vector_cache<13, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c1384141 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c1384141 in get_biconnected_components(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1719
    #3 0x7f70c1050a74 in _pedmod_get_biconnected_components /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:24
    #4 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c138412d in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c138412d in get_biconnected_components(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1719
    #2 0x7f70c1050a74 in _pedmod_get_biconnected_components /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:24
    #3 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

> out <- biconnected_components(dat$to, dat$from)
> all.equal(out_pedigree, out)
[1] TRUE
> 
> 
> 
> 
> cleanEx()
> nameEx("block_cut_tree")
> ### * block_cut_tree
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: block_cut_tree
> ### Title: Creates a Block-cut Tree Like Object
> ### Aliases: block_cut_tree block_cut_tree_pedigree
> 
> ### ** Examples
> 
> # example of a data set in pedigree and graph form
> library(pedmod)
> dat_pedigree <- data.frame(
+   id = 1:48,
+   mom = c(
+     NA, NA, 2L, 2L, 2L, NA, NA, 7L, 7L, 7L, 3L, 3L, 3L, 3L, NA, 15L, 15L, 43L,
+     18L, NA, NA, 21L, 21L, 9L, 9L, 9L, 9L, NA, NA, 29L, 29L, 29L, 30L, 30L, NA,
+     NA, 36L, 36L, 36L, 38L, 38L, NA, NA, 43L, 43L, 43L, 32L, 32L),
+   dad = c(NA, NA, 1L, 1L, 1L, NA, NA, 6L, 6L, 6L, 8L, 8L, 8L, 8L, NA, 4L, 4L,
+           42L, 5L, NA, NA, 20L, 20L, 22L, 22L, 22L, 22L, NA, NA, 28L, 28L, 28L,
+           23L, 23L, NA, NA, 35L, 35L, 35L, 31L, 31L, NA, NA, 42L, 42L, 42L,
+           45L, 45L),
+   sex = c(1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,
+           2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L,
+           1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L))
> 
> dat <- list(
+   to = c(
+     3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L, 22L, 23L,
+     24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L, 39L, 40L, 41L, 44L,
+     45L, 46L, 47L, 48L, 3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L,
+     18L, 19L, 22L, 23L, 24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L,
+     39L, 40L, 41L, 44L, 45L, 46L, 47L, 48L),
+   from = c(
+     1L, 1L, 1L, 6L, 6L, 6L, 8L, 8L, 8L, 8L, 4L, 4L, 42L, 5L, 20L, 20L, 22L, 22L,
+     22L, 22L, 28L, 28L, 28L, 23L, 23L, 35L, 35L, 35L, 31L, 31L, 42L, 42L, 42L,
+     45L, 45L, 2L, 2L, 2L, 7L, 7L, 7L, 3L, 3L, 3L, 3L, 15L, 15L, 43L, 18L, 21L,
+     21L, 9L, 9L, 9L, 9L, 29L, 29L, 29L, 30L, 30L, 36L, 36L, 36L, 38L, 38L, 43L,
+     43L, 43L, 32L, 32L))
> 
> # they give the same
> out_pedigree <- block_cut_tree_pedigree(
+   id = dat_pedigree$id, father.id = dat_pedigree$dad,
+   mother.id = dat_pedigree$mom)
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c13864dc in Rcpp::traits::r_vector_cache<14, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c13864dc in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c13864dc in get_block_cut_tree(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1775
    #3 0x7f70c1051364 in _pedmod_get_block_cut_tree /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:38
    #4 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c13864ac in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c13864ac in get_block_cut_tree(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1775
    #2 0x7f70c1051364 in _pedmod_get_block_cut_tree /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:38
    #3 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c1386381 in Rcpp::traits::r_vector_cache<13, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c1386381 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c1386381 in get_block_cut_tree(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1775
    #3 0x7f70c1051364 in _pedmod_get_block_cut_tree /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:38
    #4 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c1386351 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c1386351 in get_block_cut_tree(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1775
    #2 0x7f70c1051364 in _pedmod_get_block_cut_tree /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:38
    #3 0x58d139 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

> out <- block_cut_tree(dat$to, dat$from)
> all.equal(out_pedigree, out)
[1] TRUE
> 
> 
> 
> 
> cleanEx()
> nameEx("eval_pedigree")
> ### * eval_pedigree
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: eval_pedigree_ll
> ### Title: Approximate the Log Marginal Likelihood
> ### Aliases: eval_pedigree_ll eval_pedigree_grad eval_pedigree_hess
> 
> ### ** Examples
> 
> # three families as an example
> fam_dat <- list(
+   list(
+     y = c(FALSE, TRUE, FALSE, FALSE),
+     X = structure(c(
+       1, 1, 1, 1, 1.2922654151273, 0.358134905909256, -0.734963997107464,
+       0.855235473516044, -1.16189500386223, -0.387298334620742,
+       0.387298334620742, 1.16189500386223),
+       .Dim = 4:3, .Dimnames = list( NULL, c("(Intercept)", "X1", ""))),
+     rel_mat = structure(c(
+       1, 0.5, 0.5, 0.125, 0.5, 1, 0.5, 0.125, 0.5, 0.5,
+       1, 0.125, 0.125, 0.125, 0.125, 1), .Dim = c(4L, 4L)),
+     met_mat = structure(c(1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 1),
+                         .Dim = c(4L, 4L))),
+   list(
+     y = c(FALSE, FALSE, FALSE),
+     X = structure(c(
+       1, 1, 1, -0.0388728997202442, -0.0913782435233639,
+       -0.0801619722392612, -1, 0, 1), .Dim = c(3L, 3L)),
+     rel_mat = structure(c(
+       1, 0.5, 0.125, 0.5, 1, 0.125, 0.125, 0.125, 1), .Dim = c(3L, 3L)),
+     met_mat = structure(c(
+       1, 1, 0, 1, 1, 0, 0, 0, 1), .Dim = c(3L, 3L))),
+   list(
+     y = c(TRUE, FALSE),
+     X = structure(c(
+       1, 1, 0.305275750370738, -1.49482995913648,  -0.707106781186547,
+       0.707106781186547),
+       .Dim = 2:3, .Dimnames = list( NULL, c("(Intercept)", "X1", ""))),
+     rel_mat = structure(c(1, 0.5,  0.5, 1), .Dim = c(2L, 2L)),
+     met_mat = structure(c(1, 1, 1, 1), .Dim = c(2L,  2L))))
> 
> # get the data into the format needed for the package
> dat_arg <- lapply(fam_dat, function(x){
+   # we need the following for each family:
+   #   y: the zero-one outcomes.
+   #   X: the design matrix for the fixed effects.
+   #   scale_mats: list with the scale matrices for each type of effect.
+   list(y = as.numeric(x$y), X = x$X,
+        scale_mats = list(x$rel_mat, x$met_mat))
+ })
> 
> # get a pointer to the C++ object
> ptr <- pedigree_ll_terms(dat_arg, max_threads = 1L)
> 
> # approximate the log marginal likelihood
> beta <- c(-1, 0.3, 0.2) # fixed effect coefficients
> scs <- c(0.5, 0.33)     # scales parameters
> 
> set.seed(44492929)
> system.time(ll1 <- eval_pedigree_ll(
+   ptr = ptr, par = c(beta, log(scs)), abs_eps = -1, maxvls = 1e5,
+   rel_eps = 1e-5, minvls = 2000, use_aprx = FALSE))
   user  system elapsed 
  0.078   0.000   0.079 
> ll1 # the approximation
[1] -5.30139
attr(,"n_fails")
[1] 0
attr(,"std")
[1] 4.133979e-06
> 
> # with the approximation of pnorm and qnorm
> system.time(ll2 <- eval_pedigree_ll(
+   ptr = ptr, par = c(beta, log(scs)), abs_eps = -1, maxvls = 1e5,
+   rel_eps = 1e-5, minvls = 2000, use_aprx = TRUE))
   user  system elapsed 
  0.042   0.000   0.042 
> all.equal(ll1, ll2, tolerance = 1e-5)
[1] TRUE
> 
> # cluster weights can be used as follows to repeat the second family three
> # times and remove the third
> system.time(deriv_w_weight <- eval_pedigree_grad(
+   ptr = ptr, par = c(beta, log(scs)), abs_eps = -1, maxvls = 1e6,
+   rel_eps = 1e-3, minvls = 2000, use_aprx = TRUE,
+   cluster_weights = c(1, 3, 0)))
   user  system elapsed 
  0.252   0.000   0.254 
> 
> # the same as manually repeating second cluster and not including the third
> dum_dat <- dat_arg[c(1, 2, 2, 2)]
> dum_ptr <- pedigree_ll_terms(dum_dat, 1L)
> system.time(deriv_dum <- eval_pedigree_grad(
+   ptr = dum_ptr, par = c(beta, log(scs)), abs_eps = -1, maxvls = 1e6,
+   rel_eps = 1e-3, minvls = 2000, use_aprx = TRUE))
   user  system elapsed 
  0.242   0.000   0.243 
> all.equal(deriv_dum, deriv_w_weight, tolerance = 1e-3)
[1] TRUE
> 
> # the hessian is computed on the scale parameter scale rather than on the
> # log of the scale parameters
> system.time(hess_w_weight <- eval_pedigree_hess(
+   ptr = ptr, par = c(beta, log(scs)), abs_eps = -1, maxvls = 1e6,
+   rel_eps = 1e-3, minvls = 2000, use_aprx = TRUE,
+   cluster_weights = c(1, 3, 0)))
   user  system elapsed 
  2.816   0.001   2.829 
> 
> system.time(hess_dum <- eval_pedigree_hess(
+   ptr = dum_ptr, par = c(beta, log(scs)), abs_eps = -1, maxvls = 1e6,
+   rel_eps = 1e-3, minvls = 2000, use_aprx = TRUE))
   user  system elapsed 
  5.370   0.000   5.393 
> attr(hess_w_weight, "n_fails") <- attr(hess_dum, "n_fails") <- NULL
> all.equal(hess_w_weight, hess_dum, tolerance = 1e-3)
[1] "Attributes: < Component “vcov”: Mean relative difference: 0.001127926 >"   
[2] "Attributes: < Component “vcov_org”: Mean relative difference: 0.00243203 >"
> 
> # the results are consistent with the gradient output
> all.equal(attr(deriv_dum, "logLik"), attr(hess_dum, "logLik"),
+           tolerance = 1e-5)
[1] TRUE
> 
> hess_grad <- attr(hess_dum, "grad")
> all.equal(hess_grad, deriv_dum, check.attributes = FALSE,
+           tolerance = 1e-3)
[1] TRUE
> 
> # with loadings
> dat_arg_loadings <- lapply(fam_dat, function(x){
+   list(y = as.numeric(x$y), X = x$X, Z = x$X[, 1:2],
+        scale_mats = list(x$rel_mat, x$met_mat))
+ })
> 
> ptr_loadings <-
+   pedigree_ll_terms_loadings(dat_arg_loadings, max_threads = 1L)
> 
> scs <- c(log(0.5) / 2, 0.1, log(0.33) / 2, 0.2) # got more scales parameters
> eval_pedigree_ll(
+   ptr = ptr_loadings, par = c(beta, scs), abs_eps = -1, maxvls = 1e4,
+   rel_eps = 1e-3, minvls = 2000, use_aprx = TRUE)
[1] -5.255841
attr(,"n_fails")
[1] 0
attr(,"std")
[1] 5.106054e-05
> eval_pedigree_grad(
+   ptr = ptr_loadings, par = c(beta, scs), abs_eps = -1, maxvls = 1e4,
+   rel_eps = 1e-3, minvls = 2000, use_aprx = TRUE)
[1] -0.13953632  0.58078243 -1.61311273 -0.11081449  0.24190052 -0.33097540
[7]  0.01163456
attr(,"logLik")
[1] -5.25587
attr(,"n_fails")
[1] 3
attr(,"std")
[1] 2.596588e-05          NaN          NaN          NaN          NaN
[6]          NaN          NaN          NaN
> 
> # can recover the result from before
> scs <- c(log(0.5) / 2, 0, log(0.33) / 2, 0)
> ll3 <- eval_pedigree_ll(
+   ptr = ptr_loadings, par = c(beta, scs), abs_eps = -1, maxvls = 1e4,
+   rel_eps = 1e-3, minvls = 2000, use_aprx = TRUE)
> all.equal(ll1, ll3, tolerance = 1e-5)
[1] "Attributes: < Component “std”: Mean absolute difference: 5.192656e-05 >"
> 
> 
> 
> 
> cleanEx()
> nameEx("max_balanced_partition")
> ### * max_balanced_partition
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: max_balanced_partition
> ### Title: Finds an Approximately Balanced Connected Partition
> ### Aliases: max_balanced_partition max_balanced_partition_pedigree
> 
> ### ** Examples
> 
> # example of a data set in pedigree and graph form
> library(pedmod)
> dat_pedigree <- data.frame(
+   id = 1:48,
+   mom = c(
+     NA, NA, 2L, 2L, 2L, NA, NA, 7L, 7L, 7L, 3L, 3L, 3L, 3L, NA, 15L, 15L, 43L,
+     18L, NA, NA, 21L, 21L, 9L, 9L, 9L, 9L, NA, NA, 29L, 29L, 29L, 30L, 30L, NA,
+     NA, 36L, 36L, 36L, 38L, 38L, NA, NA, 43L, 43L, 43L, 32L, 32L),
+   dad = c(NA, NA, 1L, 1L, 1L, NA, NA, 6L, 6L, 6L, 8L, 8L, 8L, 8L, NA, 4L, 4L,
+           42L, 5L, NA, NA, 20L, 20L, 22L, 22L, 22L, 22L, NA, NA, 28L, 28L, 28L,
+           23L, 23L, NA, NA, 35L, 35L, 35L, 31L, 31L, NA, NA, 42L, 42L, 42L,
+           45L, 45L),
+   sex = c(1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,
+           2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L,
+           1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L))
> 
> dat <- list(
+   to = c(
+     3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L, 22L, 23L,
+     24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L, 39L, 40L, 41L, 44L,
+     45L, 46L, 47L, 48L, 3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L,
+     18L, 19L, 22L, 23L, 24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L,
+     39L, 40L, 41L, 44L, 45L, 46L, 47L, 48L),
+   from = c(
+     1L, 1L, 1L, 6L, 6L, 6L, 8L, 8L, 8L, 8L, 4L, 4L, 42L, 5L, 20L, 20L, 22L, 22L,
+     22L, 22L, 28L, 28L, 28L, 23L, 23L, 35L, 35L, 35L, 31L, 31L, 42L, 42L, 42L,
+     45L, 45L, 2L, 2L, 2L, 7L, 7L, 7L, 3L, 3L, 3L, 3L, 15L, 15L, 43L, 18L, 21L,
+     21L, 9L, 9L, 9L, 9L, 29L, 29L, 29L, 30L, 30L, 36L, 36L, 36L, 38L, 38L, 43L,
+     43L, 43L, 32L, 32L))
> 
> # the results may be different because of different orders!
> out_pedigree <- max_balanced_partition_pedigree(
+   id = dat_pedigree$id, father.id = dat_pedigree$dad,
+   mother.id = dat_pedigree$mom)
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c13964e5 in Rcpp::traits::r_vector_cache<14, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c13964e5 in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c13964e5 in get_max_balanced_partition(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, bool, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1830
    #3 0x7f70c1053690 in _pedmod_get_max_balanced_partition /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:58
    #4 0x58bf85 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:795
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c13964d1 in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c13964d1 in get_max_balanced_partition(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, bool, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1830
    #2 0x7f70c1053690 in _pedmod_get_max_balanced_partition /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:58
    #3 0x58bf85 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:795
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c1396206 in Rcpp::traits::r_vector_cache<13, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c1396206 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c1396206 in get_max_balanced_partition(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, bool, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1830
    #3 0x7f70c1053690 in _pedmod_get_max_balanced_partition /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:58
    #4 0x58bf85 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:795
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c13961f2 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c13961f2 in get_max_balanced_partition(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, bool, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1830
    #2 0x7f70c1053690 in _pedmod_get_max_balanced_partition /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:58
    #3 0x58bf85 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:795
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

> out <- max_balanced_partition(dat$to, dat$from)
> 
> all.equal(out_pedigree$balance_criterion, out$balance_criterion)
[1] TRUE
> all.equal(out_pedigree$removed_edges, out$removed_edges)
[1] "Mean relative difference: 0.4554974"
> 
> 
> 
> 
> cleanEx()
> nameEx("mvndst")
> ### * mvndst
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: mvndst
> ### Title: Multivariate Normal Distribution CDF and Its Derivative
> ### Aliases: mvndst mvndst_grad
> 
> ### ** Examples
> 
> # simulate covariance matrix and the upper bound
> set.seed(1)
> n <- 10L
> S <- drop(rWishart(1L, 2 * n, diag(n) / 2 / n))
> u <- rnorm(n)
> 
> system.time(pedmod_res <- mvndst(
+     lower = rep(-Inf, n), upper = u, sigma = S, mu = numeric(n),
+     maxvls = 1e6, abs_eps = 0, rel_eps = 1e-4, use_aprx = TRUE))
   user  system elapsed 
  0.036   0.000   0.036 
> pedmod_res
[1] 7.342052e-05
attr(,"n_it")
[1] 21776
attr(,"inform")
[1] 0
attr(,"abserr")
[1] 7.106154e-09
> 
> # compare with mvtnorm
> if(require(mvtnorm)){
+     mvtnorm_time <- system.time(mvtnorm_res <- mvtnorm::pmvnorm(
+         upper = u, sigma = S, algorithm = GenzBretz(
+             maxpts = 1e6, abseps = 0, releps = 1e-4)))
+     cat("mvtnorm_res:\n")
+     print(mvtnorm_res)
+ 
+     cat("mvtnorm_time:\n")
+     print(mvtnorm_time)
+ }
Loading required package: mvtnorm
mvtnorm_res:
[1] 7.341946e-05
attr(,"error")
[1] 5.195872e-09
attr(,"msg")
[1] "Normal Completion"
mvtnorm_time:
   user  system elapsed 
  0.146   0.000   0.146 
> 
> # with titling
> system.time(pedmod_res <- mvndst(
+     lower = rep(-Inf, n), upper = u, sigma = S, mu = numeric(n),
+     maxvls = 1e6, abs_eps = 0, rel_eps = 1e-4, use_tilting = TRUE))
   user  system elapsed 
  0.071   0.000   0.071 
> pedmod_res
[1] 7.341887e-05
attr(,"n_it")
[1] 21776
attr(,"inform")
[1] 0
attr(,"abserr")
[1] 3.54939e-09
> 
> # compare with TruncatedNormal
> if(require(TruncatedNormal)){
+     TruncatedNormal_time <- system.time(
+         TruncatedNormal_res <- TruncatedNormal::pmvnorm(
+             lb = rep(-Inf, n), ub = u, sigma = S,
+             B = attr(pedmod_res, "n_it"), type = "qmc"))
+     cat("TruncatedNormal_res:\n")
+     print(TruncatedNormal_res)
+ 
+     cat("TruncatedNormal_time:\n")
+     print(TruncatedNormal_time)
+ }
Loading required package: TruncatedNormal

Attaching package: ‘TruncatedNormal’

The following objects are masked from ‘package:mvtnorm’:

    pmvnorm, pmvt

Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
Warning in randtoolbox::sobol(n, dim = d - 1, init = TRUE, scrambling = 1,  :
  scrambling is currently disabled.
TruncatedNormal_res:
[1] 7.343937e-05
attr(,"relerr")
[1] 0
attr(,"upbnd")
[1] 8.143487e-05
TruncatedNormal_time:
   user  system elapsed 
  0.252   0.070   0.339 
> 
> # check the gradient
> system.time(pedmod_res <- mvndst_grad(
+   lower = rep(-Inf, n), upper = u, sigma = S, mu = numeric(n),
+   maxvls = 1e5, minvls = 1e5, abs_eps = 0, rel_eps = 1e-4, use_aprx = TRUE))
   user  system elapsed 
  0.404   0.000   0.405 
> pedmod_res
$likelihood
[1] 7.341802e-05

$d_mu
 [1] -1.574607e-04 -3.010110e-05 -7.609702e-05 -1.945725e-07 -6.204316e-05
 [6] -5.583080e-05 -3.494026e-05 -9.266995e-05 -4.978700e-05 -1.175500e-04

$d_sigma
              [,1]          [,2]         [,3]          [,4]         [,5]
 [1,] 1.235057e-04  3.582440e-05 7.386207e-05  2.798921e-07 6.586174e-05
 [2,] 3.582440e-05 -9.767467e-06 1.385365e-05  5.345597e-08 8.059805e-06
 [3,] 7.386207e-05  1.385365e-05 1.134090e-05  2.186355e-07 3.835124e-05
 [4,] 2.798921e-07  5.345597e-08 2.186355e-07 -3.832548e-07 6.622049e-08
 [5,] 6.586174e-05  8.059805e-06 3.835124e-05  6.622049e-08 3.658371e-07
 [6,] 6.374539e-05  8.621329e-06 2.795893e-05  1.009337e-07 2.572895e-05
 [7,] 3.836779e-05  7.350301e-06 2.199529e-05  1.000262e-08 1.095522e-05
 [8,] 9.810491e-05  1.867212e-05 4.775614e-05  2.553272e-08 3.545482e-05
 [9,] 5.741983e-05  1.008961e-05 2.479658e-05  1.075467e-07 2.279239e-05
[10,] 1.262442e-04  2.630631e-05 6.106946e-05  1.773326e-07 5.279605e-05
               [,6]          [,7]         [,8]          [,9]        [,10]
 [1,]  6.374539e-05  3.836779e-05 9.810491e-05  5.741983e-05 1.262442e-04
 [2,]  8.621329e-06  7.350301e-06 1.867212e-05  1.008961e-05 2.630631e-05
 [3,]  2.795893e-05  2.199529e-05 4.775614e-05  2.479658e-05 6.106946e-05
 [4,]  1.009337e-07  1.000262e-08 2.553272e-08  1.075467e-07 1.773326e-07
 [5,]  2.572895e-05  1.095522e-05 3.545482e-05  2.279239e-05 5.279605e-05
 [6,] -9.480864e-06  1.375171e-05 3.409007e-05  1.666442e-05 3.898756e-05
 [7,]  1.375171e-05 -1.215591e-05 2.090094e-05  9.701566e-06 3.331999e-05
 [8,]  3.409007e-05  2.090094e-05 1.187842e-05  3.249954e-05 8.814625e-05
 [9,]  1.666442e-05  9.701566e-06 3.249954e-05 -6.758041e-06 3.835519e-05
[10,]  3.898756e-05  3.331999e-05 8.814625e-05  3.835519e-05 5.977245e-05

attr(,"n_it")
[1] 111152
attr(,"inform")
[1] 1
attr(,"abserr")
[1] 7.717596e-08
> 
> 
> 
> 
> 
> cleanEx()

detaching ‘package:TruncatedNormal’, ‘package:mvtnorm’

> nameEx("pedigree_ll_terms")
> ### * pedigree_ll_terms
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pedigree_ll_terms
> ### Title: Get a C++ Object for Log Marginal Likelihood Approximations
> ### Aliases: pedigree_ll_terms pedigree_ll_terms_loadings
> 
> ### ** Examples
> 
> # three families as an example
> fam_dat <- list(
+   list(
+     y = c(FALSE, TRUE, FALSE, FALSE),
+     X = structure(c(
+       1, 1, 1, 1, 1.2922654151273, 0.358134905909256, -0.734963997107464,
+       0.855235473516044, -1.16189500386223, -0.387298334620742,
+       0.387298334620742, 1.16189500386223),
+       .Dim = 4:3, .Dimnames = list( NULL, c("(Intercept)", "X1", ""))),
+     rel_mat = structure(c(
+       1, 0.5, 0.5, 0.125, 0.5, 1, 0.5, 0.125, 0.5, 0.5,
+       1, 0.125, 0.125, 0.125, 0.125, 1), .Dim = c(4L, 4L)),
+     met_mat = structure(c(1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 1),
+                         .Dim = c(4L, 4L))),
+   list(
+     y = c(FALSE, FALSE, FALSE),
+     X = structure(c(
+       1, 1, 1, -0.0388728997202442, -0.0913782435233639,
+       -0.0801619722392612, -1, 0, 1), .Dim = c(3L, 3L)),
+     rel_mat = structure(c(
+       1, 0.5, 0.125, 0.5, 1, 0.125, 0.125, 0.125, 1), .Dim = c(3L, 3L)),
+     met_mat = structure(c(
+       1, 1, 0, 1, 1, 0, 0, 0, 1), .Dim = c(3L, 3L))),
+   list(
+     y = c(TRUE, FALSE),
+     X = structure(c(
+       1, 1, 0.305275750370738, -1.49482995913648,  -0.707106781186547,
+       0.707106781186547),
+       .Dim = 2:3, .Dimnames = list( NULL, c("(Intercept)", "X1", ""))),
+     rel_mat = structure(c(1, 0.5,  0.5, 1), .Dim = c(2L, 2L)),
+     met_mat = structure(c(1, 1, 1, 1), .Dim = c(2L,  2L))))
> 
> # get the data into the format needed for the package
> dat_arg <- lapply(fam_dat, function(x){
+   # we need the following for each family:
+   #   y: the zero-one outcomes.
+   #   X: the design matrix for the fixed effects.
+   #   scale_mats: list with the scale matrices for each type of effect.
+   list(y = as.numeric(x$y), X = x$X,
+        scale_mats = list(x$rel_mat, x$met_mat))
+ })
> 
> # get a pointer to the C++ object
> ptr <- pedigree_ll_terms(dat_arg, max_threads = 1L)
> 
> # get the argument for a the version with loadings
> dat_arg_loadings <- lapply(fam_dat, function(x){
+   list(y = as.numeric(x$y), X = x$X, Z = x$X[, 1:2],
+        scale_mats = list(x$rel_mat, x$met_mat))
+ })
> 
> ptr <- pedigree_ll_terms_loadings(dat_arg_loadings, max_threads = 1L)
> 
> 
> 
> 
> cleanEx()
> nameEx("pedmod_opt")
> ### * pedmod_opt
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pedmod_opt
> ### Title: Optimize the Log Marginal Likelihood
> ### Aliases: pedmod_opt pedmod_start pedmod_start_loadings
> 
> ### ** Examples
> 
> 
> 
> 
> cleanEx()
> nameEx("pedmod_profile")
> ### * pedmod_profile
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pedmod_profile
> ### Title: Computes Profile Likelihood Based Confidence Intervals
> ### Aliases: pedmod_profile
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx()
> nameEx("pedmod_profile_nleq")
> ### * pedmod_profile_nleq
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pedmod_profile_nleq
> ### Title: Computes Profile Likelihood Based Confidence Intervals for a
> ###   Nonlinear Transformation of the Variables
> ### Aliases: pedmod_profile_nleq
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx()
> nameEx("pedmod_profile_prop")
> ### * pedmod_profile_prop
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pedmod_profile_prop
> ### Title: Computes Profile Likelihood Based Confidence Intervals for the
> ###   Proportion of Variance
> ### Aliases: pedmod_profile_prop
> 
> ### ** Examples
> 
> 
> 
> 
> 
> cleanEx()
> nameEx("pedmod_sqn")
> ### * pedmod_sqn
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pedmod_sqn
> ### Title: Optimize the Log Marginal Likelihood Using a Stochastic
> ###   Quasi-Newton Method
> ### Aliases: pedmod_sqn
> 
> ### ** Examples
> 
> 
> 
> 
> cleanEx()
> nameEx("standardized_to_direct")
> ### * standardized_to_direct
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: standardized_to_direct
> ### Title: Transform Between Parameterizations
> ### Aliases: standardized_to_direct direct_to_standardized
> 
> ### ** Examples
> 
> # transform backwards and forwards
> set.seed(1)
> smp <- runif(10, -1, 1)
> res <- standardized_to_direct(smp, 2L, jacobian = TRUE)
> back_val <- direct_to_standardized(res, 2L)
> 
> all.equal(smp, back_val, check.attributes = FALSE)
[1] TRUE
> res
 [1] -0.7721713 -0.4210913  0.2399034  1.3442132 -0.9823504  1.3118825
 [7]  1.4642992  0.5295012  0.2582281 -0.8764275
attr(,"jacobian")
          [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]
 [1,] 1.646482 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
 [2,] 0.000000 1.646482 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
 [3,] 0.000000 0.000000 1.646482 0.000000 0.000000 0.000000 0.000000 0.000000
 [4,] 0.000000 0.000000 0.000000 1.646482 0.000000 0.000000 0.000000 0.000000
 [5,] 0.000000 0.000000 0.000000 0.000000 1.646482 0.000000 0.000000 0.000000
 [6,] 0.000000 0.000000 0.000000 0.000000 0.000000 1.646482 0.000000 0.000000
 [7,] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.646482 0.000000
 [8,] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.646482
 [9,] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[10,] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
             [,9]       [,10]
 [1,] -0.18438134 -0.05928466
 [2,] -0.10054942 -0.03232994
 [3,]  0.05728485  0.01841896
 [4,]  0.32097518  0.10320407
 [5,] -0.23456852 -0.07542149
 [6,]  0.31325517  0.10072183
 [7,]  0.34964969  0.11242386
 [8,]  0.12643585  0.04065328
 [9,]  1.00000000  0.00000000
[10,]  0.00000000  1.00000000
attr(,"variance proportions")
 Residual                     
0.3688810 0.4775659 0.1535531 
> 
> 
> 
> 
> cleanEx()
> nameEx("unconnected_partition")
> ### * unconnected_partition
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: unconnected_partition
> ### Title: Finds an Approximately Balanced Partition
> ### Aliases: unconnected_partition unconnected_partition_pedigree
> 
> ### ** Examples
> 
> # example of a data set in pedigree and graph form
> library(pedmod)
> dat_pedigree <- data.frame(
+   id = 1:48,
+   mom = c(
+     NA, NA, 2L, 2L, 2L, NA, NA, 7L, 7L, 7L, 3L, 3L, 3L, 3L, NA, 15L, 15L, 43L,
+     18L, NA, NA, 21L, 21L, 9L, 9L, 9L, 9L, NA, NA, 29L, 29L, 29L, 30L, 30L, NA,
+     NA, 36L, 36L, 36L, 38L, 38L, NA, NA, 43L, 43L, 43L, 32L, 32L),
+   dad = c(NA, NA, 1L, 1L, 1L, NA, NA, 6L, 6L, 6L, 8L, 8L, 8L, 8L, NA, 4L, 4L,
+           42L, 5L, NA, NA, 20L, 20L, 22L, 22L, 22L, 22L, NA, NA, 28L, 28L, 28L,
+           23L, 23L, NA, NA, 35L, 35L, 35L, 31L, 31L, NA, NA, 42L, 42L, 42L,
+           45L, 45L),
+   sex = c(1L, 2L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L,
+           2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 1L, 2L, 2L, 2L,
+           1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L))
> 
> dat <- list(
+   to = c(
+     3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L, 18L, 19L, 22L, 23L,
+     24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L, 39L, 40L, 41L, 44L,
+     45L, 46L, 47L, 48L, 3L, 4L, 5L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 16L, 17L,
+     18L, 19L, 22L, 23L, 24L, 25L, 26L, 27L, 30L, 31L, 32L, 33L, 34L, 37L, 38L,
+     39L, 40L, 41L, 44L, 45L, 46L, 47L, 48L),
+   from = c(
+     1L, 1L, 1L, 6L, 6L, 6L, 8L, 8L, 8L, 8L, 4L, 4L, 42L, 5L, 20L, 20L, 22L, 22L,
+     22L, 22L, 28L, 28L, 28L, 23L, 23L, 35L, 35L, 35L, 31L, 31L, 42L, 42L, 42L,
+     45L, 45L, 2L, 2L, 2L, 7L, 7L, 7L, 3L, 3L, 3L, 3L, 15L, 15L, 43L, 18L, 21L,
+     21L, 9L, 9L, 9L, 9L, 29L, 29L, 29L, 30L, 30L, 36L, 36L, 36L, 38L, 38L, 43L,
+     43L, 43L, 32L, 32L))
> 
> # the results may be different because of different orders!
> out_pedigree <- unconnected_partition_pedigree(
+   id = dat_pedigree$id, father.id = dat_pedigree$dad,
+   mother.id = dat_pedigree$mom)
/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c139a88c in Rcpp::traits::r_vector_cache<14, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c139a88c in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c139a88c in unconnected_partition_rcpp(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, Rcpp::Vector<13, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1866
    #3 0x7f70c1052925 in _pedmod_unconnected_partition_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:77
    #4 0x58c0b3 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:790
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 8 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c139a85c in Rcpp::Vector<14, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c139a85c in unconnected_partition_rcpp(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, Rcpp::Vector<13, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1866
    #2 0x7f70c1052925 in _pedmod_unconnected_partition_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:77
    #3 0x58c0b3 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:790
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:52: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c139a738 in Rcpp::traits::r_vector_cache<13, Rcpp::PreserveStorage>::ref(long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49
    #1 0x7f70c139a738 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #2 0x7f70c139a738 in unconnected_partition_rcpp(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, Rcpp::Vector<13, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1866
    #3 0x7f70c1052925 in _pedmod_unconnected_partition_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:77
    #4 0x58c0b3 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:790
    #5 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #6 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #7 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #8 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #9 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #10 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #11 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #12 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #13 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #14 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #15 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #16 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #17 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #18 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #19 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #20 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #21 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #22 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #23 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #24 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #25 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #26 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #27 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #28 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #29 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #30 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #31 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #32 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #33 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #34 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #35 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #36 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #37 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #38 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #39 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #40 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #41 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #42 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #43 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #44 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #45 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #46 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #47 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #48 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #49 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #50 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #51 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #52 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #53 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #55 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

/data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341:75: runtime error: reference binding to misaligned address 0x000000000001 for type 'const type', which requires 4 byte alignment
0x000000000001: note: pointer points here
<memory cannot be printed>
    #0 0x7f70c139a716 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) const /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:341
    #1 0x7f70c139a716 in unconnected_partition_rcpp(Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<13, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, Rcpp::Vector<14, Rcpp::PreserveStorage>, double, unsigned int, unsigned int, unsigned int, Rcpp::Vector<13, Rcpp::PreserveStorage>) /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/graph-partitioning.cpp:1866
    #2 0x7f70c1052925 in _pedmod_unconnected_partition_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/pedmod/src/RcppExports.cpp:77
    #3 0x58c0b3 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:790
    #4 0x653b17 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8690
    #5 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #6 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #7 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #8 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #9 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #10 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #11 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #12 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #13 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #14 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #15 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #16 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #17 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #18 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #19 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #20 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #21 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #22 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #23 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #24 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #25 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #26 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #27 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #28 0x6a0fe2 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #29 0x64de4f in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8140
    #30 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #31 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #32 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #33 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #34 0x698ed8 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #35 0x7480f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:472
    #36 0x74938b in Rf_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:522
    #37 0x749ccf in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:578
    #38 0x63f4f9 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8160
    #39 0x68e822 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7523
    #40 0x68f09a in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #41 0x694dfe in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398
    #42 0x697268 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2311
    #43 0x68f6ad in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333
    #44 0x68f6ad in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1285
    #45 0x69d4b7 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #46 0x68fad8 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1237
    #47 0x714e9e in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:263
    #48 0x715511 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:315
    #49 0x715654 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1217
    #50 0x7156a2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1224
    #51 0x41a7d8 in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #52 0x7f70d2c2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #53 0x7f70d2c295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c)
    #54 0x41d034 in _start (/data/gannet/ripley/R/gcc-SAN/bin/exec/R+0x41d034) (BuildId: 56ff6b70c40a24eccf16f0ce952f5ebd85884520)

> out <- unconnected_partition(dat$to, dat$from)
> 
> all.equal(out_pedigree$balance_criterion, out$balance_criterion)
[1] TRUE
> all.equal(out_pedigree$removed_edges, out$removed_edges)
[1] "Attributes: < Component “dim”: Mean relative difference: 0.6 >"
[2] "Numeric: lengths (20, 8) differ"                               
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  11.811 0.227 12.377 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')