* using log directory ‘/data/gannet/ripley/R/packages/tests-gcc-SAN/SPAS.Rcheck’ * using R Under development (unstable) (2026-03-16 r89642) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) GNU Fortran (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7) * running under: Fedora Linux 42 (Workstation Edition) * using session charset: UTF-8 * current time: 2026-03-17 13:34:21 UTC * using option ‘--no-stop-on-test-error’ * checking for file ‘SPAS/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SPAS’ version ‘2025.2.1’ * package encoding: UTF-8 * 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 ‘SPAS’ can be installed ... [699s/382s] OK * used C++ compiler: ‘g++ (GCC) 15.2.1 20260123 (Red Hat 15.2.1-7)’ * checking package directory ... OK * checking whether the package can be loaded ... [17s/18s] OK * checking whether the package can be loaded with stated dependencies ... [15s/16s] OK * checking whether the package can be unloaded cleanly ... [14s/14s] OK * checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK * checking whether the namespace can be unloaded cleanly ... [16s/16s] OK * checking loading without being on the library search path ... [15s/16s] OK * checking compiled code ... NOTE File ‘SPAS/libs/SPAS.so’: Found non-API call to R: ‘Rf_findVar’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and section ‘Moving into C API compliance’ for issues with the use of non-API entry points. * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [18s/28s] ERROR Running examples in ‘SPAS-Ex.R’ failed The error most likely occurred in: > ### Name: SPAS.fit.model > ### Title: Fit a Stratified-Petersen (SP) model using TMB. > ### Aliases: SPAS.fit.model > > ### ** Examples > > conne.data.csv <- textConnection(" + 9 , 21 , 0 , 0 , 0 , 0 , 171 + 0 , 101 , 22 , 1 , 0 , 0 , 763 + 0 , 0 , 128 , 49 , 0 , 0 , 934 + 0 , 0 , 0 , 48 , 12 , 0 , 434 + 0 , 0 , 0 , 0 , 7 , 0 , 49 + 0 , 0 , 0 , 0 , 0 , 0 , 4 + 351, 2736 , 3847 , 1818 , 543 , 191 , 0") > conne.data <- as.matrix(read.csv(conne.data.csv, header=FALSE)) > close(conne.data.csv) > > mod1 <- SPAS.fit.model(conne.data, model.id="Pooling rows 1/2, 5/6; pooling columns 5/6", + row.pool.in=c("12","12","3","4","56","56"), + col.pool.in=c(1,2,3,4,56,56)) ================================================================= ==1253700==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7bda8610d394 at pc 0x7fdaa52e4937 bp 0x7ffe1449e740 sp 0x7ffe1449df00 READ of size 207475 at 0x7bda8610d394 thread T0 #0 0x7fdaa52e4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7bda8522c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7bda8522c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7bda8522c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7bda8522c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7bda8522c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7bda85269882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7bda85269882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #20 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #21 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #22 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #23 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #24 0x7fdaa3c12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #25 0x7fdaa3c12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #26 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7bda8610d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7bda8610d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7bda8610d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7bda8610d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7bda8610d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bda8610d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bda8610d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bda8610d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bda8610d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7bda8610d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7bda8610d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7bda8610d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7bda8610d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7bda8610d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7bda8610d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1253700==ABORTING * checking package vignettes ... OK * checking re-building of vignette outputs ... [140s/151s] ERROR Error(s) in re-building vignettes: --- re-building ‘AutomaticPooling.Rmd’ using rmarkdown ================================================================= ==1256331==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7ba6afd0d394 at pc 0x7fa6d0ee4937 bp 0x7ffe692493b0 sp 0x7ffe69248b70 READ of size 207475 at 0x7ba6afd0d394 thread T0 #0 0x7fa6d0ee4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7ba6aee2c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7ba6aee2c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7ba6aee2c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7ba6aee2c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7ba6aee2c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7ba6aee69882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7ba6aee69882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #20 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #21 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #22 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #25 0x00000089eb43 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998 #26 0x000000a9a936 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419 #27 0x0000008e2941 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #28 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #29 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #32 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x0000008a9281 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #34 0x0000008a9281 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849 #35 0x0000008e55ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862 #36 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #37 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #43 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #44 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #45 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #47 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #48 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #49 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #50 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #51 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #52 0x0000008ea235 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #53 0x0000008ea235 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103 #54 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #55 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #57 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #58 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #59 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #63 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #64 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7fa6cf612574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #66 0x7fa6cf612627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #67 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7ba6afd0d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7ba6afd0d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7ba6afd0d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7ba6afd0d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7ba6afd0d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ba6afd0d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ba6afd0d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ba6afd0d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7ba6afd0d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7ba6afd0d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7ba6afd0d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7ba6afd0d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7ba6afd0d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7ba6afd0d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7ba6afd0d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1256331==ABORTING --- re-building ‘Conne1991.Rmd’ using rmarkdown ================================================================= ==1257474==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7b2f4650d394 at pc 0x7f2f676e4937 bp 0x7ffc17ccec60 sp 0x7ffc17cce420 READ of size 207475 at 0x7b2f4650d394 thread T0 #0 0x7f2f676e4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7b2f4562c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7b2f4562c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7b2f4562c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7b2f4562c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7b2f4562c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7b2f45669882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7b2f45669882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #20 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #21 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #22 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #25 0x00000089eb43 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998 #26 0x000000a9a936 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419 #27 0x0000008e2941 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #28 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #29 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #32 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x0000008a9281 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #34 0x0000008a9281 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849 #35 0x0000008e55ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862 #36 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #37 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #43 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #44 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #45 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #47 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #48 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #49 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #50 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #51 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #52 0x0000008ea235 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #53 0x0000008ea235 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103 #54 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #55 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #57 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #58 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #59 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #63 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #64 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7f2f65e12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #66 0x7f2f65e12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #67 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7b2f4650d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7b2f4650d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7b2f4650d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7b2f4650d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7b2f4650d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b2f4650d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b2f4650d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b2f4650d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b2f4650d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7b2f4650d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7b2f4650d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7b2f4650d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7b2f4650d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7b2f4650d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7b2f4650d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1257474==ABORTING --- re-building ‘Conne1992.Rmd’ using rmarkdown ================================================================= ==1258269==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7b4ca190d394 at pc 0x7f4cc28e4937 bp 0x7ffc5c4adf50 sp 0x7ffc5c4ad710 READ of size 207475 at 0x7b4ca190d394 thread T0 #0 0x7f4cc28e4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7b4ca0a2c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7b4ca0a2c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7b4ca0a2c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7b4ca0a2c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7b4ca0a2c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7b4ca0a69882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7b4ca0a69882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #20 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #21 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #22 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #25 0x00000089eb43 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998 #26 0x000000a9a936 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419 #27 0x0000008e2941 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #28 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #29 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #32 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x0000008a9281 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #34 0x0000008a9281 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849 #35 0x0000008e55ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862 #36 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #37 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #43 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #44 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #45 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #47 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #48 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #49 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #50 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #51 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #52 0x0000008ea235 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #53 0x0000008ea235 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103 #54 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #55 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #57 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #58 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #59 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #63 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #64 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7f4cc1012574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #66 0x7f4cc1012627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #67 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7b4ca190d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7b4ca190d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7b4ca190d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7b4ca190d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7b4ca190d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b4ca190d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b4ca190d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b4ca190d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b4ca190d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7b4ca190d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7b4ca190d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7b4ca190d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7b4ca190d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7b4ca190d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7b4ca190d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1258269==ABORTING --- re-building ‘HarrisonF2011.Rmd’ using rmarkdown ================================================================= ==1259387==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7b903050d394 at pc 0x7f90516e4937 bp 0x7ffd178cdff0 sp 0x7ffd178cd7b0 READ of size 207475 at 0x7b903050d394 thread T0 #0 0x7f90516e4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7b902f62c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7b902f62c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7b902f62c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7b902f62c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7b902f62c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7b902f669882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7b902f669882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #20 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #21 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #22 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #25 0x00000089eb43 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998 #26 0x000000a9a936 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419 #27 0x0000008e2941 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #28 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #29 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #32 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x0000008a9281 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #34 0x0000008a9281 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849 #35 0x0000008e55ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862 #36 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #37 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #43 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #44 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #45 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #47 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #48 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #49 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #50 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #51 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #52 0x0000008ea235 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #53 0x0000008ea235 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103 #54 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #55 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #57 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #58 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #59 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #63 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #64 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7f904fe12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #66 0x7f904fe12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #67 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7b903050d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7b903050d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7b903050d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7b903050d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7b903050d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b903050d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b903050d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b903050d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b903050d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7b903050d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7b903050d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7b903050d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7b903050d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7b903050d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7b903050d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1259387==ABORTING --- re-building ‘PoolingColumns.Rmd’ using rmarkdown ================================================================= ==1259494==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7b3e6350d394 at pc 0x7f3e846e4937 bp 0x7ffc4046fd60 sp 0x7ffc4046f520 READ of size 207475 at 0x7b3e6350d394 thread T0 #0 0x7f3e846e4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7b3e6262c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7b3e6262c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7b3e6262c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7b3e6262c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7b3e6262c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7b3e62669882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7b3e62669882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #20 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #21 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #22 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #25 0x00000089eb43 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998 #26 0x000000a9a936 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419 #27 0x0000008e2941 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #28 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #29 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #32 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x0000008a9281 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #34 0x0000008a9281 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849 #35 0x0000008e55ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862 #36 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #37 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #43 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #44 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #45 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #47 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #48 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #49 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #50 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #51 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #52 0x0000008ea235 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #53 0x0000008ea235 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103 #54 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #55 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #57 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #58 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #59 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #63 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #64 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7f3e82e12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #66 0x7f3e82e12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #67 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7b3e6350d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7b3e6350d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7b3e6350d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7b3e6350d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7b3e6350d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b3e6350d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b3e6350d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b3e6350d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b3e6350d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7b3e6350d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7b3e6350d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7b3e6350d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7b3e6350d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7b3e6350d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7b3e6350d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1259494==ABORTING --- re-building ‘TestingPooledPetersen.Rmd’ using rmarkdown ================================================================= ==1259635==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7b522050d394 at pc 0x7f52416e4937 bp 0x7ffca919c290 sp 0x7ffca919ba50 READ of size 207475 at 0x7b522050d394 thread T0 #0 0x7f52416e4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7b521f62c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7b521f62c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7b521f62c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7b521f62c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7b521f62c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7b521f669882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7b521f669882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #20 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #21 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #22 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #25 0x00000089eb43 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998 #26 0x000000a9a936 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419 #27 0x0000008e2941 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #28 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #29 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #32 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x0000008a9281 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #34 0x0000008a9281 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849 #35 0x0000008e55ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862 #36 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #37 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #43 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #44 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #45 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #47 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #48 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #49 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #50 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #51 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #52 0x0000008ea235 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #53 0x0000008ea235 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103 #54 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #55 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #57 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #58 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #59 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #63 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #64 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7f523fe12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #66 0x7f523fe12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #67 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7b522050d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7b522050d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7b522050d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7b522050d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7b522050d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b522050d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b522050d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b522050d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7b522050d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7b522050d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7b522050d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7b522050d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7b522050d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7b522050d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7b522050d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1259635==ABORTING --- re-building ‘ThingsThatGoWrong.Rmd’ using rmarkdown ================================================================= ==1259687==ERROR: AddressSanitizer: global-buffer-overflow on address 0x7bea0eb0d394 at pc 0x7fea2fae4937 bp 0x7fffe1f9d3c0 sp 0x7fffe1f9cb80 READ of size 207475 at 0x7bea0eb0d394 thread T0 #0 0x7fea2fae4936 in memcpy (/lib64/libasan.so.8+0xe4936) (BuildId: d3cb6206dff19da52969c009f4cd93611901c478) #1 0x7bea0dc2c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:429 #2 0x7bea0dc2c726 in std::char_traits::copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/char_traits.h:421 #3 0x7bea0dc2c726 in std::__cxx11::basic_string, std::allocator >::_S_copy(char*, char const*, unsigned long) /usr/include/c++/15/bits/basic_string.h:453 #4 0x7bea0dc2c726 in void std::__cxx11::basic_string, std::allocator >::_S_copy_chars(char*, char const*, char const*) /usr/include/c++/15/bits/basic_string.h:489 #5 0x7bea0dc2c726 in void std::__cxx11::basic_string, std::allocator >::_M_construct(char const*, char const*, std::forward_iterator_tag) [clone .constprop.0] /usr/include/c++/15/bits/basic_string.tcc:253 #6 0x7bea0dc69882 in std::__cxx11::basic_string, std::allocator >::basic_string >(char const*, std::allocator const&) /usr/include/c++/15/bits/basic_string.h:714 #7 0x7bea0dc69882 in MakeADFunObject /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 #8 0x000000751256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763 #9 0x000000755ada in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #11 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #12 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #14 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #15 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #16 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #17 0x0000008943de in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581 #18 0x000000862496 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #19 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #20 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #21 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #22 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #25 0x00000089eb43 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998 #26 0x000000a9a936 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1419 #27 0x0000008e2941 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152 #28 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #29 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000086302c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #32 0x00000092a011 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #33 0x0000008a9281 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #34 0x0000008a9281 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849 #35 0x0000008e55ac in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862 #36 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #37 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x00000089bc21 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955 #43 0x0000008d5732 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132 #44 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #45 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #47 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #48 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #49 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #50 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #51 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #52 0x0000008ea235 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #53 0x0000008ea235 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103 #54 0x0000008c2983 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515 #55 0x0000008619d2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x000000879f4a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #57 0x00000087df3a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #58 0x000000862073 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #59 0x000000862073 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x000000a07f88 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #61 0x000000a07f88 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0x000000a162fa in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #63 0x000000a16392 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #64 0x000000412fdf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7fea2e212574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #66 0x7fea2e212627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #67 0x0000004139c4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x4139c4) (BuildId: 5254acaa7b8fbfa2c9464072c13caba4a8f40e33) 0x7bea0eb0d394 is located 44 bytes before global variable '*.LC10' defined in './SPAS.so.ltrans0.ltrans' (0x7bea0eb0d3c0) of size 24 '*.LC10' is ascii string 'basic_string::_M_create' 0x7bea0eb0d394 is located 0 bytes after global variable '*.LC9' defined in './SPAS.so.ltrans0.ltrans' (0x7bea0eb0d380) of size 20 '*.LC9' is ascii string 'no_conditional_skip' SUMMARY: AddressSanitizer: global-buffer-overflow /data/gannet/ripley/R/test-dev/TMB/include/cppad/local/ad_fun.hpp:534 in MakeADFunObject Shadow bytes around the buggy address: 0x7bea0eb0d100: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bea0eb0d180: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bea0eb0d200: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bea0eb0d280: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x7bea0eb0d300: 00 00 00 00 00 00 00 00 05 f9 f9 f9 f9 f9 f9 f9 =>0x7bea0eb0d380: 00 00[04]f9 f9 f9 f9 f9 00 00 00 f9 f9 f9 f9 f9 0x7bea0eb0d400: 03 f9 f9 f9 f9 f9 f9 f9 00 07 f9 f9 f9 f9 f9 f9 0x7bea0eb0d480: 00 07 f9 f9 f9 f9 f9 f9 00 05 f9 f9 f9 f9 f9 f9 0x7bea0eb0d500: 00 00 05 f9 f9 f9 f9 f9 00 00 03 f9 f9 f9 f9 f9 0x7bea0eb0d580: 00 00 02 f9 f9 f9 f9 f9 00 06 f9 f9 f9 f9 f9 f9 0x7bea0eb0d600: 00 00 00 06 f9 f9 f9 f9 00 00 00 00 04 f9 f9 f9 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 ==1259687==ABORTING SUMMARY: processing the following files failed: ‘AutomaticPooling.Rmd’ ‘Conne1991.Rmd’ ‘Conne1992.Rmd’ ‘HarrisonF2011.Rmd’ ‘PoolingColumns.Rmd’ ‘TestingPooledPetersen.Rmd’ ‘ThingsThatGoWrong.Rmd’ Error: Vignette re-building failed. Execution halted * DONE Status: 2 ERRORs, 1 NOTE