Last updated on 2026-08-02 13:49:33 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 | 295.06 | 139.38 | 434.44 | 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/Rtmp06DOZW’ ‘~/tmp/scratch/Rtmp19mt91’
‘~/tmp/scratch/Rtmp1pCXAE’ ‘~/tmp/scratch/Rtmp1rB1A2’
‘~/tmp/scratch/Rtmp2adbvp’ ‘~/tmp/scratch/Rtmp2kR5jb’
‘~/tmp/scratch/Rtmp3YarbZ’ ‘~/tmp/scratch/Rtmp41jQFk’
‘~/tmp/scratch/Rtmp42pKNN’ ‘~/tmp/scratch/Rtmp4MhsQr’
‘~/tmp/scratch/Rtmp4MzX9w’ ‘~/tmp/scratch/Rtmp4Neibr’
‘~/tmp/scratch/Rtmp4QJ6bA’ ‘~/tmp/scratch/Rtmp4XpNmG’
‘~/tmp/scratch/Rtmp4zoO0V’ ‘~/tmp/scratch/Rtmp5JIXKO’
‘~/tmp/scratch/Rtmp63D8Pn’ ‘~/tmp/scratch/Rtmp6Xg7yC’
‘~/tmp/scratch/Rtmp6zxNm5’ ‘~/tmp/scratch/Rtmp75bXfM’
‘~/tmp/scratch/Rtmp8zC8ev’ ‘~/tmp/scratch/Rtmp94Yx1n’
‘~/tmp/scratch/RtmpA251GZ’ ‘~/tmp/scratch/RtmpAWO4uw’
‘~/tmp/scratch/RtmpAhwwRH’ ‘~/tmp/scratch/RtmpAzDGVP’
‘~/tmp/scratch/RtmpBsc0tk’ ‘~/tmp/scratch/RtmpBuRxXp’
‘~/tmp/scratch/RtmpCU4sCB’ ‘~/tmp/scratch/RtmpCguTjX’
‘~/tmp/scratch/RtmpDQMURZ’ ‘~/tmp/scratch/RtmpDWYYAS’
‘~/tmp/scratch/RtmpDcIKbf’ ‘~/tmp/scratch/RtmpDx9YKK’
‘~/tmp/scratch/RtmpE3nJyI’ ‘~/tmp/scratch/RtmpEIvPuB’
‘~/tmp/scratch/RtmpESBBq6’ ‘~/tmp/scratch/RtmpEixDYM’
‘~/tmp/scratch/RtmpEvVF3f’ ‘~/tmp/scratch/RtmpFIJieO’
‘~/tmp/scratch/RtmpFImQT9’ ‘~/tmp/scratch/RtmpFOdxn2’
‘~/tmp/scratch/RtmpFf13JK’ ‘~/tmp/scratch/RtmpG6UhdZ’
‘~/tmp/scratch/RtmpHGOruP’ ‘~/tmp/scratch/RtmpHZ1sFY’
‘~/tmp/scratch/RtmpHhpFeB’ ‘~/tmp/scratch/RtmpHk9Bty’
‘~/tmp/scratch/RtmpHnXTrd’ ‘~/tmp/scratch/RtmpJ04gL8’
‘~/tmp/scratch/RtmpJY9oLj’ ‘~/tmp/scratch/RtmpJvAJyi’
‘~/tmp/scratch/RtmpJxwRkn’ ‘~/tmp/scratch/RtmpLFRhay’
‘~/tmp/scratch/RtmpLT4ytz’ ‘~/tmp/scratch/RtmpMANkL0’
‘~/tmp/scratch/RtmpMJ8HvC’ ‘~/tmp/scratch/RtmpMQUrp0’
‘~/tmp/scratch/RtmpMy3kyA’ ‘~/tmp/scratch/RtmpN7eTN2’
‘~/tmp/scratch/RtmpN8ucWz’ ‘~/tmp/scratch/RtmpNSyiWg’
‘~/tmp/scratch/RtmpNocqPw’ ‘~/tmp/scratch/RtmpNxCoY9’
‘~/tmp/scratch/RtmpO3SEh6’ ‘~/tmp/scratch/RtmpOBnzIX’
‘~/tmp/scratch/RtmpOLwIa1’ ‘~/tmp/scratch/RtmpOSZTi6’
‘~/tmp/scratch/RtmpOUvykY’ ‘~/tmp/scratch/RtmpOksYPE’
‘~/tmp/scratch/RtmpOty3OD’ ‘~/tmp/scratch/RtmpOuUmQy’
‘~/tmp/scratch/RtmpP3y7SK’ ‘~/tmp/scratch/RtmpP4SaHX’
‘~/tmp/scratch/RtmpPUThgC’ ‘~/tmp/scratch/RtmpPWRSz8’
‘~/tmp/scratch/RtmpPfMUhf’ ‘~/tmp/scratch/RtmpQNkeEb’
‘~/tmp/scratch/RtmpR9mkIM’ ‘~/tmp/scratch/RtmpRKpBtO’
‘~/tmp/scratch/RtmpSTlG0D’ ‘~/tmp/scratch/RtmpSlV8MQ’
‘~/tmp/scratch/RtmpTwRjAK’ ‘~/tmp/scratch/RtmpV1CzoP’
‘~/tmp/scratch/RtmpWSokdD’ ‘~/tmp/scratch/RtmpXF0ler’
‘~/tmp/scratch/RtmpXQ7raV’ ‘~/tmp/scratch/RtmpXwG099’
‘~/tmp/scratch/RtmpYDaKQL’ ‘~/tmp/scratch/RtmpYJUxgM’
‘~/tmp/scratch/RtmpZAWpRE’ ‘~/tmp/scratch/RtmpZL1r76’
‘~/tmp/scratch/RtmpZcMd4n’ ‘~/tmp/scratch/RtmpaA32Pe’
‘~/tmp/scratch/Rtmpaa1a7H’ ‘~/tmp/scratch/RtmpafZl8q’
‘~/tmp/scratch/Rtmpap1SI3’ ‘~/tmp/scratch/RtmpbjcCwS’
‘~/tmp/scratch/Rtmpc0t0mN’ ‘~/tmp/scratch/Rtmpc4yWWT’
‘~/tmp/scratch/RtmpcNHW0e’ ‘~/tmp/scratch/Rtmpcjwc4b’
‘~/tmp/scratch/RtmpcoU3lN’ ‘~/tmp/scratch/RtmpctWF72’
‘~/tmp/scratch/RtmpdNxt9o’ ‘~/tmp/scratch/Rtmpdt2qFY’
‘~/tmp/scratch/Rtmpecyqwh’ ‘~/tmp/scratch/RtmpfCQNUV’
‘~/tmp/scratch/Rtmpgi2JlA’ ‘~/tmp/scratch/RtmpiAabL5’
‘~/tmp/scratch/RtmpiWAJjT’ ‘~/tmp/scratch/RtmpiZu7BT’
‘~/tmp/scratch/RtmpigWrqC’ ‘~/tmp/scratch/RtmpisN9IU’
‘~/tmp/scratch/Rtmpj3wN7Z’ ‘~/tmp/scratch/RtmpjiFlFU’
‘~/tmp/scratch/Rtmpk5aAhj’ ‘~/tmp/scratch/RtmpkIYADX’
‘~/tmp/scratch/RtmpkLEzHm’ ‘~/tmp/scratch/RtmpkWcpaL’
‘~/tmp/scratch/RtmpkaxSpq’ ‘~/tmp/scratch/RtmpkdWem7’
‘~/tmp/scratch/RtmpkjR9Bp’ ‘~/tmp/scratch/RtmplRWLnH’
‘~/tmp/scratch/Rtmplvaurv’ ‘~/tmp/scratch/Rtmpm3XxQ7’
‘~/tmp/scratch/RtmpmhUCmI’ ‘~/tmp/scratch/RtmpnhafYr’
‘~/tmp/scratch/RtmpoJKVie’ ‘~/tmp/scratch/RtmpooXQT5’
‘~/tmp/scratch/RtmpoxmzFY’ ‘~/tmp/scratch/Rtmpp3jSH3’
‘~/tmp/scratch/Rtmpp6gJxy’ ‘~/tmp/scratch/RtmppR7EHL’
‘~/tmp/scratch/RtmppgKBJy’ ‘~/tmp/scratch/RtmpqsqCVQ’
‘~/tmp/scratch/RtmprT6wpg’ ‘~/tmp/scratch/RtmprvCS5E’
‘~/tmp/scratch/Rtmps0nlxx’ ‘~/tmp/scratch/RtmpsW5T2t’
‘~/tmp/scratch/RtmptFOYGM’ ‘~/tmp/scratch/RtmptLoR90’
‘~/tmp/scratch/Rtmptryghl’ ‘~/tmp/scratch/RtmpuM7IsH’
‘~/tmp/scratch/RtmpuMw2Lt’ ‘~/tmp/scratch/Rtmpw6MePZ’
‘~/tmp/scratch/RtmpwbTxDg’ ‘~/tmp/scratch/RtmpwpAoAo’
‘~/tmp/scratch/Rtmpx3835i’ ‘~/tmp/scratch/Rtmpx57uJv’
‘~/tmp/scratch/Rtmpy612Qs’ ‘~/tmp/scratch/RtmpyEPf1Z’
‘~/tmp/scratch/RtmpyZVWxp’ ‘~/tmp/scratch/Rtmpyb1smx’
‘~/tmp/scratch/RtmpyoY4RV’ ‘~/tmp/scratch/RtmpzUskWM’
‘~/tmp/scratch/cccb2GXX.s’ ‘~/tmp/scratch/xvfb-run.00pNFa’
‘~/tmp/scratch/xvfb-run.0YFxZ3’ ‘~/tmp/scratch/xvfb-run.19duWg’
‘~/tmp/scratch/xvfb-run.2AeOxD’ ‘~/tmp/scratch/xvfb-run.2Oymn4’
‘~/tmp/scratch/xvfb-run.3pLHc5’ ‘~/tmp/scratch/xvfb-run.4d3Q7K’
‘~/tmp/scratch/xvfb-run.516GOX’ ‘~/tmp/scratch/xvfb-run.550l2b’
‘~/tmp/scratch/xvfb-run.5FoMy9’ ‘~/tmp/scratch/xvfb-run.6Og1yy’
‘~/tmp/scratch/xvfb-run.79aAxn’ ‘~/tmp/scratch/xvfb-run.7fT6Ml’
‘~/tmp/scratch/xvfb-run.Bbmloe’ ‘~/tmp/scratch/xvfb-run.DeMx6p’
‘~/tmp/scratch/xvfb-run.FHmSXy’ ‘~/tmp/scratch/xvfb-run.FSUcqI’
‘~/tmp/scratch/xvfb-run.HEQv95’ ‘~/tmp/scratch/xvfb-run.HY5FdV’
‘~/tmp/scratch/xvfb-run.K1zptF’ ‘~/tmp/scratch/xvfb-run.K4ESr3’
‘~/tmp/scratch/xvfb-run.LH7Hjm’ ‘~/tmp/scratch/xvfb-run.LMaDbW’
‘~/tmp/scratch/xvfb-run.LzxsxL’ ‘~/tmp/scratch/xvfb-run.MCENhT’
‘~/tmp/scratch/xvfb-run.NBF6RE’ ‘~/tmp/scratch/xvfb-run.Q34FZE’
‘~/tmp/scratch/xvfb-run.RXUTkK’ ‘~/tmp/scratch/xvfb-run.SSflFq’
‘~/tmp/scratch/xvfb-run.SiPSvm’ ‘~/tmp/scratch/xvfb-run.SnTwAQ’
‘~/tmp/scratch/xvfb-run.T96HSY’ ‘~/tmp/scratch/xvfb-run.TV0MJ7’
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‘~/tmp/scratch/xvfb-run.VfTYeb’ ‘~/tmp/scratch/xvfb-run.VwR9Ew’
‘~/tmp/scratch/xvfb-run.WKUKOu’ ‘~/tmp/scratch/xvfb-run.WtuPAE’
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‘~/tmp/scratch/xvfb-run.YPVT7S’ ‘~/tmp/scratch/xvfb-run.bLzABD’
‘~/tmp/scratch/xvfb-run.bXZoRN’ ‘~/tmp/scratch/xvfb-run.d844K0’
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‘~/tmp/scratch/xvfb-run.egOVfI’ ‘~/tmp/scratch/xvfb-run.f2D2eG’
‘~/tmp/scratch/xvfb-run.fSm7BI’ ‘~/tmp/scratch/xvfb-run.hLL20d’
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‘~/tmp/scratch/xvfb-run.pZBMPJ’ ‘~/tmp/scratch/xvfb-run.taAeoO’
‘~/tmp/scratch/xvfb-run.uqWptB’ ‘~/tmp/scratch/xvfb-run.uwEbln’
‘~/tmp/scratch/xvfb-run.wjDj33’ ‘~/tmp/scratch/xvfb-run.x8Q5ri’
‘~/tmp/scratch/xvfb-run.xIfyMm’ ‘~/tmp/scratch/xvfb-run.xQLv6w’
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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