Last updated on 2026-08-02 01:53:27 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 | 3.52 | 265.28 | 268.80 | 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 | 5.05 | 411.83 | 416.88 | 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/Rtmp0Cnfe9’ ‘~/tmp/scratch/Rtmp0OrcLH’
‘~/tmp/scratch/Rtmp0cX103’ ‘~/tmp/scratch/Rtmp0sCIcH’
‘~/tmp/scratch/Rtmp1BuSup’ ‘~/tmp/scratch/Rtmp1CJN17’
‘~/tmp/scratch/Rtmp1IVlti’ ‘~/tmp/scratch/Rtmp1rgVvq’
‘~/tmp/scratch/Rtmp2FKRsV’ ‘~/tmp/scratch/Rtmp2Sl5va’
‘~/tmp/scratch/Rtmp2ctZI7’ ‘~/tmp/scratch/Rtmp2lhtrf’
‘~/tmp/scratch/Rtmp3gYxle’ ‘~/tmp/scratch/Rtmp3iMg6g’
‘~/tmp/scratch/Rtmp3lZ1n7’ ‘~/tmp/scratch/Rtmp48li0g’
‘~/tmp/scratch/Rtmp4MmFAX’ ‘~/tmp/scratch/Rtmp4g23MI’
‘~/tmp/scratch/Rtmp5EwE67’ ‘~/tmp/scratch/Rtmp5IrUgz’
‘~/tmp/scratch/Rtmp61cup7’ ‘~/tmp/scratch/Rtmp61xoid’
‘~/tmp/scratch/Rtmp6dbyYT’ ‘~/tmp/scratch/Rtmp7X5BvD’
‘~/tmp/scratch/Rtmp8LRsv5’ ‘~/tmp/scratch/Rtmp8MTiiy’
‘~/tmp/scratch/Rtmp9GmfzQ’ ‘~/tmp/scratch/Rtmp9Pib4N’
‘~/tmp/scratch/Rtmp9bFrcp’ ‘~/tmp/scratch/RtmpAH1cps’
‘~/tmp/scratch/RtmpAKHbpk’ ‘~/tmp/scratch/RtmpAjARBS’
‘~/tmp/scratch/RtmpAvGIxU’ ‘~/tmp/scratch/RtmpBCBdNL’
‘~/tmp/scratch/RtmpBcdG6y’ ‘~/tmp/scratch/RtmpBesAvR’
‘~/tmp/scratch/RtmpC2Cmma’ ‘~/tmp/scratch/RtmpC4pnAP’
‘~/tmp/scratch/RtmpCIYD5z’ ‘~/tmp/scratch/RtmpDA4Wlf’
‘~/tmp/scratch/RtmpDTqxol’ ‘~/tmp/scratch/RtmpDp1tyL’
‘~/tmp/scratch/RtmpDx6oME’ ‘~/tmp/scratch/RtmpE45t3Y’
‘~/tmp/scratch/RtmpE8KObO’ ‘~/tmp/scratch/RtmpElEDze’
‘~/tmp/scratch/RtmpEo1J55’ ‘~/tmp/scratch/RtmpEwUNLh’
‘~/tmp/scratch/RtmpFcgnBr’ ‘~/tmp/scratch/RtmpG4KTbk’
‘~/tmp/scratch/RtmpG9XQxp’ ‘~/tmp/scratch/RtmpGAg7N8’
‘~/tmp/scratch/RtmpGDbZLR’ ‘~/tmp/scratch/RtmpGUwpEP’
‘~/tmp/scratch/RtmpGldxCJ’ ‘~/tmp/scratch/RtmpGn7AXx’
‘~/tmp/scratch/RtmpGodr1j’ ‘~/tmp/scratch/RtmpGv9DkZ’
‘~/tmp/scratch/RtmpH6LuFI’ ‘~/tmp/scratch/RtmpHDQ61n’
‘~/tmp/scratch/RtmpI10rAw’ ‘~/tmp/scratch/RtmpI1A6ZB’
‘~/tmp/scratch/RtmpI54iBv’ ‘~/tmp/scratch/RtmpIC4zIA’
‘~/tmp/scratch/RtmpIux2wo’ ‘~/tmp/scratch/RtmpJQKqcS’
‘~/tmp/scratch/RtmpJtIRwJ’ ‘~/tmp/scratch/RtmpK3wQsl’
‘~/tmp/scratch/RtmpKEZPGm’ ‘~/tmp/scratch/RtmpKJ9JGr’
‘~/tmp/scratch/RtmpKqdARX’ ‘~/tmp/scratch/RtmpM2kTx7’
‘~/tmp/scratch/RtmpM7CUam’ ‘~/tmp/scratch/RtmpMvVL0e’
‘~/tmp/scratch/RtmpMyWshg’ ‘~/tmp/scratch/RtmpN0EcLs’
‘~/tmp/scratch/RtmpNZwDDo’ ‘~/tmp/scratch/RtmpNdM3yu’
‘~/tmp/scratch/RtmpNwnrv2’ ‘~/tmp/scratch/RtmpOCfiep’
‘~/tmp/scratch/RtmpOcjrYG’ ‘~/tmp/scratch/RtmpPIZCqe’
‘~/tmp/scratch/RtmpPanJRX’ ‘~/tmp/scratch/RtmpPxvN7P’
‘~/tmp/scratch/RtmpQIVU5m’ ‘~/tmp/scratch/RtmpR4nlqy’
‘~/tmp/scratch/RtmpSaS5uP’ ‘~/tmp/scratch/RtmpSm2bdc’
‘~/tmp/scratch/RtmpSyUmb7’ ‘~/tmp/scratch/RtmpTnYeBc’
‘~/tmp/scratch/RtmpTyaRmz’ ‘~/tmp/scratch/RtmpUPSbxu’
‘~/tmp/scratch/RtmpV6Dh50’ ‘~/tmp/scratch/RtmpX8FFkO’
‘~/tmp/scratch/RtmpXPJqz1’ ‘~/tmp/scratch/RtmpXmbN5V’
‘~/tmp/scratch/RtmpXnVjeS’ ‘~/tmp/scratch/RtmpXuucFu’
‘~/tmp/scratch/RtmpXz6CLO’ ‘~/tmp/scratch/RtmpYNSnWi’
‘~/tmp/scratch/RtmpYQCG38’ ‘~/tmp/scratch/RtmpYR8KhL’
‘~/tmp/scratch/RtmpYrdlU2’ ‘~/tmp/scratch/RtmpYuoWS4’
‘~/tmp/scratch/RtmpZTStwn’ ‘~/tmp/scratch/RtmpaDmVy9’
‘~/tmp/scratch/RtmpaKrw3f’ ‘~/tmp/scratch/RtmpaMYGQ3’
‘~/tmp/scratch/RtmpagMPJL’ ‘~/tmp/scratch/RtmpbSZ6YK’
‘~/tmp/scratch/RtmpcDfEs8’ ‘~/tmp/scratch/RtmpdfUVnC’
‘~/tmp/scratch/RtmpeBi9X4’ ‘~/tmp/scratch/RtmpeKwwaL’
‘~/tmp/scratch/RtmpeLKwP4’ ‘~/tmp/scratch/RtmpeYRQN9’
‘~/tmp/scratch/RtmpfXBIVa’ ‘~/tmp/scratch/RtmpgpjCSD’
‘~/tmp/scratch/RtmpgykNlh’ ‘~/tmp/scratch/RtmphJqVbn’
‘~/tmp/scratch/RtmphiaHjU’ ‘~/tmp/scratch/Rtmpi7uGxo’
‘~/tmp/scratch/Rtmpi9NZJV’ ‘~/tmp/scratch/RtmpiY6eFo’
‘~/tmp/scratch/RtmpihAy5w’ ‘~/tmp/scratch/RtmpirnSpS’
‘~/tmp/scratch/RtmpisTsYy’ ‘~/tmp/scratch/RtmpjhS77t’
‘~/tmp/scratch/RtmpjlvXE4’ ‘~/tmp/scratch/RtmpjrrpFN’
‘~/tmp/scratch/RtmpkGDXma’ ‘~/tmp/scratch/RtmpkGKd4j’
‘~/tmp/scratch/RtmpkVoAY8’ ‘~/tmp/scratch/RtmpknkStE’
‘~/tmp/scratch/Rtmpl0437p’ ‘~/tmp/scratch/Rtmpl41XPA’
‘~/tmp/scratch/Rtmplfcnub’ ‘~/tmp/scratch/RtmpmLDtKc’
‘~/tmp/scratch/RtmpmQv1Da’ ‘~/tmp/scratch/RtmpmX22hW’
‘~/tmp/scratch/RtmpmgbTy9’ ‘~/tmp/scratch/RtmpmsdXf2’
‘~/tmp/scratch/RtmpnVaP3x’ ‘~/tmp/scratch/RtmpnYk8Is’
‘~/tmp/scratch/Rtmpnxlbeh’ ‘~/tmp/scratch/RtmponjO40’
‘~/tmp/scratch/RtmpptrznJ’ ‘~/tmp/scratch/Rtmpq4Jp0e’
‘~/tmp/scratch/RtmpqJuLkV’ ‘~/tmp/scratch/RtmpqaCzSq’
‘~/tmp/scratch/RtmprBcDHD’ ‘~/tmp/scratch/Rtmps6Xa7w’
‘~/tmp/scratch/Rtmps6kMXc’ ‘~/tmp/scratch/RtmpsaRVoH’
‘~/tmp/scratch/RtmpsrsVjm’ ‘~/tmp/scratch/RtmptWrURd’
‘~/tmp/scratch/RtmptuEi1b’ ‘~/tmp/scratch/Rtmpu32T11’
‘~/tmp/scratch/RtmpuD7d44’ ‘~/tmp/scratch/Rtmpv6BiLc’
‘~/tmp/scratch/RtmpvgLwmf’ ‘~/tmp/scratch/RtmpvvHdhb’
‘~/tmp/scratch/Rtmpw8C8WP’ ‘~/tmp/scratch/RtmpwOpchc’
‘~/tmp/scratch/RtmpwUkDyP’ ‘~/tmp/scratch/RtmpwstxLx’
‘~/tmp/scratch/Rtmpx8hbzc’ ‘~/tmp/scratch/RtmpxOVZva’
‘~/tmp/scratch/RtmpxzHT7c’ ‘~/tmp/scratch/RtmpyBuP0H’
‘~/tmp/scratch/RtmpyvqANf’ ‘~/tmp/scratch/Rtmpz0xElc’
‘~/tmp/scratch/RtmpzGOFWV’ ‘~/tmp/scratch/RtmpzQh5Ye’
‘~/tmp/scratch/RtmpzWOIXx’ ‘~/tmp/scratch/RtmpzdCPCe’
‘~/tmp/scratch/RtmpzfjWf1’ ‘~/tmp/scratch/Rtmpzymzqp’
‘~/tmp/scratch/xvfb-run.01RgM4’ ‘~/tmp/scratch/xvfb-run.0EWJr0’
‘~/tmp/scratch/xvfb-run.1qjBtH’ ‘~/tmp/scratch/xvfb-run.3mFrNi’
‘~/tmp/scratch/xvfb-run.4R96dq’ ‘~/tmp/scratch/xvfb-run.5gohJC’
‘~/tmp/scratch/xvfb-run.5tNokm’ ‘~/tmp/scratch/xvfb-run.6MZcY9’
‘~/tmp/scratch/xvfb-run.6bhoOM’ ‘~/tmp/scratch/xvfb-run.6kr0X0’
‘~/tmp/scratch/xvfb-run.AiHsiq’ ‘~/tmp/scratch/xvfb-run.B3HNIq’
‘~/tmp/scratch/xvfb-run.ELlXnn’ ‘~/tmp/scratch/xvfb-run.ENaqh5’
‘~/tmp/scratch/xvfb-run.Fsp0Sp’ ‘~/tmp/scratch/xvfb-run.G4cy6v’
‘~/tmp/scratch/xvfb-run.GNs5Tw’ ‘~/tmp/scratch/xvfb-run.GeTo02’
‘~/tmp/scratch/xvfb-run.HYfUdd’ ‘~/tmp/scratch/xvfb-run.I1O62d’
‘~/tmp/scratch/xvfb-run.J6KJ7G’ ‘~/tmp/scratch/xvfb-run.JLwdLT’
‘~/tmp/scratch/xvfb-run.KQr7lw’ ‘~/tmp/scratch/xvfb-run.KmZvPC’
‘~/tmp/scratch/xvfb-run.MSrnIk’ ‘~/tmp/scratch/xvfb-run.NQMIAX’
‘~/tmp/scratch/xvfb-run.NjvEO8’ ‘~/tmp/scratch/xvfb-run.Nm2BwB’
‘~/tmp/scratch/xvfb-run.OTWKey’ ‘~/tmp/scratch/xvfb-run.OoBuo4’
‘~/tmp/scratch/xvfb-run.PuiM1p’ ‘~/tmp/scratch/xvfb-run.Pz2Zeo’
‘~/tmp/scratch/xvfb-run.Q93I1B’ ‘~/tmp/scratch/xvfb-run.QakaXD’
‘~/tmp/scratch/xvfb-run.RQYWVZ’ ‘~/tmp/scratch/xvfb-run.SMChks’
‘~/tmp/scratch/xvfb-run.U7O9Rk’ ‘~/tmp/scratch/xvfb-run.UvKiOY’
‘~/tmp/scratch/xvfb-run.UyRutF’ ‘~/tmp/scratch/xvfb-run.VLNr1Q’
‘~/tmp/scratch/xvfb-run.WM94Qa’ ‘~/tmp/scratch/xvfb-run.WcN5km’
‘~/tmp/scratch/xvfb-run.XjvUS6’ ‘~/tmp/scratch/xvfb-run.YM0coD’
‘~/tmp/scratch/xvfb-run.ZZxbLN’ ‘~/tmp/scratch/xvfb-run.Ze77IP’
‘~/tmp/scratch/xvfb-run.ZukmuT’ ‘~/tmp/scratch/xvfb-run.bAnGpi’
‘~/tmp/scratch/xvfb-run.dceFl9’ ‘~/tmp/scratch/xvfb-run.elGzQY’
‘~/tmp/scratch/xvfb-run.elQy0w’ ‘~/tmp/scratch/xvfb-run.hiPFZJ’
‘~/tmp/scratch/xvfb-run.iBeRjb’ ‘~/tmp/scratch/xvfb-run.iMW5jM’
‘~/tmp/scratch/xvfb-run.iiKXBq’ ‘~/tmp/scratch/xvfb-run.ijyPSh’
‘~/tmp/scratch/xvfb-run.iy3vt2’ ‘~/tmp/scratch/xvfb-run.jfuyrV’
‘~/tmp/scratch/xvfb-run.kdJkzY’ ‘~/tmp/scratch/xvfb-run.lzcfs3’
‘~/tmp/scratch/xvfb-run.mQlAK9’ ‘~/tmp/scratch/xvfb-run.mYO8mg’
‘~/tmp/scratch/xvfb-run.mZn5U0’ ‘~/tmp/scratch/xvfb-run.nCJHBn’
‘~/tmp/scratch/xvfb-run.nF0IRu’ ‘~/tmp/scratch/xvfb-run.o2AGxd’
‘~/tmp/scratch/xvfb-run.ooUIoB’ ‘~/tmp/scratch/xvfb-run.pufU3g’
‘~/tmp/scratch/xvfb-run.qToRg9’ ‘~/tmp/scratch/xvfb-run.qwy40r’
‘~/tmp/scratch/xvfb-run.s9H6xk’ ‘~/tmp/scratch/xvfb-run.ss1GkN’
‘~/tmp/scratch/xvfb-run.uTTqAl’ ‘~/tmp/scratch/xvfb-run.ugyfaC’
‘~/tmp/scratch/xvfb-run.ui4yEc’ ‘~/tmp/scratch/xvfb-run.wBTywW’
‘~/tmp/scratch/xvfb-run.xSvqFb’ ‘~/tmp/scratch/xvfb-run.yhpnn2’
‘~/tmp/scratch/xvfb-run.zI5XAv’ ‘~/tmp/scratch/xvfb-run.zp65Yl’
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