R Under development (unstable) (2026-08-05 r90355) -- "Unsuffered Consequences"
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> pkgname <- "rchime"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('rchime')
Loading required package: Rcpp
Loading required package: strollur

Attaching package: ‘strollur’

The following objects are masked from ‘package:base’:

    assign, names, summary

> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("rchime")
> ### * rchime
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: rchime
> ### Title: rchime
> ### Aliases: rchime rchime.strollur rchime.data.frame
> 
> ### ** Examples
> 
> 
> # Let's use a strollur object with 500 sequences
> 
> data <- strollur::load_dataset(
+   rchime_example("strollur_multi_sample_small.rds")
+ )
> 
> rchime(data)
ℹ The de novo method runs with a single processor.

vsearch_main.cc:1346:10: runtime error: left shift of negative value -959796983
    #0 0x7fe8ae5966e3 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 0x7fe8ae596e4f in Vsearch_Main::dust(char*, int) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1397:24
    #2 0x7fe8ae5972c3 in Vsearch_Main::dust_all(unsigned long) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/vsearch_main.cc:1417:9
    #3 0x7fe8ae597af6 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:1483:7
    #4 0x7fe8ae533f17 in ChimeraVsearch::removeChimeras() /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/chimera_vsearch.cpp:143:37
    #5 0x7fe8ae572d49 in rchimeDenovo(std::__1::vector<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::allocator<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::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::allocator<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::vector<float, std::__1::allocator<float>>, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float>>>>, Rcpp::Nullable<Rcpp::Vector<19, Rcpp::PreserveStorage>>) /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/rcpp_rchime.cpp:286:36
    #6 0x7fe8ae4ffa90 in _rchime_rchimeDenovo /data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime/src/RcppExports.cpp:54:34
    #7 0x55a6fca7e585 in R_doDotCall (/data/localhost/ripley/R/R-clang/bin/exec/R+0x8f585)
    #8 0x55a6fcaca4b7 in bcEval_loop eval.c
    #9 0x55a6fcab883b in bcEval eval.c
    #10 0x55a6fcab7ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4)
    #11 0x55a6fcad0158 in R_execClosure eval.c
    #12 0x55a6fcacf64a in applyClosure_core eval.c
    #13 0x55a6fcab8f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16)
    #14 0x55a6fcb1caa1 in dispatchMethod objects.c
    #15 0x55a6fcb1c4c8 in Rf_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12d4c8)
    #16 0x55a6fcb1cffd in do_usemethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0x12dffd)
    #17 0x55a6fcabf4d5 in bcEval_loop eval.c
    #18 0x55a6fcab883b in bcEval eval.c
    #19 0x55a6fcab7ff4 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc8ff4)
    #20 0x55a6fcad0158 in R_execClosure eval.c
    #21 0x55a6fcacf64a in applyClosure_core eval.c
    #22 0x55a6fcab8f16 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9f16)
    #23 0x55a6fcab8447 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xc9447)
    #24 0x55a6fcb05777 in Rf_ReplIteration (/data/localhost/ripley/R/R-clang/bin/exec/R+0x116777)
    #25 0x55a6fcb0727e in run_Rmainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x11827e)
    #26 0x55a6fcb072ea in Rf_mainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1182ea)
    #27 0x55a6fc9f0db7 in main (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1db7)
    #28 0x7fe8bbb0b680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7)
    #29 0x7fe8bbb0b797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 17f2e1fd905f485786f6fd6e3bede4ad737137e7)
    #30 0x55a6fc9f0cd4 in _start (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1cd4)

SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior vsearch_main.cc:1346:10 
→ rchime removed `128` chimeras from your dataset.
→ It took `2.00326061248779` seconds to detect and remove the chimeras.
> data
multi_sample - 500 sequences:

            starts ends nbases ambigs polymers numns numseqs
Minimum:         1  250    250      0        3     0    1.00
2.5%-tile:       1  252    252      0        4     0  167.20
25%-tile:        1  252    252      0        4     0 1672.00
Median:          1  253    253      0        4     0 3344.00
75%-tile:        1  253    253      0        5     0 5016.00
97.5%-tile:      1  253    253      0        6     0 6520.80
Maximum:         1  255    255      0        6     0 6688.00
Mean:            1  252    252      0        4     0 3344.14

scrap_summary:
      type      trash_code unique total
1 sequence rchime_chimeras     90   128

Number of unique seqs: 410 
Total number of seqs: 6688 

Total number of samples: 20 
Total number of custom reports: 1 

> 
> 
> # Detect and remove chimeras from the dataset using de novo approach by
> # sample (recommended)
> 
> table <- readRDS(rchime_example("miseq_data_frame_by_sample_small.rds"))
> 
> data <- rchime(data = table)
ℹ The de novo method runs with a single processor.

→ rchime removed `128` chimeras from your dataset.
→ It took `1.85767507553101` seconds to detect and remove the chimeras.
> data
            starts ends nbases ambigs polymers numns numseqs
Minimum:         1  250    250      0        3     0    1.00
2.5%-tile:       1  252    252      0        4     0  167.20
25%-tile:        1  252    252      0        4     0 1672.00
Median:          1  253    253      0        4     0 3344.00
75%-tile:        1  253    253      0        5     0 5016.00
97.5%-tile:      1  253    253      0        6     0 6520.80
Maximum:         1  255    255      0        6     0 6688.00
Mean:            1  252    252      0        4     0 3344.14

scrap_summary:
      type      trash_code unique total
1 sequence rchime_chimeras     90   128

Number of unique seqs: 410 
Total number of seqs: 6688 

Total number of samples: 20 
Total number of custom reports: 1 

> 
> 
> 
> 
> cleanEx()
> nameEx("rchime_example")
> ### * rchime_example
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: rchime_example
> ### Title: Get path to rchime example files
> ### Aliases: rchime_example
> 
> ### ** Examples
> 
> rchime_example()
[1] "/data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime.Rcheck/rchime/extdata"
> rchime_example("silva.gold.rds")
[1] "/data/localhost/ripley/R/packages/tests-clang-UBSAN/rchime.Rcheck/rchime/extdata/silva.gold.rds"
> 
> 
> 
> cleanEx()
> nameEx("silva_gold")
> ### * silva_gold
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: silva_gold
> ### Title: silva_gold
> ### Aliases: silva_gold
> 
> ### ** Examples
> 
> 
> reference <- silva_gold()
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  6.858 0.428 7.664 0.003 0.014 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')