Last updated on 2026-08-03 09:50:44 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 303.33 | 146.91 | 450.24 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 299.03 | 134.16 | 433.19 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 337.00 | 241.39 | 578.39 | NOTE | |
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 322.00 | 103.06 | 425.06 | ERROR | |
| r-devel-windows-x86_64 | 0.2.0 | 368.00 | 192.00 | 560.00 | NOTE | |
| r-patched-linux-x86_64 | 0.2.0 | 353.33 | 179.31 | 532.64 | NOTE | |
| r-release-linux-x86_64 | 0.2.0 | 379.22 | 178.28 | 557.50 | NOTE | |
| r-release-macos-arm64 | 0.2.0 | 65.00 | -5.00 | 60.00 | NOTE | |
| r-release-macos-x86_64 | 0.2.0 | 208.00 | 128.00 | 336.00 | NOTE | |
| r-release-windows-x86_64 | 0.2.0 | 377.00 | 196.00 | 573.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.2.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.2.0 | 195.00 | 28.00 | 223.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.2.0 | 521.00 | 262.00 | 783.00 | NOTE |
Version: 0.2.0
Check: DESCRIPTION meta-information
Result: NOTE
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘getPrevalence.R’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.2.0
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
‘~/tmp/scratch/Rtmp1Le8LN’ ‘~/tmp/scratch/Rtmp1aVznL’
‘~/tmp/scratch/Rtmp2UKymi’ ‘~/tmp/scratch/Rtmp2zbVcl’
‘~/tmp/scratch/Rtmp3AdQsq’ ‘~/tmp/scratch/Rtmp3MxiyU’
‘~/tmp/scratch/Rtmp3ckO1d’ ‘~/tmp/scratch/Rtmp4MrDP7’
‘~/tmp/scratch/Rtmp58oEov’ ‘~/tmp/scratch/Rtmp5He5Vm’
‘~/tmp/scratch/Rtmp5WA2SB’ ‘~/tmp/scratch/Rtmp5f1IdJ’
‘~/tmp/scratch/Rtmp6e7XIa’ ‘~/tmp/scratch/Rtmp7hzwLe’
‘~/tmp/scratch/Rtmp8DLwU4’ ‘~/tmp/scratch/Rtmp9Eps1A’
‘~/tmp/scratch/Rtmp9JeHSe’ ‘~/tmp/scratch/Rtmp9TuKm2’
‘~/tmp/scratch/Rtmp9X6S8F’ ‘~/tmp/scratch/Rtmp9l94NE’
‘~/tmp/scratch/RtmpA32EVY’ ‘~/tmp/scratch/RtmpAHJS4r’
‘~/tmp/scratch/RtmpARVhcY’ ‘~/tmp/scratch/RtmpB1nwhg’
‘~/tmp/scratch/RtmpBOQI4f’ ‘~/tmp/scratch/RtmpBkpcVO’
‘~/tmp/scratch/RtmpCEPpxB’ ‘~/tmp/scratch/RtmpCyktCv’
‘~/tmp/scratch/RtmpD2rCCb’ ‘~/tmp/scratch/RtmpDJu6qO’
‘~/tmp/scratch/RtmpDXacOi’ ‘~/tmp/scratch/RtmpDsJ1Ro’
‘~/tmp/scratch/RtmpDxoocX’ ‘~/tmp/scratch/RtmpDzNUyY’
‘~/tmp/scratch/RtmpE4yKSV’ ‘~/tmp/scratch/RtmpEwq9Db’
‘~/tmp/scratch/RtmpF2U4OK’ ‘~/tmp/scratch/RtmpFSH6Jx’
‘~/tmp/scratch/RtmpFhPX0i’ ‘~/tmp/scratch/RtmpGT7VxL’
‘~/tmp/scratch/RtmpH86jKC’ ‘~/tmp/scratch/RtmpHDv5f4’
‘~/tmp/scratch/RtmpJ68s8P’ ‘~/tmp/scratch/RtmpJtmpLV’
‘~/tmp/scratch/RtmpKsNm8c’ ‘~/tmp/scratch/RtmpKvGkpC’
‘~/tmp/scratch/RtmpL2KI4k’ ‘~/tmp/scratch/RtmpLwiVOm’
‘~/tmp/scratch/RtmpMReO9z’ ‘~/tmp/scratch/RtmpN5oNZs’
‘~/tmp/scratch/RtmpN7qpr7’ ‘~/tmp/scratch/RtmpNBok7l’
‘~/tmp/scratch/RtmpOVRLYO’ ‘~/tmp/scratch/RtmpPH6A1q’
‘~/tmp/scratch/RtmpQSiK5z’ ‘~/tmp/scratch/RtmpQWLgqO’
‘~/tmp/scratch/RtmpQxTilm’ ‘~/tmp/scratch/RtmpRGzCvX’
‘~/tmp/scratch/RtmpROFXEP’ ‘~/tmp/scratch/RtmpRaxNvU’
‘~/tmp/scratch/RtmpRbrvH3’ ‘~/tmp/scratch/RtmpSQl5mO’
‘~/tmp/scratch/RtmpT3Tgr6’ ‘~/tmp/scratch/RtmpTVIlxA’
‘~/tmp/scratch/RtmpTufKcD’ ‘~/tmp/scratch/RtmpU1gPaE’
‘~/tmp/scratch/RtmpUVSRYI’ ‘~/tmp/scratch/RtmpUXzrVx’
‘~/tmp/scratch/RtmpUY2I8k’ ‘~/tmp/scratch/RtmpUccAyJ’
‘~/tmp/scratch/RtmpUdYsJs’ ‘~/tmp/scratch/RtmpV6OGyu’
‘~/tmp/scratch/RtmpV8ItGH’ ‘~/tmp/scratch/RtmpVYgInW’
‘~/tmp/scratch/RtmpVbtP6U’ ‘~/tmp/scratch/RtmpVoRMRC’
‘~/tmp/scratch/RtmpW0Q174’ ‘~/tmp/scratch/RtmpW2mCZX’
‘~/tmp/scratch/RtmpWy82wg’ ‘~/tmp/scratch/RtmpXDkK4b’
‘~/tmp/scratch/RtmpXJAA9W’ ‘~/tmp/scratch/RtmpXOmId0’
‘~/tmp/scratch/RtmpXWnoFK’ ‘~/tmp/scratch/RtmpY1NZg5’
‘~/tmp/scratch/RtmpY9doqS’ ‘~/tmp/scratch/RtmpZuW4DE’
‘~/tmp/scratch/RtmpaGLKAb’ ‘~/tmp/scratch/RtmpaL7SFQ’
‘~/tmp/scratch/RtmpaVcOsn’ ‘~/tmp/scratch/Rtmpas9LPG’
‘~/tmp/scratch/Rtmpb1hM8J’ ‘~/tmp/scratch/Rtmpb5ph6H’
‘~/tmp/scratch/RtmpbnljBv’ ‘~/tmp/scratch/RtmpbuVwlY’
‘~/tmp/scratch/Rtmpc296Wm’ ‘~/tmp/scratch/Rtmpc2wsbx’
‘~/tmp/scratch/Rtmpc6Yeuz’ ‘~/tmp/scratch/Rtmpczh71Q’
‘~/tmp/scratch/Rtmpd1ib16’ ‘~/tmp/scratch/RtmpdaHqrd’
‘~/tmp/scratch/RtmpdcAc7X’ ‘~/tmp/scratch/Rtmpe1yMZD’
‘~/tmp/scratch/RtmpeYbszR’ ‘~/tmp/scratch/RtmpfB0G1g’
‘~/tmp/scratch/Rtmpgddo9U’ ‘~/tmp/scratch/RtmpghvvNo’
‘~/tmp/scratch/RtmphAuObi’ ‘~/tmp/scratch/RtmphdKtcn’
‘~/tmp/scratch/RtmphyhhRd’ ‘~/tmp/scratch/RtmpiVexvW’
‘~/tmp/scratch/RtmpioNfOh’ ‘~/tmp/scratch/RtmpiwwiCw’
‘~/tmp/scratch/Rtmpj2KyLk’ ‘~/tmp/scratch/Rtmpj49IBg’
‘~/tmp/scratch/RtmpjD9zTP’ ‘~/tmp/scratch/RtmpjLAEYt’
‘~/tmp/scratch/RtmpjNK4zp’ ‘~/tmp/scratch/RtmpjRtbEJ’
‘~/tmp/scratch/RtmpjY40so’ ‘~/tmp/scratch/RtmpkP3BWj’
‘~/tmp/scratch/RtmpkiqB92’ ‘~/tmp/scratch/Rtmpkv62CS’
‘~/tmp/scratch/Rtmpl94dte’ ‘~/tmp/scratch/RtmplZ2Y6X’
‘~/tmp/scratch/RtmplwiFk3’ ‘~/tmp/scratch/Rtmpm3Owba’
‘~/tmp/scratch/Rtmpn3dGYl’ ‘~/tmp/scratch/RtmpoX9ZrC’
‘~/tmp/scratch/RtmpojXSoB’ ‘~/tmp/scratch/RtmppY0EsM’
‘~/tmp/scratch/RtmppgpYyn’ ‘~/tmp/scratch/Rtmpq7Nqu0’
‘~/tmp/scratch/RtmpqtIMVP’ ‘~/tmp/scratch/RtmpqyYiwu’
‘~/tmp/scratch/RtmpsFmeBh’ ‘~/tmp/scratch/RtmpsflMKS’
‘~/tmp/scratch/RtmpsmB8YE’ ‘~/tmp/scratch/Rtmpt1vZzn’
‘~/tmp/scratch/RtmptG8t7N’ ‘~/tmp/scratch/RtmptUUv7x’
‘~/tmp/scratch/RtmpuYb1MB’ ‘~/tmp/scratch/Rtmpv2ITqU’
‘~/tmp/scratch/RtmpvZ2OAx’ ‘~/tmp/scratch/RtmpwtDRkD’
‘~/tmp/scratch/RtmpwxIPG2’ ‘~/tmp/scratch/Rtmpx79t3l’
‘~/tmp/scratch/RtmpxUXgsQ’ ‘~/tmp/scratch/RtmpxuOKDt’
‘~/tmp/scratch/Rtmpy8OC2Q’ ‘~/tmp/scratch/RtmpyniwvD’
‘~/tmp/scratch/RtmpysDTRL’ ‘~/tmp/scratch/Rtmpz0F2BI’
‘~/tmp/scratch/RtmpzBpCK1’ ‘~/tmp/scratch/RtmpzFJkhk’
‘~/tmp/scratch/RtmpzZqFL3’ ‘~/tmp/scratch/RtmpzbOjcO’
‘~/tmp/scratch/RtmpzhK7t9’ ‘~/tmp/scratch/ccYCfFgo.s’
‘~/tmp/scratch/ccySb52d.s’ ‘~/tmp/scratch/xvfb-run.09qult’
‘~/tmp/scratch/xvfb-run.0KWX6x’ ‘~/tmp/scratch/xvfb-run.1A9wQM’
‘~/tmp/scratch/xvfb-run.1P6njl’ ‘~/tmp/scratch/xvfb-run.1rQc3c’
‘~/tmp/scratch/xvfb-run.2jBvxV’ ‘~/tmp/scratch/xvfb-run.3RYjFu’
‘~/tmp/scratch/xvfb-run.4Po1gz’ ‘~/tmp/scratch/xvfb-run.7Ika9E’
‘~/tmp/scratch/xvfb-run.8FXrP0’ ‘~/tmp/scratch/xvfb-run.8PGVCQ’
‘~/tmp/scratch/xvfb-run.9a0hMT’ ‘~/tmp/scratch/xvfb-run.9fcyxz’
‘~/tmp/scratch/xvfb-run.9tAdP0’ ‘~/tmp/scratch/xvfb-run.9xuiPj’
‘~/tmp/scratch/xvfb-run.9zffqM’ ‘~/tmp/scratch/xvfb-run.Awl1pv’
‘~/tmp/scratch/xvfb-run.EWJSll’ ‘~/tmp/scratch/xvfb-run.F4i3WJ’
‘~/tmp/scratch/xvfb-run.FSPOgO’ ‘~/tmp/scratch/xvfb-run.Ggi2ZR’
‘~/tmp/scratch/xvfb-run.HXeVAp’ ‘~/tmp/scratch/xvfb-run.JZ9JHr’
‘~/tmp/scratch/xvfb-run.MYRm3T’ ‘~/tmp/scratch/xvfb-run.N8TXT6’
‘~/tmp/scratch/xvfb-run.N9II0h’ ‘~/tmp/scratch/xvfb-run.Ooknvs’
‘~/tmp/scratch/xvfb-run.PWFn3X’ ‘~/tmp/scratch/xvfb-run.QeYl3U’
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‘~/tmp/scratch/xvfb-run.XKOAdX’ ‘~/tmp/scratch/xvfb-run.cbglLu’
‘~/tmp/scratch/xvfb-run.ccjjJd’ ‘~/tmp/scratch/xvfb-run.cvgXCW’
‘~/tmp/scratch/xvfb-run.dnkt5c’ ‘~/tmp/scratch/xvfb-run.iJmGsV’
‘~/tmp/scratch/xvfb-run.iRnT6L’ ‘~/tmp/scratch/xvfb-run.jdVX5E’
‘~/tmp/scratch/xvfb-run.k6VkQE’ ‘~/tmp/scratch/xvfb-run.knof2b’
‘~/tmp/scratch/xvfb-run.l4e3CR’ ‘~/tmp/scratch/xvfb-run.lJXlyw’
‘~/tmp/scratch/xvfb-run.mhss3j’ ‘~/tmp/scratch/xvfb-run.muj4nT’
‘~/tmp/scratch/xvfb-run.p0eOIy’ ‘~/tmp/scratch/xvfb-run.pH7Ryc’
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‘~/tmp/scratch/xvfb-run.qZO1kJ’ ‘~/tmp/scratch/xvfb-run.qo7dAp’
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‘~/tmp/scratch/xvfb-run.tWUS9A’ ‘~/tmp/scratch/xvfb-run.uKOwjH’
‘~/tmp/scratch/xvfb-run.vrkeM3’ ‘~/tmp/scratch/xvfb-run.w1AqYE’
‘~/tmp/scratch/xvfb-run.wclIOD’ ‘~/tmp/scratch/xvfb-run.wqkkFe’
‘~/tmp/scratch/xvfb-run.x7skWz’ ‘~/tmp/scratch/xvfb-run.xrTIgb’
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Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘RcppParallel’ ‘rstantools’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘PoolTestR-Ex.R’ failed
The error most likely occurred in:
> ### Name: PoolRegBayes
> ### Title: Bayesian Mixed or Fixed Effect Logistic Regression with
> ### Presence/Absence Tests on Pooled Samples
> ### Aliases: PoolRegBayes
>
> ### ** Examples
>
> # Perform logistic-type regression modelling for a synthetic dataset consisting
> # of pools (sizes 1, 5, or 10) taken from 4 different regions and 3 different
> # years. Within each region specimens are collected at 4 different villages,
> # and within each village specimens are collected at 8 different sites.
>
>
> ### Models in a frequentist framework
> #ignoring hierarchical sampling frame within each region
> Mod <- PoolReg(Result ~ Region + Year,
+ data = SimpleExampleData,
+ poolSize = NumInPool)
[1] "Model has no group/random effects. Using a fixed effect model (glm)"
> summary(Mod)
Call:
stats::glm(formula = formula, family = stats::binomial(PoolLink(data[[poolSize]])),
data = data)
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -1.97190 0.12559 -15.701 < 2e-16 ***
RegionB -1.20591 0.17890 -6.741 1.58e-11 ***
RegionC -2.40943 0.27082 -8.897 < 2e-16 ***
RegionD -0.11001 0.14466 -0.760 0.4470
Year -0.13874 0.07716 -1.798 0.0722 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 1304.34 on 1151 degrees of freedom
Residual deviance: 990.58 on 1147 degrees of freedom
AIC: 1000.6
Number of Fisher Scoring iterations: 6
>
> #accounting hierarchical sampling frame within each region
> HierMod <- PoolReg(Result ~ Region + Year + (1|Village) + (1|Site),
+ data = SimpleExampleData,
+ poolSize = NumInPool)
[1] "Detected group/random effects. Using a mixed effect model (glmer)"
Error: Downdated VtV is not positive definite
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc