--- re-building ‘limitations.Rmd’ using rmarkdown /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/validator/Validator.cpp:340:7: runtime error: downcast of address 0x7babe0427400 which does not point to an object of type 'TConstraint' 0x7babe0427400: note: object is of type 'VConstraintSpeciesReference20611' 00 00 00 00 30 b7 65 d1 4b 7b 00 00 83 50 00 00 02 00 00 00 70 51 22 df 4b 7b 00 00 01 be be be ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'VConstraintSpeciesReference20611' #0 0x7b4bce7634a6 in ValidatorConstraints::add(VConstraint*) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xd634a6) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #1 0x7b4bced6c0c9 in ConsistencyValidator::init() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x136c0c9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #2 0x7b4bce62413a in SBMLInternalValidator::checkConsistency(bool) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xc2413a) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #3 0x7b4bcdffd1f0 in SBMLDocument::checkConsistency() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5fd1f0) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #4 0x7b4bcea67e2c in SBMLReactionConverter::isDocumentValid() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1067e2c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #5 0x7b4bcea76ae9 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1076ae9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #6 0x7b4bce0054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #7 0x7b4bcdb90623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string, std::allocator >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #8 0x7b4bcdb0d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #9 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760 #10 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708 #11 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #12 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #14 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #15 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #16 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #17 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #18 0x00000087b017 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1191 #19 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #20 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #21 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #22 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #23 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #24 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #25 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #26 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #27 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #28 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #30 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #31 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #32 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #33 0x0000008afe54 in Rf_evalList /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3685 #34 0x00000087a96c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1249 #35 0x00000088f23e in do_begin /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3003 #36 0x00000087a5a6 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230 #37 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #38 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #39 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #40 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #41 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #42 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #43 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #44 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #45 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #46 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #47 0x00000088f23e in do_begin /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3003 #48 0x00000087a5a6 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230 #49 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #50 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #51 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #52 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #53 0x0000008af57e in do_set /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3587 #54 0x00000087a5a6 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230 #55 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #56 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #57 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #58 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #60 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #61 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #62 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #63 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #64 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #65 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #66 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #67 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #68 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #69 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #70 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #71 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #72 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #73 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #74 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #75 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #76 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #77 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #78 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #79 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #80 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #81 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #82 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #83 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #84 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #85 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #86 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #87 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #88 0x00000089842b in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #89 0x000000902c77 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8125 #90 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #91 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #92 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #93 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #94 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #95 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #96 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264 #97 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319 #98 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239 #99 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246 #100 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29 #101 0x7f4be380a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #102 0x7f4be380a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #103 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca) /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/LocalParameter.cpp:655:17: runtime error: downcast of address 0x7cebe0368a80 which does not point to an object of type 'LocalParameter' 0x7cebe0368a80: note: object is of type 'Parameter' 00 00 00 00 30 8d 66 d1 4b 7b 00 00 98 8a 36 e0 eb 7c 00 00 01 00 00 00 00 00 00 00 6b 00 be be ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'Parameter' #0 0x7b4bcdf31ab7 in ListOfParameters::get(std::__cxx11::basic_string, std::allocator > const&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x531ab7) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #1 0x7b4bceec4b3a in CiElementMathCheck::checkCiElement(Model const&, ASTNode const&, SBase const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x14c4b3a) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #2 0x7b4bcef0dc57 in MathMLBase::checkChildren(Model const&, ASTNode const&, SBase const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x150dc57) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #3 0x7b4bcef11c3c in MathMLBase::check_(Model const&, Model const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1511c3c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #4 0x7b4bce77c6b4 in ValidatingVisitor::visit(Model const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xd7c6b4) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #5 0x7b4bcde2c0da in Model::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x42c0da) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #6 0x7b4bcdfc3df6 in SBMLDocument::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5c3df6) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #7 0x7b4bce7b6479 in Validator::validate(SBMLDocument const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xdb6479) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #8 0x7b4bce624925 in SBMLInternalValidator::checkConsistency(bool) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xc24925) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #9 0x7b4bcdffd1f0 in SBMLDocument::checkConsistency() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5fd1f0) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #10 0x7b4bcea67e2c in SBMLReactionConverter::isDocumentValid() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1067e2c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #11 0x7b4bcea76ae9 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1076ae9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #12 0x7b4bce0054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #13 0x7b4bcdb90623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string, std::allocator >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #14 0x7b4bcdb0d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #15 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760 #16 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708 #17 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #18 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #20 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #21 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #22 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x00000087b017 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1191 #25 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #26 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #27 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #28 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #29 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #30 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #31 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #32 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #33 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #34 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #36 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #37 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #38 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #39 0x0000008afe54 in Rf_evalList /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3685 #40 0x00000087a96c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1249 #41 0x00000088f23e in do_begin /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3003 #42 0x00000087a5a6 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230 #43 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #44 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #45 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #46 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #47 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #48 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #49 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #50 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #51 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #52 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #53 0x00000088f23e in do_begin /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3003 #54 0x00000087a5a6 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230 #55 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #56 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #57 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #58 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #59 0x0000008af57e in do_set /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3587 #60 0x00000087a5a6 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1230 #61 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #62 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #63 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #64 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #65 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #66 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #67 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #68 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #69 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #70 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #71 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #72 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #73 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #74 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #75 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #76 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #77 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #78 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #79 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #80 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #81 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #82 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #83 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #84 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #85 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #86 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #87 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #88 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #89 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #90 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #91 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #92 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #93 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #94 0x00000089842b in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #95 0x000000902c77 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8125 #96 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #97 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #98 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #99 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #100 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #101 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #102 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264 #103 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319 #104 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239 #105 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246 #106 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29 #107 0x7f4be380a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #108 0x7f4be380a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #109 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca) [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘limitations.Rmd’ --- re-building ‘r2sbml.Rmd’ using rmarkdown /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/validator/Validator.cpp:340:7: runtime error: downcast of address 0x7b7e0f076300 which does not point to an object of type 'TConstraint' 0x7b7e0f076300: note: object is of type 'VConstraintSpeciesReference20611' 00 00 00 00 30 b7 25 00 1e 7b 00 00 83 50 00 00 02 00 00 00 70 b1 e1 0d 1e 7b 00 00 01 be be be ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'VConstraintSpeciesReference20611' #0 0x7b1dfd3634a6 in ValidatorConstraints::add(VConstraint*) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xd634a6) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #1 0x7b1dfd96c0c9 in ConsistencyValidator::init() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x136c0c9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #2 0x7b1dfd22413a in SBMLInternalValidator::checkConsistency(bool) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xc2413a) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #3 0x7b1dfcbfd1f0 in SBMLDocument::checkConsistency() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5fd1f0) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #4 0x7b1dfd667e2c in SBMLReactionConverter::isDocumentValid() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1067e2c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #5 0x7b1dfd676ae9 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1076ae9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #6 0x7b1dfcc054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #7 0x7b1dfc790623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string, std::allocator >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #8 0x7b1dfc70d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #9 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760 #10 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708 #11 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #12 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #14 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #15 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #16 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #17 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #18 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #19 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #20 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #21 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #22 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #23 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #24 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #25 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #26 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #27 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #28 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #29 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #30 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #32 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #33 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #34 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #35 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #36 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #37 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #38 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #39 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #40 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #41 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #42 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #43 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #44 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #45 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #46 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #47 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #48 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #49 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #50 0x00000089842b in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #51 0x000000902c77 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8125 #52 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #53 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #54 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #55 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #56 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #57 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #58 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264 #59 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319 #60 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239 #61 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246 #62 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29 #63 0x7f1e1240a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #64 0x7f1e1240a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #65 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca) /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/LocalParameter.cpp:655:17: runtime error: downcast of address 0x7cbe0f0d4680 which does not point to an object of type 'LocalParameter' 0x7cbe0f0d4680: note: object is of type 'Parameter' 00 00 00 00 30 8d 26 00 1e 7b 00 00 98 46 0d 0f be 7c 00 00 08 00 00 00 00 00 00 00 76 65 71 5f ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'Parameter' #0 0x7b1dfcb31ab7 in ListOfParameters::get(std::__cxx11::basic_string, std::allocator > const&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x531ab7) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #1 0x7b1dfd5dcf86 in getNewId(Model*, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xfdcf86) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #2 0x7b1dfd5f565b in SBMLLocalParameterConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xff565b) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #3 0x7b1dfcc054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #4 0x7b1dfd6772e1 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10772e1) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #5 0x7b1dfcc054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #6 0x7b1dfc790623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string, std::allocator >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #7 0x7b1dfc70d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #8 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760 #9 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708 #10 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #11 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #12 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #13 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #14 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #15 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #16 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #17 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #18 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #19 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #20 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #21 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #22 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #23 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #24 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #25 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #26 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #28 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #29 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #30 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #31 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #32 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #33 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #34 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #36 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #37 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #38 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #39 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #40 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #41 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #42 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #43 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #44 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #45 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #46 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #47 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #48 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #49 0x00000089842b in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #50 0x000000902c77 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8125 #51 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #52 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #54 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #55 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #56 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #57 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264 #58 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319 #59 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239 #60 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246 #61 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29 #62 0x7f1e1240a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #63 0x7f1e1240a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #64 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca) /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/validator/Validator.cpp:93:22: runtime error: member call on address 0x7b7e0f29eba0 which does not point to an object of type 'TConstraint' 0x7b7e0f29eba0: note: object is of type 'VConstraintSpeciesReference20611' 00 00 00 00 30 b7 25 00 1e 7b 00 00 83 50 00 00 02 00 00 00 70 19 e6 0d 1e 7b 00 00 00 be be be ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'VConstraintSpeciesReference20611' #0 0x7b1dfd3a6cc8 in ValidatingVisitor::visit(ModifierSpeciesReference const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xda6cc8) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #1 0x7b1dfc9e43be in ListOf::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x3e43be) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #2 0x7b1dfcb4a58d in Reaction::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x54a58d) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #3 0x7b1dfc9e43be in ListOf::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x3e43be) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #4 0x7b1dfca2c946 in Model::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x42c946) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #5 0x7b1dfcbc3df6 in SBMLDocument::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5c3df6) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #6 0x7b1dfd3b6479 in Validator::validate(SBMLDocument const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xdb6479) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #7 0x7b1dfd2241c3 in SBMLInternalValidator::checkConsistency(bool) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xc241c3) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #8 0x7b1dfcbfd1f0 in SBMLDocument::checkConsistency() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5fd1f0) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #9 0x7b1dfd667e2c in SBMLReactionConverter::isDocumentValid() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1067e2c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #10 0x7b1dfd676ae9 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1076ae9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #11 0x7b1dfcc054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #12 0x7b1dfc790623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string, std::allocator >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #13 0x7b1dfc70d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #14 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760 #15 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708 #16 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #17 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #19 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #20 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #21 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #22 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #23 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #24 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #25 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #26 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #27 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #28 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #29 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #30 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #31 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #32 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #33 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #35 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #36 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #37 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #38 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #39 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #40 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #42 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #43 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #44 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #45 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #46 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #47 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #48 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #49 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #50 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #51 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #52 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #53 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #54 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #55 0x00000089842b in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #56 0x000000902c77 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8125 #57 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #58 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #60 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #61 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #62 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #63 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264 #64 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319 #65 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239 #66 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246 #67 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29 #68 0x7f1e1240a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #69 0x7f1e1240a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #70 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca) /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/validator/constraints/ConsistencyConstraints.cpp:1830:36: runtime error: member call on address 0x7cae0fcdd880 which does not point to an object of type 'SpeciesReference' 0x7cae0fcdd880: note: object is of type 'ModifierSpeciesReference' 00 00 00 00 d0 21 26 00 1e 7b 00 00 98 d8 cd 0f ae 7c 00 00 00 00 00 00 00 00 00 00 00 be be be ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'ModifierSpeciesReference' #0 0x7b1dfd94b29d in VConstraintSpeciesReference21111::check_(Model const&, SpeciesReference const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x134b29d) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #1 0x7b1dfd3a6513 in ValidatingVisitor::visit(ModifierSpeciesReference const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xda6513) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #2 0x7b1dfc9e43be in ListOf::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x3e43be) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #3 0x7b1dfcb4a58d in Reaction::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x54a58d) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #4 0x7b1dfc9e43be in ListOf::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x3e43be) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #5 0x7b1dfca2c946 in Model::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x42c946) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #6 0x7b1dfcbc3df6 in SBMLDocument::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5c3df6) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #7 0x7b1dfd3b6479 in Validator::validate(SBMLDocument const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xdb6479) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #8 0x7b1dfd2241c3 in SBMLInternalValidator::checkConsistency(bool) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xc241c3) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #9 0x7b1dfcbfd1f0 in SBMLDocument::checkConsistency() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5fd1f0) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #10 0x7b1dfd667e2c in SBMLReactionConverter::isDocumentValid() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1067e2c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #11 0x7b1dfd676ae9 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1076ae9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #12 0x7b1dfcc054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #13 0x7b1dfc790623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string, std::allocator >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #14 0x7b1dfc70d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #15 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760 #16 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708 #17 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #18 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #20 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #21 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #22 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #23 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #24 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #25 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #26 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #28 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #29 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #30 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #31 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #32 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #33 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #35 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #36 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #37 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #38 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #39 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #40 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #41 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #42 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #43 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #44 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #45 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #46 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #47 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #48 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #49 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #50 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #51 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #52 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #53 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #54 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #55 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #56 0x00000089842b in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #57 0x000000902c77 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8125 #58 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #59 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #60 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #61 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #62 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #63 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #64 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264 #65 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319 #66 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239 #67 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246 #68 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29 #69 0x7f1e1240a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #70 0x7f1e1240a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #71 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca) /data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml/src/libsbml-src/src/sbml/Reaction.cpp:82:28: runtime error: downcast of address 0x7cae0fcdd880 which does not point to an object of type 'SpeciesReference' 0x7cae0fcdd880: note: object is of type 'ModifierSpeciesReference' 00 00 00 00 d0 21 26 00 1e 7b 00 00 98 d8 cd 0f ae 7c 00 00 00 00 00 00 00 00 00 00 00 be be be ^~~~~~~~~~~~~~~~~~~~~~~ vptr for 'ModifierSpeciesReference' #0 0x7b1dfcb55c3b in GetSpeciesRef(ListOf&, std::__cxx11::basic_string, std::allocator > const&) [clone .lto_priv.0] (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x555c3b) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #1 0x7b1dfcb6b00f in Reaction::getModifier(std::__cxx11::basic_string, std::allocator > const&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x56b00f) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #2 0x7b1dfd96004c in VConstraintLocalParameter21173::check_(Model const&, LocalParameter const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x136004c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #3 0x7b1dfd39b11a in ValidatingVisitor::visit(Parameter const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xd9b11a) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #4 0x7b1dfc9e43be in ListOf::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x3e43be) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #5 0x7b1dfc9d0570 in KineticLaw::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x3d0570) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #6 0x7b1dfcb4a7cb in Reaction::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x54a7cb) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #7 0x7b1dfc9e43be in ListOf::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x3e43be) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #8 0x7b1dfca2c946 in Model::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x42c946) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #9 0x7b1dfcbc3df6 in SBMLDocument::accept(SBMLVisitor&) const (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5c3df6) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #10 0x7b1dfd3b6479 in Validator::validate(SBMLDocument const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xdb6479) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #11 0x7b1dfd2241c3 in SBMLInternalValidator::checkConsistency(bool) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0xc241c3) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #12 0x7b1dfcbfd1f0 in SBMLDocument::checkConsistency() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x5fd1f0) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #13 0x7b1dfd667e2c in SBMLReactionConverter::isDocumentValid() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1067e2c) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #14 0x7b1dfd676ae9 in SBMLReactionConverter::convert() (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x1076ae9) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #15 0x7b1dfcc054cd in SBMLDocument::convert(ConversionProperties const&) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x6054cd) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #16 0x7b1dfc790623 in convertReactions(SEXPREC*, SEXPREC*, std::__cxx11::basic_string, std::allocator >) (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x190623) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #17 0x7b1dfc70d632 in _r2sbml_convertReactions (/data/localhost/ripley/R/packages/tests-gcc-SAN/r2sbml.Rcheck/r2sbml/libs/r2sbml.so+0x10d632) (BuildId: 77187ecca3a85a09dc5ba75135705c28320ffbf3) #18 0x00000075fa3a in R_doDotCall /data/localhost/ripley/R/svn/R-devel/src/main/dotcode.c:760 #19 0x000000904867 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8708 #20 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #21 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #22 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #23 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #24 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #25 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #26 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #27 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #28 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #29 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #32 0x0000008ba443 in do_withVisible /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:4020 #33 0x000000abf461 in do_internal /data/localhost/ripley/R/svn/R-devel/src/main/names.c:1425 #34 0x0000008faa7c in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8174 #35 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #36 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #37 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #38 0x00000087b13c in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1185 #39 0x000000947c4a in forcePromise.part.0.lto_priv.0 /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:976 #40 0x0000008c3e6f in forcePromise /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:956 #41 0x0000008c3e6f in getvar /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:5869 #42 0x0000008fe104 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7884 #43 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #44 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #46 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #47 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #48 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #49 0x0000008b74f9 in do_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:3977 #50 0x0000008f0d0b in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8154 #51 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #52 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #54 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #55 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #56 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #57 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #58 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #59 0x00000089842b in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #60 0x000000902c77 in bcEval_loop /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:8125 #61 0x0000008dbc1b in bcEval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:7537 #62 0x000000879aca in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1167 #63 0x000000892f4a in R_execClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2400 #64 0x000000896c4d in applyClosure_core /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2316 #65 0x00000087a178 in Rf_applyClosure /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:2335 #66 0x00000087a178 in Rf_eval /data/localhost/ripley/R/svn/R-devel/src/main/eval.c:1278 #67 0x000000a25478 in Rf_ReplIteration /data/localhost/ripley/R/svn/R-devel/src/main/main.c:264 #68 0x000000a25478 in R_ReplConsole /data/localhost/ripley/R/svn/R-devel/src/main/main.c:319 #69 0x000000a431da in run_Rmainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1239 #70 0x000000a43272 in Rf_mainloop /data/localhost/ripley/R/svn/R-devel/src/main/main.c:1246 #71 0x0000004122df in main /data/localhost/ripley/R/svn/R-devel/src/main/Rmain.c:29 #72 0x7f1e1240a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #73 0x7f1e1240a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c) #74 0x000000412ca4 in _start (/data/localhost/ripley/R/gcc-SAN3/bin/exec/R+0x412ca4) (BuildId: 71398c2e2422cbe6c955a1152125cb4edf0131ca) [WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead. --- finished re-building ‘r2sbml.Rmd’