--- re-building ‘chimera_report.Rmd’ using rmarkdown vsearch_main.cc:1346:10: runtime error: left shift of negative value -964019831 #0 0x7f8ae4e9a6e3 in Vsearch_Main::wo(int, char const*, int*, int*) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1346:10 #1 0x7f8ae4e9ae4f in Vsearch_Main::dust(char*, int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1397:24 #2 0x7f8ae4e9b2c3 in Vsearch_Main::dust_all(unsigned long) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1417:9 #3 0x7f8ae4e9baf6 in Vsearch_Main::vmain(std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector>&, unsigned int, unsigned int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1483:7 #4 0x7f8ae4e37f17 in ChimeraVsearch::removeChimeras() /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/chimera_vsearch.cpp:143:37 #5 0x7f8ae4e76d49 in rchimeDenovo(std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>, std::__1::allocator, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>>>, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>, std::__1::allocator, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>>>, std::__1::vector>, std::__1::allocator>>>, Rcpp::Nullable>) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/rcpp_rchime.cpp:286:36 #6 0x7f8ae4e03a90 in _rchime_rchimeDenovo /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/RcppExports.cpp:54:34 #7 0x560cba810585 in R_doDotCall (/data/localhost/ripley/R/R-clang/bin/exec/R+0x8f585) #8 0x560cba85c4b7 in bcEval_loop eval.c #9 0x560cba84a83b in bcEval eval.c #10 0x560cba849ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #11 0x560cba862158 in R_execClosure eval.c #12 0x560cba86164a in applyClosure_core eval.c #13 0x560cba84af16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #14 0x560cba8aeaa1 in dispatchMethod objects.c #15 0x560cba8ae4c8 in Rf_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12d4c8) #16 0x560cba8aeffd in do_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12dffd) #17 0x560cba8514d5 in bcEval_loop eval.c #18 0x560cba84a83b in bcEval eval.c #19 0x560cba849ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #20 0x560cba862158 in R_execClosure eval.c #21 0x560cba86164a in applyClosure_core eval.c #22 0x560cba84af16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #23 0x560cba84a447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #24 0x560cba868927 in do_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7927) #25 0x560cba851273 in bcEval_loop eval.c #26 0x560cba84a83b in bcEval eval.c #27 0x560cba849ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #28 0x560cba84aa93 in forcePromise eval.c #29 0x560cba84a0bd in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc90bd) #30 0x560cba868e06 in do_withVisible (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7e06) #31 0x560cba8ac807 in do_internal (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12b807) #32 0x560cba8514d5 in bcEval_loop eval.c #33 0x560cba84a83b in bcEval eval.c #34 0x560cba849ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #35 0x560cba84aa93 in forcePromise eval.c #36 0x560cba84a0bd in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc90bd) #37 0x560cba84aa93 in forcePromise eval.c #38 0x560cba85e5bf in getvar eval.c #39 0x560cba84ec78 in bcEval_loop eval.c #40 0x560cba84a83b in bcEval eval.c #41 0x560cba849ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #42 0x560cba862158 in R_execClosure eval.c #43 0x560cba86164a in applyClosure_core eval.c #44 0x560cba84af16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #45 0x560cba84a447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #46 0x560cba868927 in do_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7927) #47 0x560cba851273 in bcEval_loop eval.c #48 0x560cba84a83b in bcEval eval.c #49 0x560cba849ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #50 0x560cba862158 in R_execClosure eval.c #51 0x560cba86164a in applyClosure_core eval.c #52 0x560cba84af16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #53 0x560cba84a447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #54 0x560cba862158 in R_execClosure eval.c #55 0x560cba86164a in applyClosure_core eval.c #56 0x560cba850b05 in bcEval_loop eval.c #57 0x560cba84a83b in bcEval eval.c #58 0x560cba849ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #59 0x560cba862158 in R_execClosure eval.c #60 0x560cba86164a in applyClosure_core eval.c #61 0x560cba84af16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #62 0x560cba84a447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #63 0x560cba897777 in Rf_ReplIteration (/data/localhost/ripley/R/R-clang/bin/exec/R+0x116777) #64 0x560cba89927e in run_Rmainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x11827e) #65 0x560cba8992ea in Rf_mainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1182ea) #66 0x560cba782db7 in main (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1db7) #67 0x7f8af2f0b680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7) #68 0x7f8af2f0b797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7) #69 0x560cba782cd4 in _start (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1cd4) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior vsearch_main.cc:1346:10 --- finished re-building ‘chimera_report.Rmd’ --- re-building ‘denovo_based_detection.Rmd’ using rmarkdown vsearch_main.cc:1346:10: runtime error: left shift of negative value -964019831 #0 0x7f8d7a5626e3 in Vsearch_Main::wo(int, char const*, int*, int*) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1346:10 #1 0x7f8d7a562e4f in Vsearch_Main::dust(char*, int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1397:24 #2 0x7f8d7a5632c3 in Vsearch_Main::dust_all(unsigned long) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1417:9 #3 0x7f8d7a563af6 in Vsearch_Main::vmain(std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector>&, unsigned int, unsigned int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1483:7 #4 0x7f8d7a4fff17 in ChimeraVsearch::removeChimeras() /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/chimera_vsearch.cpp:143:37 #5 0x7f8d7a53ed49 in rchimeDenovo(std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>, std::__1::allocator, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>>>, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>, std::__1::allocator, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>>>, std::__1::vector>, std::__1::allocator>>>, Rcpp::Nullable>) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/rcpp_rchime.cpp:286:36 #6 0x7f8d7a4cba90 in _rchime_rchimeDenovo /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/RcppExports.cpp:54:34 #7 0x55e4d760f585 in R_doDotCall (/data/localhost/ripley/R/R-clang/bin/exec/R+0x8f585) #8 0x55e4d765b4b7 in bcEval_loop eval.c #9 0x55e4d764983b in bcEval eval.c #10 0x55e4d7648ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #11 0x55e4d7661158 in R_execClosure eval.c #12 0x55e4d766064a in applyClosure_core eval.c #13 0x55e4d7649f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #14 0x55e4d76adaa1 in dispatchMethod objects.c #15 0x55e4d76ad4c8 in Rf_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12d4c8) #16 0x55e4d76adffd in do_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12dffd) #17 0x55e4d76504d5 in bcEval_loop eval.c #18 0x55e4d764983b in bcEval eval.c #19 0x55e4d7648ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #20 0x55e4d7661158 in R_execClosure eval.c #21 0x55e4d766064a in applyClosure_core eval.c #22 0x55e4d7649f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #23 0x55e4d7649447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #24 0x55e4d7667927 in do_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7927) #25 0x55e4d7650273 in bcEval_loop eval.c #26 0x55e4d764983b in bcEval eval.c #27 0x55e4d7648ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #28 0x55e4d7649a93 in forcePromise eval.c #29 0x55e4d76490bd in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc90bd) #30 0x55e4d7667e06 in do_withVisible (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7e06) #31 0x55e4d76ab807 in do_internal (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12b807) #32 0x55e4d76504d5 in bcEval_loop eval.c #33 0x55e4d764983b in bcEval eval.c #34 0x55e4d7648ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #35 0x55e4d7649a93 in forcePromise eval.c #36 0x55e4d76490bd in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc90bd) #37 0x55e4d7649a93 in forcePromise eval.c #38 0x55e4d765d5bf in getvar eval.c #39 0x55e4d764dc78 in bcEval_loop eval.c #40 0x55e4d764983b in bcEval eval.c #41 0x55e4d7648ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #42 0x55e4d7661158 in R_execClosure eval.c #43 0x55e4d766064a in applyClosure_core eval.c #44 0x55e4d7649f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #45 0x55e4d7649447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #46 0x55e4d7667927 in do_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7927) #47 0x55e4d7650273 in bcEval_loop eval.c #48 0x55e4d764983b in bcEval eval.c #49 0x55e4d7648ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #50 0x55e4d7661158 in R_execClosure eval.c #51 0x55e4d766064a in applyClosure_core eval.c #52 0x55e4d7649f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #53 0x55e4d7649447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #54 0x55e4d7661158 in R_execClosure eval.c #55 0x55e4d766064a in applyClosure_core eval.c #56 0x55e4d764fb05 in bcEval_loop eval.c #57 0x55e4d764983b in bcEval eval.c #58 0x55e4d7648ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4) #59 0x55e4d7661158 in R_execClosure eval.c #60 0x55e4d766064a in applyClosure_core eval.c #61 0x55e4d7649f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16) #62 0x55e4d7649447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447) #63 0x55e4d7696777 in Rf_ReplIteration (/data/localhost/ripley/R/R-clang/bin/exec/R+0x116777) #64 0x55e4d769827e in run_Rmainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x11827e) #65 0x55e4d76982ea in Rf_mainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1182ea) #66 0x55e4d7581db7 in main (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1db7) #67 0x7f8d8860a680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7) #68 0x7f8d8860a797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7) #69 0x55e4d7581cd4 in _start (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1cd4) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior vsearch_main.cc:1346:10 --- finished re-building ‘denovo_based_detection.Rmd’ --- re-building ‘rchime.Rmd’ using rmarkdown --- finished re-building ‘rchime.Rmd’ --- re-building ‘reference_based_detection.Rmd’ using rmarkdown vsearch_main.cc:1346:10: runtime error: left shift of negative value -2046395799 #0 0x7f37ade9a6e3 in Vsearch_Main::wo(int, char const*, int*, int*) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1346:10 #1 0x7f37ade9ae4f in Vsearch_Main::dust(char*, int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1397:24 #2 0x7f37ade9b2c3 in Vsearch_Main::dust_all(unsigned long) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1417:9 #3 0x7f37ade9bcb1 in Vsearch_Main::vmain(std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>>&, std::__1::vector>&, unsigned int, unsigned int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1475:7 #4 0x7f37ade37529 in processReferenceVsearch(chimeraData*) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/chimera_vsearch.cpp:95:34 #5 0x7f37ade5be51 in std::__1::__packaged_task_function::operator()() const /usr/local/clang22me/bin/../include/c++/v1/future:1600:10 #6 0x7f37ade5be51 in std::__1::packaged_task::operator()() /usr/local/clang22me/bin/../include/c++/v1/future:1761:5 #7 0x7f37ade5bcd1 in std::__1::__invoke_result_impl>::type std::__1::__invoke[abi:nqe220108]>(std::__1::packaged_task&&) /usr/local/clang22me/bin/../include/c++/v1/__type_traits/invoke.h:90:27 #8 0x7f37ade5bcd1 in void std::__1::__thread_execute[abi:nqe220108]>, std::__1::packaged_task, 0ul>(std::__1::tuple>, std::__1::packaged_task>&, std::__1::__integer_sequence) /usr/local/clang22me/bin/../include/c++/v1/__thread/thread.h:161:3 #9 0x7f37ade5bcd1 in void* std::__1::__thread_proxy[abi:nqe220108]>, std::__1::packaged_task>>(void*) /usr/local/clang22me/bin/../include/c++/v1/__thread/thread.h:169:3 #10 0x7f37bbf7ac18 in start_thread (/lib64/libc.so.6+0x72c18) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7) #11 0x7f37bbffe5cb in __GI___clone3 (/lib64/libc.so.6+0xf65cb) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior vsearch_main.cc:1346:10 --- finished re-building ‘reference_based_detection.Rmd’