R Under development (unstable) (2026-06-24 r90190) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # 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(strollur) Attaching package: 'strollur' The following objects are masked from 'package:base': assign, names, summary > > test_check("strollur") bins is not a valid type for the abundance function. Types include: 'bin', 'sequence', sample' and 'treatment'. Added 3 sequences. Added 2425 sequences. Added 2 resource references. Assigned 3 sequence abundances. Assigned 2425 sequence abundances. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin representative sequences. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Assigned 531 otu bins. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence taxonomies. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin representative sequences. Assigned 531 otu bin taxonomies. Assigned 2425 asv bins. Assigned 2425 asv bin taxonomies. Assigned 63 phylotype bins. Assigned 63 phylotype bin taxonomies. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence taxonomies. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin representative sequences. Assigned 531 otu bin taxonomies. Assigned 2425 asv bins. Assigned 2425 asv bin taxonomies. Assigned 63 phylotype bins. Assigned 63 phylotype bin taxonomies. Added metadata. Added 2 resource references. Added a contigs_report. Assigned 3 otu bins. Added 3 sequences. Assigned 3 sequence abundances. Assigned 3 otu bins. Assigned 531 otu bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Added 531 sequences. Assigned 531 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin taxonomies. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 19 samples to treatments. Added 2425 sequences. Assigned 2425 sequence taxonomies. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Added 531 sequences. Assigned 531 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin taxonomies. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence taxonomies. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin representative sequences. Assigned 531 otu bin taxonomies. Assigned 2425 asv bins. Assigned 2425 asv bin taxonomies. Assigned 63 phylotype bins. Assigned 63 phylotype bin taxonomies. Added metadata. Added 2 resource references. Added a contigs_report. Added 4 sequences. Added 1 resource references. Assigned 4 sequence abundances. Assigned 2 otu bins. Added 4 sequences. Assigned 4 sequence abundances. Assigned 2 otu bins. Added 1 resource references. Added 2425 sequences. Added 19 sequences. > The strollur objects public field 'sequence_tree' are not equivalent. > The strollur objects public field 'sequence_tree' are not equivalent. Assigned 531 otu bins. Assigned 531 otu bins. > The strollur objects public field 'sample_tree' are not equivalent. > The strollur objects public field 'sample_tree' are not equivalent. > The strollur objects public field 'raw' are not equivalent. The strollur objects have different dataset names. Added 2425 sequences. The strollur objects have different sequence data statuses. Added 2425 sequences. Assigned 2425 sequence taxonomies. The strollur objects have different classification statuses. Assigned 2425 sequence taxonomies. The strollur objects have different number of unique sequences. Added 4 sequences. Added 4 sequences. The strollur objects include different sequence names. Added 4 sequences. Added 4 sequences. The strollur objects include different sequence strings. Added 4 sequences. Added 4 sequences. The strollur objects include different sequence comments. Assigned 4 sequence taxonomies. Assigned 4 sequence taxonomies. The strollur objects include different sequence taxonomies. Assigned 2 otu bins. Added 4 sequences. The strollur objects include different sequence bin assignment statuses. Assigned 2 otu bins. Added 1 resource references. The strollur objects include different resource_references. Assigned 4 sequence abundances. Assigned 4 sequence abundances. The strollur objects include different sequence abundance data. Assigned 4 sequence abundances. Assigned 2 otu bins. Assigned 2 otu bins. The strollur objects include different bin data. Added a contigs_report. Added 2425 sequences. The strollur objects include different report data. Added metadata. The strollur objects include different metadata. Added 4 sequences. Added 4 sequences. The strollur objects include different sequence trash codes. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Added a contigs_report. Added metadata. Added 2 resource references. starts ends nbases ambigs polymers numns numseqs Minimum: 1 375 249.0000 0 3.000000 0 1.000 2.5%-tile: 1 375 252.0000 0 4.000000 0 2849.075 25%-tile: 1 375 252.0000 0 4.000000 0 28490.750 Median: 1 375 253.0000 0 4.000000 0 56981.500 75%-tile: 1 375 253.0000 0 5.000000 0 85472.250 97.5%-tile: 1 375 254.0000 0 6.000000 0 111113.925 Maximum: 1 375 256.0000 0 6.000000 0 113963.000 Mean: 1 375 252.7406 0 4.496082 0 56981.643 Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Added 2425 sequences. Added 4 sequences. Added 4 sequences. Added 4 sequences. Added 4 sequences. Added 1 resource references. Assigned 4 sequence abundances. Assigned 2 otu bins. Assigned 531 otu bins. Assigned 531 otu bin taxonomies. Assigned 2425 sequence abundances. Assigned 2425 sequence abundances. Assigned 2425 sequence abundances. Assigned 4 sequence abundances. Assigned 4 sequence abundances. Assigned 4 sequence abundances. Assigned 3 otu bins. Assigned 3 otu bins. Assigned 3 otu bins. Assigned 531 otu bins. Assigned 531 otu bins. Assigned 4 sequence taxonomies. Added 1 resource references. Assigned 4 sequence taxonomies. Assigned 4 sequence taxonomies. Assigned 4 sequence taxonomies. Assigned 2 otu bins. Assigned 4 otu bins. Assigned 4 otu bin taxonomies. Added 1 resource references. Assigned 4 otu bin taxonomies. Assigned 531 otu bins. Assigned 531 otu bin taxonomies. Added metadata. Added 2 resource references. Added 1 resource references. Added 2 resource references. Added a align_report. Added 2 sequences. Your report does not contain an entry for every sequence in your dataset, ignoring report. Added a contigs_report. Added a contigs_report. Added 2 sequences. Your report does not contain an entry for every sequence in your dataset, ignoring report. Added a chimera_report. Added a chimera_report. Added a contigs_report. Added a alignment_report. Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns Minimum: 252.0 249 2 251 0 0 2.5%-tile: 252.0 249 2 251 0 0 25%-tile: 252.0 249 2 251 0 0 Median: 253.0 249 2 251 1 0 75%-tile: 253.0 249 2 251 2 0 97.5%-tile: 253.0 249 2 251 7 0 Maximum: 253.0 249 2 251 7 0 Mean: 252.6 249 2 251 2 0 Expected_Errors Minimum: 1.00000000 2.5%-tile: 1.00000000 25%-tile: 1.00000000 Median: 1.00000000 75%-tile: 1.00000000 97.5%-tile: 1.00000000 Maximum: 1.00000000 Mean: 0.01306454 QueryLength TemplateLength SearchScore QueryStart QueryEnd Minimum: 252.0 292.0 58.000 1 252.0 2.5%-tile: 252.0 292.0 59.000 1 252.0 25%-tile: 252.0 292.0 67.000 1 252.0 Median: 253.0 293.0 72.000 1 253.0 75%-tile: 253.0 293.0 75.000 1 253.0 97.5%-tile: 253.0 293.0 82.000 1 253.0 Maximum: 253.0 293.0 83.000 1 253.0 Mean: 252.6 292.6 70.434 1 252.6 TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery Minimum: 20 271.0 252.0 0 2.5%-tile: 20 271.0 252.0 0 25%-tile: 20 271.0 252.0 0 Median: 20 272.0 253.0 0 75%-tile: 20 272.0 253.0 0 97.5%-tile: 20 272.0 253.0 0 Maximum: 20 272.0 253.0 0 Mean: 20 271.6 252.6 0 GapsInTemplate LongestInsert SimBtwnQuery&Template Minimum: 0 0 93.000 2.5%-tile: 0 0 93.000 25%-tile: 0 0 95.000 Median: 0 0 95.000 75%-tile: 0 0 97.000 97.5%-tile: 0 0 98.000 Maximum: 0 0 98.000 Mean: 0 0 94.692 Added 4 sequences. Added 4 sequences. Added 4 sequences. > [WARNING]: Your tree does not contain a node for every sequence in your dataset, ignoring tree. Missing tree nodes for: seq4 . Added 2425 sequences. Added 4 sequences. > [Warning]: Your dataset does not contain sample data, ignoring sample tree. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 19 samples to treatments. > [WARNING]: Your tree does not contain a node for every sample in your dataset, ignoring tree. Missing tree nodes for: F3D0, F3D1, F3D141, F3D142, F3D143, F3D144, F3D145, F3D146, F3D147, F3D148, F3D149, F3D150, F3D2, F3D3, F3D5, F3D6, F3D7, F3D8, F3D9 . Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. data frame with 0 columns and 0 rows data frame with 0 columns and 0 rows Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 2425 sequence taxonomies. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 2425 sequence taxonomies. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin representative sequences. Added 2425 sequences. Assigned 2425 sequence abundances. Added 1 sequences. Added 2425 sequences. Added 2425 sequences. Added 3 sequences. Assigned 3 otu bins. Assigned 3 otu bins. Assigned 3 otu bins. Assigned 3 otu bins. Assigned 4 sequence abundances. Assigned 2 otu bins. Assigned 4 sequence abundances. Assigned 2 sequence abundances. Assigned 4 sequence taxonomies. Assigned 4 sequence abundances. Assigned 3 samples to treatments. Assigned 4 sequence abundances. Assigned 4 sequence abundances. Assigned 2 otu bins. Assigned 3 otu bins. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 4 sequence taxonomies. Assigned 3 otu bins. Assigned 4 sequence taxonomies. Added 100 sequences. Assigned 100 sequence abundances. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 19 samples to treatments. Added 6 sequences. Assigned 6 sequence abundances. Assigned 531 otu bins. Assigned 531 otu bin taxonomies. Assigned 531 asv bins. Assigned 531 phylotype bins. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bins. Assigned 531 otu bins. Added 591 sequences. Assigned 591 sequence abundances. Added 531 sequences. Assigned 531 sequence abundances. Assigned 531 sequence taxonomies. Added metadata. Added 759 sequences. Assigned 759 sequence abundances. Assigned 759 asv bins. Assigned 759 asv bin taxonomies. Added a contigs_report. Added 3 sequences. Added 3 sequences. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. starts ends nbases ambigs polymers numns numseqs Minimum: 1 375 249.0000 0 3.000000 0 1.00 2.5%-tile: 1 375 252.0000 0 4.000000 0 2694.30 25%-tile: 1 375 252.0000 0 4.000000 0 26943.00 Median: 1 375 253.0000 0 4.000000 0 53886.00 75%-tile: 1 375 253.0000 0 5.000000 0 80829.00 97.5%-tile: 1 375 254.0000 0 6.000000 0 105077.70 Maximum: 1 375 256.0000 0 6.000000 0 107772.00 Mean: 1 375 252.7345 0 4.493546 0 53886.14 Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Assigned 531 otu bins. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. adding: tmp/RtmpDCS9Q8/tmp/ (stored 0%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.sequence.tree (deflated 77%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.sample.tree (deflated 57%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.resource_reference (deflated 43%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.contigs_report (deflated 81%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.metadata (deflated 48%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.phylotype.cons.taxonomy (deflated 85%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.asv.cons.taxonomy (deflated 96%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.otu.cons.taxonomy (deflated 95%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.phylotype.shared (deflated 67%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.asv.shared (deflated 89%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.otu.shared (deflated 79%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.phylotype.list (deflated 83%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.asv.list (deflated 82%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.otu.list (deflated 82%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.design (deflated 65%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.count_table (deflated 81%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.taxonomy (deflated 91%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.fasta (deflated 92%) Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Added 2 resource references. Added metadata. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. adding: tmp/RtmpDCS9Q8/tmp/ (stored 0%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.design (deflated 65%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.phylotype.cons.taxonomy (deflated 85%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.asv.cons.taxonomy (deflated 96%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.otu.cons.taxonomy (deflated 95%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.phylotype.shared (deflated 67%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.asv.shared (deflated 89%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.otu.shared (deflated 79%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.count_table (deflated 81%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.phylotype.list (deflated 83%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.asv.list (deflated 82%) adding: tmp/RtmpDCS9Q8/tmp/miseq_sop.otu.list (deflated 82%) Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Added a alignment_report. Added a contigs_report. adding: tmp/RtmpDCS9Q8/tmp/ (stored 0%) adding: tmp/RtmpDCS9Q8/tmp/strollur.1782356107.contigs_report (deflated 44%) adding: tmp/RtmpDCS9Q8/tmp/strollur.1782356107.alignment_report (deflated 57%) Added a alignment_report. Added a contigs_report. Added a chimera_report. adding: tmp/RtmpDCS9Q8/tmp/ (stored 0%) adding: tmp/RtmpDCS9Q8/tmp/strollur.1782356107.chimera_report (deflated 82%) adding: tmp/RtmpDCS9Q8/tmp/strollur.1782356107.count_table (deflated 79%) Added a chimera_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Added 6 sequences. Assigned 6 sequence abundances. Added 6 sequences. Assigned 6 sequence abundances. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Assigned 531 otu bins. Assigned 19 samples to treatments. Assigned 531 otu bins. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 531 sequences. Assigned 531 sequence abundances. Assigned 531 sequence taxonomies. Added 19216 sequences. Assigned 19216 sequence abundances. Assigned 19216 sequence taxonomies. Added metadata. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Added metadata. Assigned 19 samples to treatments. Added 2425 sequences. Assigned 2425 sequence abundances. Assigned 2425 sequence taxonomies. Assigned 531 otu bins. Assigned 2425 asv bins. Assigned 63 phylotype bins. Assigned 19 samples to treatments. Assigned 531 otu bin taxonomies. Assigned 531 otu bin representative sequences. Added metadata. Added 2 resource references. Added a contigs_report. Assigned 531 otu bins. Added 2425 sequences. Added 2 resource references. Added 2425 sequences. Added a align_report. Added 4 sequences. Assigned 531 otu bins. Assigned 2 otu bins. Assigned 2 otu bin representative sequences. Assigned 531 otu bins. Assigned 531 otu bin taxonomies. Assigned 4 sequence abundances. Assigned 4 sequence taxonomies. Assigned 4 sequence taxonomies. Assigned 531 otu bins. Assigned 19 samples to treatments. Assigned 531 otu bins. Assigned 531 otu bin taxonomies. Assigned 4 sequence abundances. ================================================================= ==1812309==ERROR: AddressSanitizer: heap-buffer-overflow on address 0x7b3efd8e8894 at pc 0x7b1ef028f8ed bp 0x7ffcde48f430 sp 0x7ffcde48f428 READ of size 4 at 0x7b3efd8e8894 thread T0 #0 0x7b1ef028f8ec in AbundTable::setAbundance(int, std::__1::vector> const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/strollur/src/abundtable.cpp:717:56 #1 0x7b1ef030e8f2 in Dataset::setAbundances(std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>> const&, std::__1::vector>, std::__1::allocator>>> const&, std::__1::basic_string, std::__1::allocator> const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/strollur/src/dataset.cpp:1786:31 #2 0x7b1ef036e961 in xdev_set_abundances(Rcpp::Environment_Impl const&, std::__1::vector, std::__1::allocator>, std::__1::allocator, std::__1::allocator>>> const&, std::__1::vector>, std::__1::allocator>>> const&, std::__1::basic_string, std::__1::allocator> const&) /data/gannet/ripley/R/packages/tests-clang-ASAN/strollur/src/rcpp_xint_xdev_functions.cpp:1153:19 #3 0x7b1ef0266679 in _strollur_xdev_set_abundances /data/gannet/ripley/R/packages/tests-clang-ASAN/strollur/src/RcppExports.cpp:477:34 #4 0x55ce441a5016 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11 #5 0x55ce4426dc7d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #6 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #7 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #8 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #9 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #10 0x55ce4425730e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #11 0x55ce44254c78 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #12 0x55ce4425655a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #13 0x55ce44281101 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867:6 #14 0x55ce44281101 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880:20 #15 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #16 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #17 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #18 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #19 0x55ce4425730e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #20 0x55ce44254c78 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #21 0x55ce442adb15 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #22 0x55ce44254790 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #23 0x55ce442ab1b9 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #24 0x55ce44254790 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #25 0x55ce442b25a3 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #26 0x55ce442626ca in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #27 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #28 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #29 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #30 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #31 0x55ce4425730e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #32 0x55ce44254c78 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #33 0x55ce442b2f0a in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3993:9 #34 0x55ce442626ca in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #35 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #36 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #37 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #38 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #39 0x55ce442a5694 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #40 0x55ce442a5694 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2465:8 #41 0x55ce4405cd11 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75:8 #42 0x55ce4435c409 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1424:11 #43 0x55ce44267ee3 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8170:15 #44 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #45 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #46 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #47 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #48 0x55ce4425730e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #49 0x55ce44254c78 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #50 0x55ce44325b31 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264:23 #51 0x55ce44328360 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317:11 #52 0x55ce44328360 in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235:5 #53 0x55ce443283f2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242:5 #54 0x55ce44029d3c in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29:5 #55 0x7f1f00911574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #56 0x7f1f00911627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #57 0x55ce43f417d4 in _start (/data/gannet/ripley/R/clang-ASAN/bin/exec/R+0x17d4) 0x7b3efd8e8894 is located 0 bytes after 4-byte region [0x7b3efd8e8890,0x7b3efd8e8894) allocated by thread T0 here: #0 0x55ce43fe6bb4 in malloc /home/runner/work/llvm-project/llvm-project/compiler-rt/lib/asan/asan_malloc_linux.cpp:67:3 #1 0x7f1efe41f3fb in operator new(unsigned long) (/lib64/libstdc++.so.6+0x1f3fb) (BuildId: 51787ae23973475ac7373bc252b400c7229de8e7) #2 0x7b1ef027f34e in Rcpp::traits::RangeExporter>>::get() /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/internal/Exporter.h:46:13 #3 0x7b1ef027f34e in std::__1::vector> Rcpp::internal::as>>(SEXPREC*, Rcpp::traits::r_type_generic_tag) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/as.h:88:29 #4 0x7b1ef027f34e in std::__1::vector> Rcpp::as>>(SEXPREC*) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/as.h:151:16 #5 0x7b1ef027f34e in void Rcpp::internal::export_range__dispatch>*>, std::__1::vector>>(SEXPREC*, std::__1::__wrap_iter>*>, Rcpp::traits::r_type_generic_tag) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/api/meat/export.h:32:22 #6 0x7b1ef0266597 in void Rcpp::internal::export_range>*>>(SEXPREC*, std::__1::__wrap_iter>*>) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/internal/export.h:94:4 #7 0x7b1ef0266597 in Rcpp::traits::RangeExporter>, std::__1::allocator>>>>::get() /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/internal/Exporter.h:47:11 #8 0x7b1ef0266597 in std::__1::vector>, std::__1::allocator>>> Rcpp::internal::as>, std::__1::allocator>>>>(SEXPREC*, Rcpp::traits::r_type_generic_tag) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/as.h:88:29 #9 0x7b1ef0266597 in std::__1::vector>, std::__1::allocator>>> Rcpp::as>, std::__1::allocator>>>>(SEXPREC*) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/as.h:151:16 #10 0x7b1ef0266597 in Rcpp::ConstReferenceInputParameter>, std::__1::allocator>>>>::ConstReferenceInputParameter(SEXPREC*) /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/InputParameter.h:72:54 #11 0x7b1ef0266597 in _strollur_xdev_set_abundances /data/gannet/ripley/R/packages/tests-clang-ASAN/strollur/src/RcppExports.cpp:475:73 #12 0x55ce441a5016 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763:11 #13 0x55ce4426dc7d in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8700:21 #14 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #15 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #16 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #17 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #18 0x55ce4425730e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #19 0x55ce44254c78 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #20 0x55ce4425655a in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976:13 #21 0x55ce44281101 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5867:6 #22 0x55ce44281101 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7880:20 #23 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #24 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #25 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #26 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 #27 0x55ce4425730e in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2333:16 #28 0x55ce44254c78 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1278:12 #29 0x55ce442adb15 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3585:8 #30 0x55ce44254790 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #31 0x55ce442ab1b9 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3001:10 #32 0x55ce44254790 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1230:12 #33 0x55ce442b25a3 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3975:13 #34 0x55ce442626ca in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8150:14 #35 0x55ce44255cc4 in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7533:16 #36 0x55ce44254251 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167:8 #37 0x55ce4429c9ec in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2398:39 #38 0x55ce4429bba8 in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2314:16 SUMMARY: AddressSanitizer: heap-buffer-overflow /data/gannet/ripley/R/packages/tests-clang-ASAN/strollur/src/abundtable.cpp:717:56 in AbundTable::setAbundance(int, std::__1::vector> const&) Shadow bytes around the buggy address: 0x7b3efd8e8600: fa fa fa fa fa fa fd fa fa fa fd fa fa fa fd fa 0x7b3efd8e8680: fa fa fd fa fa fa 04 fa fa fa fa fa fa fa fd fa 0x7b3efd8e8700: fa fa fd fa fa fa fa fa fa fa fa fa fa fa fa fa 0x7b3efd8e8780: fa fa 04 fa fa fa fa fa fa fa fd fd fa fa fa fa 0x7b3efd8e8800: fa fa fd fd fa fa fa fa fa fa fd fa fa fa fa fa =>0x7b3efd8e8880: fa fa[04]fa fa fa fd fd fa fa fd fa fa fa fa fa 0x7b3efd8e8900: fa fa fa fa fa fa fd fa fa fa fa fa fa fa fd fd 0x7b3efd8e8980: fa fa fd fa fa fa fa fa fa fa fd fa fa fa 04 fa 0x7b3efd8e8a00: fa fa fd fd fa fa fd fa fa fa fa fa fa fa fd fa 0x7b3efd8e8a80: fa fa fd fa fa fa fa fa fa fa fa fa fa fa fd fa 0x7b3efd8e8b00: fa fa fa fa fa fa fd fa fa fa fa fa fa fa fd fa Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user: f7 Container overflow: fc Array cookie: ac Intra object redzone: bb ASan internal: fe Left alloca redzone: ca Right alloca redzone: cb ==1812309==ABORTING