* using log directory ‘/data/gannet/ripley/R/packages/tests-clang-SAN/ELMSurv.Rcheck’ * using R Under development (unstable) (2019-05-27 r76612) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘ELMSurv/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ELMSurv’ version ‘0.6’ * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package ‘ELMSurv’ can be installed ... [193s/97s] OK * checking package directory ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking compiled code ... OK * checking examples ... ERROR Running examples in ‘ELMSurv-Ex.R’ failed The error most likely occurred in: > ### Name: ELMBJ > ### Title: ELMBJ > ### Aliases: ELMBJ > > ### ** Examples > > set.seed(123) > require(ELMSurv) > require(survival) Loading required package: survival > #Lung DATA > data(lung) > lung=na.omit(lung) > lung[,3]=lung[,3]-1 > n=dim(lung)[1] > L=sample(1:n,ceiling(n*0.5)) > trset<-lung[L,] > teset<-lung[-L,] > rii=c(2,3) > #A kernel ELM base model > kerelmsurv=ELMBJ(trset[,-rii],Surv(trset[,rii[1]],trset[,rii[2]])) ================================================================= ==13701==ERROR: AddressSanitizer: stack-use-after-scope on address 0x7ffff4b3de00 at pc 0x7f63fcd54db5 bp 0x7ffff4b3dc10 sp 0x7ffff4b3dc08 READ of size 8 at 0x7ffff4b3de00 thread T0 #0 0x7f63fcd54db4 in Rcpp::PreserveStorage >::get__() const /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/storage/PreserveStorage.h:26:20 #1 0x7f63fcd54db4 in Rcpp::Vector<14, Rcpp::PreserveStorage>::size() const /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/vector/Vector.h:278 #2 0x7f63fcd54db4 in Rcpp::sugar::Vectorized<&(log), true, Rcpp::Vector<14, Rcpp::PreserveStorage> >::size() const /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/sugar/block/Vectorized_Math.h:40 #3 0x7f63fcd54db4 in void Rcpp::Vector<14, Rcpp::PreserveStorage>::assign_sugar_expression > >(Rcpp::sugar::Vectorized<&(log), true, Rcpp::Vector<14, Rcpp::PreserveStorage> > const&) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/vector/Vector.h:1041 #4 0x7f63fcd4f761 in void Rcpp::Vector<14, Rcpp::PreserveStorage>::assign_object > >(Rcpp::sugar::Vectorized<&(log), true, Rcpp::Vector<14, Rcpp::PreserveStorage> > const&, Rcpp::traits::integral_constant) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/vector/Vector.h:1055:9 #5 0x7f63fcd4f761 in Rcpp::Vector<14, Rcpp::PreserveStorage>& Rcpp::Vector<14, Rcpp::PreserveStorage>::operator= > >(Rcpp::sugar::Vectorized<&(log), true, Rcpp::Vector<14, Rcpp::PreserveStorage> > const&) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/vector/Vector.h:249 #6 0x7f63fcd4f761 in bjimpute(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) /data/gannet/ripley/R/packages/tests-clang-SAN/ELMSurv/src/bj.cpp:24 #7 0x7f63fcd41745 in _ELMSurv_bjimpute /data/gannet/ripley/R/packages/tests-clang-SAN/ELMSurv/src/RcppExports.cpp:65:34 #8 0x76fdaf in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:579:17 #9 0x8dbfb1 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7290:21 #10 0x8c1c47 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620:8 #11 0x91fb3b in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #12 0x91cd2f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1706:16 #13 0x8e1ac8 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:6740:12 #14 0x8c1c47 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:620:8 #15 0x91fb3b in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c #16 0x91cd2f in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1706:16 #17 0x8c2d69 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:743:12 #18 0x92c0fb in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2808:8 #19 0x8c27cf in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:695:12 #20 0x9f5973 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:260:2 #21 0x9f9cd0 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:310:11 #22 0x9f9ab5 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1086:5 #23 0x54399a in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #24 0x7f640eafd11a in __libc_start_main (/lib64/libc.so.6+0x2311a) #25 0x42f4d9 in _start (/data/gannet/ripley/R/R-clang-SAN/bin/exec/R+0x42f4d9) Address 0x7ffff4b3de00 is located in stack of thread T0 at offset 192 in frame #0 0x7f63fcd4f23f in bjimpute(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*) /data/gannet/ripley/R/packages/tests-clang-SAN/ELMSurv/src/bj.cpp:9 This frame has 52 object(s): [32, 48) 'retval.i662' [64, 80) 'retval.i623' [96, 104) 'exporter.i.i569' [128, 136) 'exporter.i.i' [160, 176) 'retval.i' [192, 208) 'ref.tmp.i' <== Memory access at offset 192 is inside this variable [224, 232) 'y.addr' [256, 264) 'cen.addr' [288, 296) 'inibeta.addr' [320, 324) 'maxit' (line 12) [336, 360) 'xNM' (line 16) [400, 416) 'agg.tmp' [432, 436) 'n' (line 17) [448, 452) 'p' (line 18) [464, 480) 'cennew' (line 21) [496, 512) 'ynew' (line 23) [528, 536) 'ref.tmp' (line 24) [560, 576) 'beta' (line 26) [592, 600) 'ref.tmp45' (line 28) [624, 648) 'betamat' (line 32) [688, 692) 'ref.tmp60' (line 32) [704, 728) 'ref.tmp75' (line 34) [768, 792) 'newx' (line 36) [832, 864) 'ref.tmp85' (line 36) [896, 912) 'ref.tmp86' (line 36) [928, 952) 'agg.tmp87' [992, 1016) 'ref.tmp98' (line 36) [1056, 1072) 'ystar' (line 41) [1088, 1104) 'eps' (line 42) [1120, 1136) 'epstar' (line 43) [1152, 1168) 'tmp' (line 44) [1184, 1344) 'tmp145' (line 49) [1408, 1568) 'ref.tmp146' (line 49) [1632, 1656) 'agg.tmp147' [1696, 1712) 'agg.tmp154' [1728, 1744) 'epstemp' (line 50) [1760, 1776) 'ref.tmp191' (line 51) [1792, 1808) 'ref.tmp210' (line 52) [1824, 1840) 'agg.tmp211' [1856, 1872) 'agg.tmp218' [1888, 2048) 'coef' (line 54) [2112, 2136) 'ref.tmp238' (line 54) [2176, 2336) 'ref.tmp239' (line 54) [2400, 2560) 'ref.tmp252' (line 54) [2624, 2640) 'betatemp' (line 56) [2656, 2680) 'ref.tmp305' (line 59) [2720, 2728) 'ref.tmp318' (line 62) [2752, 2760) 'ref.tmp319' (line 62) [2784, 2800) 'ref.tmp320' (line 62) [2816, 2840) 'ref.tmp321' (line 62) [2880, 2896) 'ref.tmp382' (line 67) [2912, 2920) 'ref.tmp409' (line 78) HINT: this may be a false positive if your program uses some custom stack unwind mechanism, swapcontext or vfork (longjmp and C++ exceptions *are* supported) SUMMARY: AddressSanitizer: stack-use-after-scope /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/storage/PreserveStorage.h:26:20 in Rcpp::PreserveStorage >::get__() const Shadow bytes around the buggy address: 0x10007e95fb70: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x10007e95fb80: 00 00 00 00 f1 f1 f1 f1 f8 f8 f2 f2 f8 f2 f2 f2 0x10007e95fb90: f8 f3 f3 f3 00 00 00 00 00 00 00 00 00 00 00 00 0x10007e95fba0: 00 00 00 00 00 00 00 00 f1 f1 f1 f1 f8 f8 f2 f2 0x10007e95fbb0: f8 f8 f2 f2 f8 f2 f2 f2 f8 f2 f2 f2 f8 f8 f2 f2 =>0x10007e95fbc0:[f8]f8 f2 f2 00 f2 f2 f2 00 f2 f2 f2 00 f2 f2 f2 0x10007e95fbd0: 04 f2 00 00 00 f2 f2 f2 f2 f2 00 00 f2 f2 04 f2 0x10007e95fbe0: 04 f2 00 00 f2 f2 00 00 f2 f2 00 f2 f2 f2 f8 f8 0x10007e95fbf0: f2 f2 f8 f2 f2 f2 f8 f8 f8 f2 f2 f2 f2 f2 f8 f2 0x10007e95fc00: f8 f8 f8 f2 f2 f2 f2 f2 f8 f8 f8 f2 f2 f2 f2 f2 0x10007e95fc10: f8 f8 f8 f8 f2 f2 f2 f2 f8 f8 f2 f2 00 00 00 f2 Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb Shadow gap: cc ==13701==ABORTING * DONE Status: 1 ERROR