Last updated on 2026-08-01 02:57:45 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.8 | 5.48 | 448.25 | 453.73 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.8 | 3.55 | 269.15 | 272.70 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.1.8 | 8.00 | 549.11 | 557.11 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.8 | 289.20 | ERROR | |||
| r-devel-windows-x86_64 | 0.1.8 | 9.00 | 370.00 | 379.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.8 | 5.88 | 409.37 | 415.25 | OK | |
| r-release-linux-x86_64 | 0.1.8 | 4.52 | 410.21 | 414.73 | OK | |
| r-release-macos-arm64 | 0.1.8 | 1.00 | 102.00 | 103.00 | OK | |
| r-release-macos-x86_64 | 0.1.8 | 4.00 | 612.00 | 616.00 | OK | |
| r-release-windows-x86_64 | 0.1.8 | 9.00 | 349.00 | 358.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.8 | OK | ||||
| r-oldrel-macos-x86_64 | 0.1.8 | 3.00 | 270.00 | 273.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.8 | 11.00 | 512.00 | 523.00 | OK |
Version: 0.1.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [160s/196s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(ulrb)
>
> test_check("ulrb")
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 2 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 5 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
Joining with `by = join_by(Sample, Level)`
Saving _problems/test-define_rb-264.R
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Ignoring unknown labels:
* fill : ""
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Missing argument sample_names. This is a vector with the names of the samples, as in the data input
Taxa_id assumes each column is a taxonomic unit.
Taxa_id assumes each column is a taxonomic unit.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-define_rb.R:263:3'): No warning, if there are no clusters with zero taxa ──
Expected `define_rb(no_singles, check_singles = TRUE)` not to throw any warnings.
Actually got a <rlang_warning> with message:
There were 4 warnings in `mutate()`.
The first warning was:
i In argument: `pam_object = purrr::map(...)`.
i In group 1: `Sample = "ERR2044665"`.
Caused by warning in `structure()`:
! Replacing special names '.Names' is deprecated; use 'names' instead.
i Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.8
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp0BJ1Cr’ ‘~/tmp/scratch/Rtmp0ezyRX’
‘~/tmp/scratch/Rtmp0psoYc’ ‘~/tmp/scratch/Rtmp0zOjFT’
‘~/tmp/scratch/Rtmp1Hgacl’ ‘~/tmp/scratch/Rtmp1ewrxH’
‘~/tmp/scratch/Rtmp1ykrhI’ ‘~/tmp/scratch/Rtmp21euu1’
‘~/tmp/scratch/Rtmp21kLja’ ‘~/tmp/scratch/Rtmp2M0NIz’
‘~/tmp/scratch/Rtmp2Org1H’ ‘~/tmp/scratch/Rtmp2cziXv’
‘~/tmp/scratch/Rtmp31DzJm’ ‘~/tmp/scratch/Rtmp3MeLFg’
‘~/tmp/scratch/Rtmp3Mhw3N’ ‘~/tmp/scratch/Rtmp3RAKdz’
‘~/tmp/scratch/Rtmp3nGqRo’ ‘~/tmp/scratch/Rtmp3qRaDF’
‘~/tmp/scratch/Rtmp3s6Cqm’ ‘~/tmp/scratch/Rtmp4Aylb6’
‘~/tmp/scratch/Rtmp4NTJbi’ ‘~/tmp/scratch/Rtmp4gCNvu’
‘~/tmp/scratch/Rtmp4tHKK3’ ‘~/tmp/scratch/Rtmp53eD63’
‘~/tmp/scratch/Rtmp5zu16S’ ‘~/tmp/scratch/Rtmp6SWIzC’
‘~/tmp/scratch/Rtmp6Y8Idc’ ‘~/tmp/scratch/Rtmp6vWTjJ’
‘~/tmp/scratch/Rtmp72giIG’ ‘~/tmp/scratch/Rtmp7x0232’
‘~/tmp/scratch/Rtmp89SZKB’ ‘~/tmp/scratch/Rtmp8NKkqK’
‘~/tmp/scratch/Rtmp8oOT5q’ ‘~/tmp/scratch/Rtmp9G2H8h’
‘~/tmp/scratch/Rtmp9ZqxUV’ ‘~/tmp/scratch/RtmpA4HiUO’
‘~/tmp/scratch/RtmpAv4OcW’ ‘~/tmp/scratch/RtmpB2uW47’
‘~/tmp/scratch/RtmpB85tAm’ ‘~/tmp/scratch/RtmpBcrAdg’
‘~/tmp/scratch/RtmpCqWkRd’ ‘~/tmp/scratch/RtmpCrdYuN’
‘~/tmp/scratch/RtmpCrnZBY’ ‘~/tmp/scratch/RtmpCt5VKD’
‘~/tmp/scratch/RtmpD4nvca’ ‘~/tmp/scratch/RtmpD7xFVO’
‘~/tmp/scratch/RtmpDFJCOX’ ‘~/tmp/scratch/RtmpDr1n3G’
‘~/tmp/scratch/RtmpDus3iY’ ‘~/tmp/scratch/RtmpDx6IJa’
‘~/tmp/scratch/RtmpFWRF5d’ ‘~/tmp/scratch/RtmpFe84DN’
‘~/tmp/scratch/RtmpFiuQQF’ ‘~/tmp/scratch/RtmpGJoXeW’
‘~/tmp/scratch/RtmpGnsyTn’ ‘~/tmp/scratch/RtmpGwWxuI’
‘~/tmp/scratch/RtmpHwa5Rq’ ‘~/tmp/scratch/RtmpIbaSCa’
‘~/tmp/scratch/RtmpIc4PEC’ ‘~/tmp/scratch/RtmpIphjtf’
‘~/tmp/scratch/RtmpJ4Y9qB’ ‘~/tmp/scratch/RtmpJAufug’
‘~/tmp/scratch/RtmpJDfUB3’ ‘~/tmp/scratch/RtmpJQGT00’
‘~/tmp/scratch/RtmpJjnuh9’ ‘~/tmp/scratch/RtmpKJ3z7Y’
‘~/tmp/scratch/RtmpL3Elaw’ ‘~/tmp/scratch/RtmpLPAUy5’
‘~/tmp/scratch/RtmpLfaeCt’ ‘~/tmp/scratch/RtmpM3RtOB’
‘~/tmp/scratch/RtmpM7VN4B’ ‘~/tmp/scratch/RtmpME16BG’
‘~/tmp/scratch/RtmpMRQ0SO’ ‘~/tmp/scratch/RtmpMUrq1j’
‘~/tmp/scratch/RtmpNgK9xP’ ‘~/tmp/scratch/RtmpOEKJtY’
‘~/tmp/scratch/RtmpOEyOnd’ ‘~/tmp/scratch/RtmpOIvcb6’
‘~/tmp/scratch/RtmpOLstbE’ ‘~/tmp/scratch/RtmpOR9TdM’
‘~/tmp/scratch/RtmpOnnAs6’ ‘~/tmp/scratch/RtmpP5gOAt’
‘~/tmp/scratch/RtmpPYQcUS’ ‘~/tmp/scratch/RtmpPkHv02’
‘~/tmp/scratch/RtmpQWVNy9’ ‘~/tmp/scratch/RtmpQiIwKP’
‘~/tmp/scratch/RtmpQki9KF’ ‘~/tmp/scratch/RtmpR3bbsk’
‘~/tmp/scratch/RtmpRLHwbC’ ‘~/tmp/scratch/RtmpRRyeEX’
‘~/tmp/scratch/RtmpRc5Oll’ ‘~/tmp/scratch/RtmpRg1u7k’
‘~/tmp/scratch/RtmpS9H98t’ ‘~/tmp/scratch/RtmpS9HuQC’
‘~/tmp/scratch/RtmpSq59tQ’ ‘~/tmp/scratch/RtmpT4MwdC’
‘~/tmp/scratch/RtmpTJGSu2’ ‘~/tmp/scratch/RtmpTbezrl’
‘~/tmp/scratch/RtmpTyIUci’ ‘~/tmp/scratch/RtmpU8k41U’
‘~/tmp/scratch/RtmpUEPn2I’ ‘~/tmp/scratch/RtmpUImnxJ’
‘~/tmp/scratch/RtmpUQHr9C’ ‘~/tmp/scratch/RtmpUepIAY’
‘~/tmp/scratch/RtmpUnbtL9’ ‘~/tmp/scratch/RtmpUv6fpW’
‘~/tmp/scratch/RtmpVLNpMU’ ‘~/tmp/scratch/RtmpVqUfUW’
‘~/tmp/scratch/RtmpW7OaFI’ ‘~/tmp/scratch/RtmpWEbQyB’
‘~/tmp/scratch/RtmpWJ2HEg’ ‘~/tmp/scratch/RtmpWLYwF7’
‘~/tmp/scratch/RtmpWNNJwh’ ‘~/tmp/scratch/RtmpWsTnDW’
‘~/tmp/scratch/RtmpXfc2nJ’ ‘~/tmp/scratch/RtmpYotJ5l’
‘~/tmp/scratch/RtmpZFIEl6’ ‘~/tmp/scratch/RtmpZWAP8L’
‘~/tmp/scratch/RtmpZnW4OX’ ‘~/tmp/scratch/Rtmpa3GDrX’
‘~/tmp/scratch/RtmpaK3KFO’ ‘~/tmp/scratch/RtmpaXSrMC’
‘~/tmp/scratch/Rtmpb7dFEV’ ‘~/tmp/scratch/RtmpbdBrGn’
‘~/tmp/scratch/Rtmpd0P1cf’ ‘~/tmp/scratch/RtmpdT6pkB’
‘~/tmp/scratch/RtmpdXPna3’ ‘~/tmp/scratch/RtmpengWTe’
‘~/tmp/scratch/Rtmpeqvviz’ ‘~/tmp/scratch/RtmpfKh0XD’
‘~/tmp/scratch/RtmpfZ4r5v’ ‘~/tmp/scratch/RtmpfwhutJ’
‘~/tmp/scratch/RtmpgAhsDr’ ‘~/tmp/scratch/RtmpgJUAvp’
‘~/tmp/scratch/RtmpgZNrwc’ ‘~/tmp/scratch/RtmphQ2lT1’
‘~/tmp/scratch/RtmphQcQQG’ ‘~/tmp/scratch/RtmphkdLGd’
‘~/tmp/scratch/RtmpiXgfcS’ ‘~/tmp/scratch/Rtmpirj1co’
‘~/tmp/scratch/RtmpkY3QZ3’ ‘~/tmp/scratch/RtmpkcWoNe’
‘~/tmp/scratch/RtmpkiX4qR’ ‘~/tmp/scratch/Rtmpkn9Qq4’
‘~/tmp/scratch/RtmpkpRGYI’ ‘~/tmp/scratch/Rtmpkqfbms’
‘~/tmp/scratch/RtmpkxBrUE’ ‘~/tmp/scratch/Rtmpl5wE6y’
‘~/tmp/scratch/Rtmpl9221g’ ‘~/tmp/scratch/RtmplbO5ID’
‘~/tmp/scratch/RtmpllhiE3’ ‘~/tmp/scratch/RtmpmPafMR’
‘~/tmp/scratch/RtmpmTiYuE’ ‘~/tmp/scratch/RtmpmxBOgn’
‘~/tmp/scratch/Rtmpn4NAzZ’ ‘~/tmp/scratch/RtmpnYhh3X’
‘~/tmp/scratch/RtmpncCniM’ ‘~/tmp/scratch/Rtmpo9KIca’
‘~/tmp/scratch/RtmpoEXklg’ ‘~/tmp/scratch/RtmpoFzcMz’
‘~/tmp/scratch/RtmpoRFFC5’ ‘~/tmp/scratch/Rtmpod84V6’
‘~/tmp/scratch/RtmpogGo01’ ‘~/tmp/scratch/Rtmpp791Eh’
‘~/tmp/scratch/Rtmppcq6CI’ ‘~/tmp/scratch/RtmpqkC2hs’
‘~/tmp/scratch/Rtmpqx0ukR’ ‘~/tmp/scratch/RtmprjjgPh’
‘~/tmp/scratch/RtmprnjyXv’ ‘~/tmp/scratch/Rtmpt0MF0n’
‘~/tmp/scratch/Rtmpt81xg0’ ‘~/tmp/scratch/RtmptPJKSX’
‘~/tmp/scratch/Rtmptcu6FK’ ‘~/tmp/scratch/RtmptuWqf8’
‘~/tmp/scratch/RtmpuUCs26’ ‘~/tmp/scratch/RtmpvCycO0’
‘~/tmp/scratch/RtmpvWU8ZN’ ‘~/tmp/scratch/RtmpvlGLXh’
‘~/tmp/scratch/Rtmpw2GFRo’ ‘~/tmp/scratch/RtmpwwqKpo’
‘~/tmp/scratch/RtmpxFmqlJ’ ‘~/tmp/scratch/RtmpxoXKpW’
‘~/tmp/scratch/RtmpyG81kq’ ‘~/tmp/scratch/Rtmpyxi93B’
‘~/tmp/scratch/RtmpzIGI1V’ ‘~/tmp/scratch/RtmpzXs4Oi’
‘~/tmp/scratch/xvfb-run.037wpq’ ‘~/tmp/scratch/xvfb-run.0Y4o2R’
‘~/tmp/scratch/xvfb-run.0vXJhD’ ‘~/tmp/scratch/xvfb-run.1AVr1R’
‘~/tmp/scratch/xvfb-run.3CQM3Y’ ‘~/tmp/scratch/xvfb-run.3e5bst’
‘~/tmp/scratch/xvfb-run.56grD5’ ‘~/tmp/scratch/xvfb-run.5UJL1q’
‘~/tmp/scratch/xvfb-run.5uexXy’ ‘~/tmp/scratch/xvfb-run.6uS17H’
‘~/tmp/scratch/xvfb-run.7oeIVI’ ‘~/tmp/scratch/xvfb-run.9JjTnh’
‘~/tmp/scratch/xvfb-run.AqWWHA’ ‘~/tmp/scratch/xvfb-run.B5deE7’
‘~/tmp/scratch/xvfb-run.BXsiLq’ ‘~/tmp/scratch/xvfb-run.Bc5sOa’
‘~/tmp/scratch/xvfb-run.C9n7DH’ ‘~/tmp/scratch/xvfb-run.D7044Q’
‘~/tmp/scratch/xvfb-run.DpvFme’ ‘~/tmp/scratch/xvfb-run.EIGCra’
‘~/tmp/scratch/xvfb-run.ElXtxi’ ‘~/tmp/scratch/xvfb-run.Ew8tko’
‘~/tmp/scratch/xvfb-run.FWxzXM’ ‘~/tmp/scratch/xvfb-run.Fisnnq’
‘~/tmp/scratch/xvfb-run.HZM5Bv’ ‘~/tmp/scratch/xvfb-run.IFQPZk’
‘~/tmp/scratch/xvfb-run.IJykK4’ ‘~/tmp/scratch/xvfb-run.ILbr79’
‘~/tmp/scratch/xvfb-run.Im3v8M’ ‘~/tmp/scratch/xvfb-run.KAqnWA’
‘~/tmp/scratch/xvfb-run.KYdTbJ’ ‘~/tmp/scratch/xvfb-run.L86h6f’
‘~/tmp/scratch/xvfb-run.LcQhhJ’ ‘~/tmp/scratch/xvfb-run.LqTY2e’
‘~/tmp/scratch/xvfb-run.MWIEES’ ‘~/tmp/scratch/xvfb-run.MZc9zE’
‘~/tmp/scratch/xvfb-run.PKeN0q’ ‘~/tmp/scratch/xvfb-run.PKnqYi’
‘~/tmp/scratch/xvfb-run.R1sOYI’ ‘~/tmp/scratch/xvfb-run.TA9cGN’
‘~/tmp/scratch/xvfb-run.TLODjj’ ‘~/tmp/scratch/xvfb-run.U4vhiE’
‘~/tmp/scratch/xvfb-run.UGRYDf’ ‘~/tmp/scratch/xvfb-run.UWMAc1’
‘~/tmp/scratch/xvfb-run.UbN4GU’ ‘~/tmp/scratch/xvfb-run.UlvIlJ’
‘~/tmp/scratch/xvfb-run.Ut9cYj’ ‘~/tmp/scratch/xvfb-run.VOewVD’
‘~/tmp/scratch/xvfb-run.Vx8O7S’ ‘~/tmp/scratch/xvfb-run.Xcbb5o’
‘~/tmp/scratch/xvfb-run.YnahKL’ ‘~/tmp/scratch/xvfb-run.Zg0EsG’
‘~/tmp/scratch/xvfb-run.a8jcVj’ ‘~/tmp/scratch/xvfb-run.aJNVKT’
‘~/tmp/scratch/xvfb-run.enTGxj’ ‘~/tmp/scratch/xvfb-run.gMIchH’
‘~/tmp/scratch/xvfb-run.hKVOUX’ ‘~/tmp/scratch/xvfb-run.halBDA’
‘~/tmp/scratch/xvfb-run.j7lpol’ ‘~/tmp/scratch/xvfb-run.kXCfkj’
‘~/tmp/scratch/xvfb-run.mQiRM6’ ‘~/tmp/scratch/xvfb-run.mZ6kfW’
‘~/tmp/scratch/xvfb-run.miAs93’ ‘~/tmp/scratch/xvfb-run.mlymww’
‘~/tmp/scratch/xvfb-run.sD8cB8’ ‘~/tmp/scratch/xvfb-run.sNwv8B’
‘~/tmp/scratch/xvfb-run.smPyLc’ ‘~/tmp/scratch/xvfb-run.tHoWJs’
‘~/tmp/scratch/xvfb-run.tW6i2e’ ‘~/tmp/scratch/xvfb-run.tnH7ak’
‘~/tmp/scratch/xvfb-run.tnPqvl’ ‘~/tmp/scratch/xvfb-run.u8hJSt’
‘~/tmp/scratch/xvfb-run.ufNQwX’ ‘~/tmp/scratch/xvfb-run.vPEGBH’
‘~/tmp/scratch/xvfb-run.wAC4J7’ ‘~/tmp/scratch/xvfb-run.x0ebUY’
‘~/tmp/scratch/xvfb-run.xaH58Z’ ‘~/tmp/scratch/xvfb-run.yWxyMk’
‘~/tmp/scratch/xvfb-run.you7qW’ ‘~/tmp/scratch/xvfb-run.zHQfZU’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [241s/269s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(ulrb)
>
> test_check("ulrb")
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 2 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 5 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
Joining with `by = join_by(Sample, Level)`
Saving _problems/test-define_rb-264.R
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Ignoring unknown labels:
* fill : ""
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Missing argument sample_names. This is a vector with the names of the samples, as in the data input
Taxa_id assumes each column is a taxonomic unit.
Taxa_id assumes each column is a taxonomic unit.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-define_rb.R:263:3'): No warning, if there are no clusters with zero taxa ──
Expected `define_rb(no_singles, check_singles = TRUE)` not to throw any warnings.
Actually got a <rlang_warning> with message:
There were 4 warnings in `mutate()`.
The first warning was:
i In argument: `pam_object = purrr::map(...)`.
i In group 1: `Sample = "ERR2044665"`.
Caused by warning in `structure()`:
! Replacing special names '.Names' is deprecated; use 'names' instead.
i Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.8
Check: tests
Result: ERROR
Running ‘testthat.R’ [101s/103s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(ulrb)
>
> test_check("ulrb")
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 2 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 5 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
Joining with `by = join_by(Sample, Level)`
Saving _problems/test-define_rb-264.R
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Ignoring unknown labels:
* fill : ""
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Missing argument sample_names. This is a vector with the names of the samples, as in the data input
Taxa_id assumes each column is a taxonomic unit.
Taxa_id assumes each column is a taxonomic unit.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-define_rb.R:263:3'): No warning, if there are no clusters with zero taxa ──
Expected `define_rb(no_singles, check_singles = TRUE)` not to throw any warnings.
Actually got a <rlang_warning> with message:
There were 4 warnings in `mutate()`.
The first warning was:
i In argument: `pam_object = purrr::map(...)`.
i In group 1: `Sample = "ERR2044665"`.
Caused by warning in `structure()`:
! Replacing special names '.Names' is deprecated; use 'names' instead.
i Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.1.8
Check: tests
Result: ERROR
Running 'testthat.R' [121s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # 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/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> library(testthat)
> library(ulrb)
>
> test_check("ulrb")
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
If half the observations within a classification are below 0.5 Silhouette score, we consider that the clustering was 'Bad'.
Check 'Evaluation' collumn for more details.
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 2 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 9 based on Calinski-Harabasz.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
K= 5 based on Average Silhouette Score.
Joining with `by = join_by(Sample, Level)`
Automatic option set to TRUE, so classification vector was overwritten
Joining with `by = join_by(Sample, Level)`
Saving _problems/test-define_rb-264.R
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Ignoring unknown labels:
* fill : ""
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Joining with `by = join_by(Sample, Level)`
Missing argument sample_names. This is a vector with the names of the samples, as in the data input
Taxa_id assumes each column is a taxonomic unit.
Taxa_id assumes each column is a taxonomic unit.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-define_rb.R:263:3'): No warning, if there are no clusters with zero taxa ──
Expected `define_rb(no_singles, check_singles = TRUE)` not to throw any warnings.
Actually got a <rlang_warning> with message:
There were 4 warnings in `mutate()`.
The first warning was:
i In argument: `pam_object = purrr::map(...)`.
i In group 1: `Sample = "ERR2044665"`.
Caused by warning in `structure()`:
! Replacing special names '.Names' is deprecated; use 'names' instead.
i Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
[ FAIL 1 | WARN 235 | SKIP 0 | PASS 153 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64