* using log directory ‘/srv/hornik/tmp/CRAN_pretest/rbiom.Rcheck’
* using R Under development (unstable) (2025-01-11 r87563)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.6 (1+b1)
    Debian flang-new version 19.1.6 (1+b1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘rbiom/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rbiom’ version ‘2.0.8’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [5s/8s] NOTE
Maintainer: ‘Daniel P. Smith <dansmith01@gmail.com>’

Days since last update: 1
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rbiom’ can be installed ... [26s/26s] OK
* used C++ compiler: ‘Debian clang version 19.1.6 (1+b1)’
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking whether startup messages can be suppressed ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [19s/20s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [2s/2s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [38s/37s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [10s/10s] ERROR
  Running ‘testthat.r’ [10s/9s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  > library(rbiom)
  > 
  > test_check("rbiom")
  [ FAIL 1 | WARN 0 | SKIP 32 | PASS 179 ]
  
  ══ Skipped tests (32) ══════════════════════════════════════════════════════════
  • On CRAN (32): 'test-as_rbiom.r:16:3', 'test-bdiv_heatmap.r:5:3',
    'test-bdiv_ord_plot.r:6:3', 'test-biom_merge.r:11:3', 'test-biom_ply.r:9:3',
    'test-biom_ply.r:48:3', 'test-boxplot.r:10:3', 'test-boxplot_build.r:3:3',
    'test-cache.r:3:3', 'test-corrplot.r:11:3', 'test-distmat_ord_table.r:6:3',
    'test-import_table.r:13:3', 'test-plot_heatmap.r:15:3',
    'test-plot_palettes.r:6:3', 'test-provenance.r:3:3', 'test-rarefy.r:3:3',
    'test-rbiom-deprecated.r:3:3', 'test-rbiom_objects.r:24:3',
    'test-read_biom.r:3:3', 'test-read_fasta.r:3:3', 'test-read_tree.r:7:3',
    'test-s3_methods.r:3:3', 'test-stats_emmeans.r:8:3',
    'test-stats_wilcox.r:3:3', 'test-taxa_heatmap.r:5:3', 'test-taxa_map.r:3:3',
    'test-taxa_stacked.r:5:3', 'test-taxa_table.r:3:3', 'test-utils.r:3:3',
    'test-validate.r:3:3', 'test-write_biom.r:15:3', 'test-write_xlsx.r:3:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-bdiv_table.r:7:3'): bdiv_table ───────────────────────────────
  round(...) (`actual`) not equal to c(0.2, 0.37, 0.42, 0.14, 0.21, 0.32, 0.25, 0.3, 0.41, 0.4) (`expected`).
  
    `actual`: 0.200 0.380 0.430 0.150 0.230 0.320 0.250 0.270 0.410 0.410
  `expected`: 0.200 0.370 0.420 0.140 0.210 0.320 0.250 0.300 0.410 0.400
  
  [ FAIL 1 | WARN 0 | SKIP 32 | PASS 179 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [5s/5s] OK
* checking HTML version of manual ... [3s/3s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE