==3579219== Memcheck, a memory error detector ==3579219== Copyright (C) 2002-2024, and GNU GPL'd, by Julian Seward et al. ==3579219== Using Valgrind-3.24.0 and LibVEX; rerun with -h for copyright info ==3579219== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R --vanilla ==3579219== R Under development (unstable) (2026-06-17 r90170) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "hypergraph.sizing" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('hypergraph.sizing') > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("complete.hypergraph") > ### * complete.hypergraph > > flush(stderr()); flush(stdout()) > > ### Name: complete.hypergraph > ### Title: Complete Hypergraph > ### Aliases: complete.hypergraph > > ### ** Examples > > H<-complete.hypergraph(10,3) > H $vertices [1] 10 $edges $edges[[1]] [1] 1 $edges[[2]] [1] 2 $edges[[3]] [1] 3 $edges[[4]] [1] 4 $edges[[5]] [1] 5 $edges[[6]] [1] 6 $edges[[7]] [1] 7 $edges[[8]] [1] 8 $edges[[9]] [1] 9 $edges[[10]] [1] 10 $edges[[11]] [1] 1 2 $edges[[12]] [1] 1 3 $edges[[13]] [1] 1 4 $edges[[14]] [1] 1 5 $edges[[15]] [1] 1 6 $edges[[16]] [1] 1 7 $edges[[17]] [1] 1 8 $edges[[18]] [1] 1 9 $edges[[19]] [1] 1 10 $edges[[20]] [1] 2 3 $edges[[21]] [1] 2 4 $edges[[22]] [1] 2 5 $edges[[23]] [1] 2 6 $edges[[24]] [1] 2 7 $edges[[25]] [1] 2 8 $edges[[26]] [1] 2 9 $edges[[27]] [1] 2 10 $edges[[28]] [1] 3 4 $edges[[29]] [1] 3 5 $edges[[30]] [1] 3 6 $edges[[31]] [1] 3 7 $edges[[32]] [1] 3 8 $edges[[33]] [1] 3 9 $edges[[34]] [1] 3 10 $edges[[35]] [1] 4 5 $edges[[36]] [1] 4 6 $edges[[37]] [1] 4 7 $edges[[38]] [1] 4 8 $edges[[39]] [1] 4 9 $edges[[40]] [1] 4 10 $edges[[41]] [1] 5 6 $edges[[42]] [1] 5 7 $edges[[43]] [1] 5 8 $edges[[44]] [1] 5 9 $edges[[45]] [1] 5 10 $edges[[46]] [1] 6 7 $edges[[47]] [1] 6 8 $edges[[48]] [1] 6 9 $edges[[49]] [1] 6 10 $edges[[50]] [1] 7 8 $edges[[51]] [1] 7 9 $edges[[52]] [1] 7 10 $edges[[53]] [1] 8 9 $edges[[54]] [1] 8 10 $edges[[55]] [1] 9 10 $edges[[56]] [1] 1 2 3 $edges[[57]] [1] 1 2 4 $edges[[58]] [1] 1 2 5 $edges[[59]] [1] 1 2 6 $edges[[60]] [1] 1 2 7 $edges[[61]] [1] 1 2 8 $edges[[62]] [1] 1 2 9 $edges[[63]] [1] 1 2 10 $edges[[64]] [1] 1 3 4 $edges[[65]] [1] 1 3 5 $edges[[66]] [1] 1 3 6 $edges[[67]] [1] 1 3 7 $edges[[68]] [1] 1 3 8 $edges[[69]] [1] 1 3 9 $edges[[70]] [1] 1 3 10 $edges[[71]] [1] 1 4 5 $edges[[72]] [1] 1 4 6 $edges[[73]] [1] 1 4 7 $edges[[74]] [1] 1 4 8 $edges[[75]] [1] 1 4 9 $edges[[76]] [1] 1 4 10 $edges[[77]] [1] 1 5 6 $edges[[78]] [1] 1 5 7 $edges[[79]] [1] 1 5 8 $edges[[80]] [1] 1 5 9 $edges[[81]] [1] 1 5 10 $edges[[82]] [1] 1 6 7 $edges[[83]] [1] 1 6 8 $edges[[84]] [1] 1 6 9 $edges[[85]] [1] 1 6 10 $edges[[86]] [1] 1 7 8 $edges[[87]] [1] 1 7 9 $edges[[88]] [1] 1 7 10 $edges[[89]] [1] 1 8 9 $edges[[90]] [1] 1 8 10 $edges[[91]] [1] 1 9 10 $edges[[92]] [1] 2 3 4 $edges[[93]] [1] 2 3 5 $edges[[94]] [1] 2 3 6 $edges[[95]] [1] 2 3 7 $edges[[96]] [1] 2 3 8 $edges[[97]] [1] 2 3 9 $edges[[98]] [1] 2 3 10 $edges[[99]] [1] 2 4 5 $edges[[100]] [1] 2 4 6 $edges[[101]] [1] 2 4 7 $edges[[102]] [1] 2 4 8 $edges[[103]] [1] 2 4 9 $edges[[104]] [1] 2 4 10 $edges[[105]] [1] 2 5 6 $edges[[106]] [1] 2 5 7 $edges[[107]] [1] 2 5 8 $edges[[108]] [1] 2 5 9 $edges[[109]] [1] 2 5 10 $edges[[110]] [1] 2 6 7 $edges[[111]] [1] 2 6 8 $edges[[112]] [1] 2 6 9 $edges[[113]] [1] 2 6 10 $edges[[114]] [1] 2 7 8 $edges[[115]] [1] 2 7 9 $edges[[116]] [1] 2 7 10 $edges[[117]] [1] 2 8 9 $edges[[118]] [1] 2 8 10 $edges[[119]] [1] 2 9 10 $edges[[120]] [1] 3 4 5 $edges[[121]] [1] 3 4 6 $edges[[122]] [1] 3 4 7 $edges[[123]] [1] 3 4 8 $edges[[124]] [1] 3 4 9 $edges[[125]] [1] 3 4 10 $edges[[126]] [1] 3 5 6 $edges[[127]] [1] 3 5 7 $edges[[128]] [1] 3 5 8 $edges[[129]] [1] 3 5 9 $edges[[130]] [1] 3 5 10 $edges[[131]] [1] 3 6 7 $edges[[132]] [1] 3 6 8 $edges[[133]] [1] 3 6 9 $edges[[134]] [1] 3 6 10 $edges[[135]] [1] 3 7 8 $edges[[136]] [1] 3 7 9 $edges[[137]] [1] 3 7 10 $edges[[138]] [1] 3 8 9 $edges[[139]] [1] 3 8 10 $edges[[140]] [1] 3 9 10 $edges[[141]] [1] 4 5 6 $edges[[142]] [1] 4 5 7 $edges[[143]] [1] 4 5 8 $edges[[144]] [1] 4 5 9 $edges[[145]] [1] 4 5 10 $edges[[146]] [1] 4 6 7 $edges[[147]] [1] 4 6 8 $edges[[148]] [1] 4 6 9 $edges[[149]] [1] 4 6 10 $edges[[150]] [1] 4 7 8 $edges[[151]] [1] 4 7 9 $edges[[152]] [1] 4 7 10 $edges[[153]] [1] 4 8 9 $edges[[154]] [1] 4 8 10 $edges[[155]] [1] 4 9 10 $edges[[156]] [1] 5 6 7 $edges[[157]] [1] 5 6 8 $edges[[158]] [1] 5 6 9 $edges[[159]] [1] 5 6 10 $edges[[160]] [1] 5 7 8 $edges[[161]] [1] 5 7 9 $edges[[162]] [1] 5 7 10 $edges[[163]] [1] 5 8 9 $edges[[164]] [1] 5 8 10 $edges[[165]] [1] 5 9 10 $edges[[166]] [1] 6 7 8 $edges[[167]] [1] 6 7 9 $edges[[168]] [1] 6 7 10 $edges[[169]] [1] 6 8 9 $edges[[170]] [1] 6 8 10 $edges[[171]] [1] 6 9 10 $edges[[172]] [1] 7 8 9 $edges[[173]] [1] 7 8 10 $edges[[174]] [1] 7 9 10 $edges[[175]] [1] 8 9 10 > > > > cleanEx() > nameEx("count.indep.hyper") > ### * count.indep.hyper > > flush(stderr()); flush(stdout()) > > ### Name: count.indep.hyper > ### Title: Count the Number of Independent Sets for a Hypergraph > ### Aliases: count.indep.hyper count.vc.hyper > > ### ** Examples > > set.seed(1) > edge.orders<-rpois(15,1.6)+1 > > H<-list("vertices"=10,lapply(edge.orders,function(s){sample(seq_len(10),s)})) > > ind.set<-count.indep.hyper(H) ==3579219== Invalid write of size 8 ==3579219== at 0x1232FF3A: hypergraph::countindep(unsigned int) (packages/tests-vg/hypergraph.sizing/src/Hypergraph2.cpp:339) ==3579219== by 0x1233052F: count_indep_hyper_approx (packages/tests-vg/hypergraph.sizing/src/Hypergraph2.cpp:432) ==3579219== by 0x4ABEA7: do_dotCode (svn/R-devel/src/main/dotcode.c:1978) ==3579219== by 0x4E638C: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3579219== by 0x4F42D7: bcEval (svn/R-devel/src/main/eval.c:7533) ==3579219== by 0x4F42D7: bcEval (svn/R-devel/src/main/eval.c:7518) ==3579219== by 0x4F460A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3579219== by 0x4F659D: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3579219== by 0x4F725F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3579219== by 0x4F471A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3579219== by 0x4F471A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3579219== by 0x4F967C: do_set (svn/R-devel/src/main/eval.c:3585) ==3579219== by 0x4F4972: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3579219== by 0x52BA0B: Rf_ReplIteration (svn/R-devel/src/main/main.c:264) ==3579219== Address 0xf06d9c0 is 0 bytes after a block of size 0 alloc'd ==3579219== at 0x484577A: operator new[](unsigned long) (/builddir/build/BUILD/valgrind-3.24.0/coregrind/m_replacemalloc/vg_replace_malloc.c:729) ==3579219== by 0x1232FE84: hypergraph::countindep(unsigned int) (packages/tests-vg/hypergraph.sizing/src/Hypergraph2.cpp:325) ==3579219== by 0x1233052F: count_indep_hyper_approx (packages/tests-vg/hypergraph.sizing/src/Hypergraph2.cpp:432) ==3579219== by 0x4ABEA7: do_dotCode (svn/R-devel/src/main/dotcode.c:1978) ==3579219== by 0x4E638C: bcEval_loop (svn/R-devel/src/main/eval.c:8150) ==3579219== by 0x4F42D7: bcEval (svn/R-devel/src/main/eval.c:7533) ==3579219== by 0x4F42D7: bcEval (svn/R-devel/src/main/eval.c:7518) ==3579219== by 0x4F460A: Rf_eval (svn/R-devel/src/main/eval.c:1167) ==3579219== by 0x4F659D: R_execClosure (svn/R-devel/src/main/eval.c:2398) ==3579219== by 0x4F725F: applyClosure_core (svn/R-devel/src/main/eval.c:2314) ==3579219== by 0x4F471A: Rf_applyClosure (svn/R-devel/src/main/eval.c:2333) ==3579219== by 0x4F471A: Rf_eval (svn/R-devel/src/main/eval.c:1278) ==3579219== by 0x4F967C: do_set (svn/R-devel/src/main/eval.c:3585) ==3579219== by 0x4F4972: Rf_eval (svn/R-devel/src/main/eval.c:1230) ==3579219== > > > > cleanEx() > nameEx("get.p.vals.hypergraph") > ### * get.p.vals.hypergraph > > flush(stderr()); flush(stdout()) > > ### Name: get.p.vals.hypergraph > ### Title: Calculate p-values for set-wise variable selection from a > ### hypergraph > ### Aliases: get.p.vals.hypergraph > > ### ** Examples > > set.seed(1) > X<-matrix(rnorm(200),20,10)%*%(diag(rep(1,10))-c(0.4,0.4,rep(0,8))%*%t(c(0.4,0.4,rep(0,8)))) > Y<-rnorm(20)+X%*%c(0,2,0,2,2,0,0,0,0,0) > H<-complete.hypergraph(10,2) > get.p.vals.hypergraph(X,Y,H,"gaussian") [1] 0.4496155831 0.0150359942 0.0550711220 0.0006867266 0.0006715078 [6] 0.8484137847 0.2850358784 0.9403905081 0.1945213765 0.3537068694 [11] 0.0241170075 0.1431446500 0.0007501197 0.0004036611 0.6961942377 [16] 0.5129163572 0.7389553831 0.3032680109 0.3199403425 0.0164986688 [21] 0.0001342205 0.0004410718 0.0412059204 0.0284633097 0.0430611851 [26] 0.0065408703 0.0134914935 0.0005023246 0.0003680815 0.1354077724 [31] 0.1237564427 0.1419696227 0.0944957745 0.1126241912 0.0011699945 [36] 0.0019589334 0.0010410618 0.0017936442 0.0023139789 0.0012088633 [41] 0.0022551952 0.0007526939 0.0018623807 0.0021460090 0.0021572531 [46] 0.4550217655 0.9756857489 0.3983037632 0.6261306806 0.5034792178 [51] 0.2041230804 0.3171589212 0.4111920035 0.5980974460 0.3772423590 > > > > cleanEx() > nameEx("get.threshold.hyper") > ### * get.threshold.hyper > > flush(stderr()); flush(stdout()) > > ### Name: get.threshold.hyper > ### Title: Calculate a Threshold to Control FDR for Hypergraph-Based GLSUP > ### Aliases: get.threshold.hyper > > ### ** Examples > > set.seed(1) > edge.orders<-rpois(15,1.6)+1 > > H<-list("vertices"=10,"edges"=lapply(edge.orders,function(s){sample(seq_len(10),s)})) > get.threshold.hyper(H,0.05,assumption="PRDS") [1] 117.108 > > > > > cleanEx() > nameEx("make.test") > ### * make.test > > flush(stderr()); flush(stdout()) > > ### Name: make.test > ### Title: Standard hypothesis tests. > ### Aliases: make.test > > ### ** Examples > > set.seed(1) > X<-matrix(rnorm(200),20,10)%*%(diag(rep(1,10))-c(0.4,0.4,rep(0,8))%*%t(c(0.4,0.4,rep(0,8)))) > Y<-rnorm(20)+X%*%c(0,2,0,2,2,0,0,0,0,0) > > tst<-make.test("gaussian") > > m1<-tst$model(Y~X) > X_sub<-X[,-c(1,2)] > m2<-tst$model(Y~X_sub) > > tst$p.val(m1,m2) [1] 0.02411701 > > > > cleanEx() > nameEx("sizing.hyper") > ### * sizing.hyper > > flush(stderr()); flush(stdout()) > > ### Name: sizing.hyper > ### Title: Create a Hypergraph-Based Sizing Function for GLSUP > ### Aliases: sizing.hyper > > ### ** Examples > > set.seed(1) > edge.orders<-rpois(15,1.6)+1 > > H<-list("vertices"=10,lapply(edge.orders,function(s){sample(seq_len(10),s)})) > > sizing<-sizing.hyper(H) > sizing(seq_len(15)) numeric(0) > > > > ### *