R Under development (unstable) (2026-08-05 r90355) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(rchime)
Loading required package: Rcpp
Loading required package: strollur

Attaching package: 'strollur'

The following objects are masked from 'package:base':

    assign, names, summary

> 
> test_check("rchime")
vsearch_main.cc:1346:10: runtime error: left shift of negative value -2046395799
    #0 0x7f5587b246e3 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 0x7f5587b24e4f in Vsearch_Main::dust(char*, int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1397:24
    #2 0x7f5587b252c3 in Vsearch_Main::dust_all(unsigned long) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1417:9
    #3 0x7f5587b25cb1 in Vsearch_Main::vmain(std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>&, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>&, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>&, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>&, std::__1::vector<float, std::__1::allocator<float>>&, unsigned int, unsigned int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1475:7
    #4 0x7f5587ac1529 in processReferenceVsearch(chimeraData*) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/chimera_vsearch.cpp:95:34
    #5 0x7f5587acc25b in ChimeraVsearch::removeChimeras(std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>&, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>&) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/chimera_vsearch.cpp:302:5
    #6 0x7f5587afda5d in rchimeReference(std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>, std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>, std::__1::allocator<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>>>, Rcpp::Nullable<Rcpp::Vector<19, Rcpp::PreserveStorage>>) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/rcpp_rchime.cpp:103:35
    #7 0x7f5587a8c8d4 in _rchime_rchimeReference /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/RcppExports.cpp:26:34
    #8 0x5634a5098f3a in R_doDotCall (/data/localhost/ripley/R/R-clang/bin/exec/R+0x8ff3a)
    #9 0x5634a50e44b7 in bcEval_loop eval.c
    #10 0x5634a50d283b in bcEval eval.c
    #11 0x5634a50d1ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4)
    #12 0x5634a50ea158 in R_execClosure eval.c
    #13 0x5634a50e964a in applyClosure_core eval.c
    #14 0x5634a50d2f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16)
    #15 0x5634a5136aa1 in dispatchMethod objects.c
    #16 0x5634a51364c8 in Rf_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12d4c8)
    #17 0x5634a5136ffd in do_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12dffd)
    #18 0x5634a50d94d5 in bcEval_loop eval.c
    #19 0x5634a50d283b in bcEval eval.c
    #20 0x5634a50d1ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4)
    #21 0x5634a50ea158 in R_execClosure eval.c
    #22 0x5634a50e964a in applyClosure_core eval.c
    #23 0x5634a50d2f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16)
    #24 0x5634a50d2447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447)
    #25 0x5634a50ef4b7 in do_set (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe64b7)
    #26 0x5634a50d221f in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc921f)
    #27 0x5634a50ee7aa in do_begin (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe57aa)
    #28 0x5634a50d221f in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc921f)
    #29 0x5634a50f0927 in do_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7927)
    #30 0x5634a50d9273 in bcEval_loop eval.c
    #31 0x5634a50d283b in bcEval eval.c
    #32 0x5634a50d1ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4)
    #33 0x5634a50ea158 in R_execClosure eval.c
    #34 0x5634a50e964a in applyClosure_core eval.c
    #35 0x5634a50d2f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16)
    #36 0x5634a50d2447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447)
    #37 0x5634a50f0d07 in do_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7d07)
    #38 0x5634a50d9273 in bcEval_loop eval.c
    #39 0x5634a50d283b in bcEval eval.c
    #40 0x5634a50d1ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4)
    #41 0x5634a50ea158 in R_execClosure eval.c
    #42 0x5634a50e964a in applyClosure_core eval.c
    #43 0x5634a50ecaf8 in R_forceAndCall (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe3af8)
    #44 0x5634a501e9db in do_lapply (/data/localhost/ripley/R/R-clang/bin/exec/R+0x159db)
    #45 0x5634a5134807 in do_internal (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12b807)
    #46 0x5634a50d94d5 in bcEval_loop eval.c
    #47 0x5634a50d283b in bcEval eval.c
    #48 0x5634a50d1ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4)
    #49 0x5634a50ea158 in R_execClosure eval.c
    #50 0x5634a50e964a in applyClosure_core eval.c
    #51 0x5634a50d2f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16)
    #52 0x5634a50d2447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447)
    #53 0x5634a511f777 in Rf_ReplIteration (/data/localhost/ripley/R/R-clang/bin/exec/R+0x116777)
    #54 0x5634a512127e in run_Rmainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x11827e)
    #55 0x5634a51212ea in Rf_mainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1182ea)
    #56 0x5634a500adb7 in main (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1db7)
    #57 0x7f559550b680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7)
    #58 0x7f559550b797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7)
    #59 0x5634a500acd4 in _start (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1cd4)

SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior vsearch_main.cc:1346:10 
> rchime removed `12` chimeras from your dataset.
> It took `4.87426996231079` seconds to detect and remove the chimeras.
Added a chimera_accnos report.
> rchime detected `12` chimeras in your dataset.
> It took `4.16680955886841` seconds to detect the chimeras.
Added 3 sequences.
> rchime complete, no chimeras found.
> It took `3.78863286972046` seconds to detect and remove the chimeras.
Added a chimera_accnos report.
> rchime detected `12` chimeras in your dataset.
> It took `5.17378163337708` seconds to detect the chimeras.
> rchime removed `12` chimeras from your dataset.
> It took `4.00957751274109` seconds to detect and remove the chimeras.
> rchime removed `79` chimeras from your dataset.
> It took `6.89392876625061` seconds to detect and remove the chimeras.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 259 ]
> 
> proc.time()
   user  system elapsed 
 96.562   0.927  72.149