Last updated on 2026-08-01 02:57:29 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 | 302.68 | 140.10 | 442.78 | 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 | 365.86 | 179.91 | 545.77 | 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/Rtmp0Y0OKZ’ ‘~/tmp/scratch/Rtmp15Y2b7’
‘~/tmp/scratch/Rtmp1IBTly’ ‘~/tmp/scratch/Rtmp1YSnjC’
‘~/tmp/scratch/Rtmp1pCyGr’ ‘~/tmp/scratch/Rtmp1s8hZG’
‘~/tmp/scratch/Rtmp20hNLC’ ‘~/tmp/scratch/Rtmp25eIEE’
‘~/tmp/scratch/Rtmp26zt5A’ ‘~/tmp/scratch/Rtmp2Aipnh’
‘~/tmp/scratch/Rtmp2D0K3d’ ‘~/tmp/scratch/Rtmp2DKZFr’
‘~/tmp/scratch/Rtmp2mWJDO’ ‘~/tmp/scratch/Rtmp31B1rC’
‘~/tmp/scratch/Rtmp3CmNli’ ‘~/tmp/scratch/Rtmp3esof9’
‘~/tmp/scratch/Rtmp3rDGc3’ ‘~/tmp/scratch/Rtmp4Qt9t4’
‘~/tmp/scratch/Rtmp4ZzNST’ ‘~/tmp/scratch/Rtmp4mByTP’
‘~/tmp/scratch/Rtmp4tkx6i’ ‘~/tmp/scratch/Rtmp5CU3mX’
‘~/tmp/scratch/Rtmp5SdkRG’ ‘~/tmp/scratch/Rtmp5xAOhL’
‘~/tmp/scratch/Rtmp8KjPoB’ ‘~/tmp/scratch/Rtmp8gufzq’
‘~/tmp/scratch/Rtmp8okqo9’ ‘~/tmp/scratch/Rtmp8x4F8R’
‘~/tmp/scratch/Rtmp9CQPZl’ ‘~/tmp/scratch/Rtmp9j1aU5’
‘~/tmp/scratch/Rtmp9n0vVP’ ‘~/tmp/scratch/RtmpAqNSwZ’
‘~/tmp/scratch/RtmpAyNjgS’ ‘~/tmp/scratch/RtmpB0OKjx’
‘~/tmp/scratch/RtmpBLBCwd’ ‘~/tmp/scratch/RtmpBZNadB’
‘~/tmp/scratch/RtmpBgw43g’ ‘~/tmp/scratch/RtmpCMI37w’
‘~/tmp/scratch/RtmpCtNUkV’ ‘~/tmp/scratch/RtmpDOqdmX’
‘~/tmp/scratch/RtmpEmDai2’ ‘~/tmp/scratch/RtmpErKZLJ’
‘~/tmp/scratch/RtmpFJaARS’ ‘~/tmp/scratch/RtmpFm5BWG’
‘~/tmp/scratch/RtmpFsCMfS’ ‘~/tmp/scratch/RtmpGAZ4gE’
‘~/tmp/scratch/RtmpGJ3ImM’ ‘~/tmp/scratch/RtmpGZbrvu’
‘~/tmp/scratch/RtmpH0H0Zq’ ‘~/tmp/scratch/RtmpHDq36V’
‘~/tmp/scratch/RtmpHRGqga’ ‘~/tmp/scratch/RtmpIHXTlz’
‘~/tmp/scratch/RtmpIhA6Ra’ ‘~/tmp/scratch/RtmpIhN4Ww’
‘~/tmp/scratch/RtmpJOgNsI’ ‘~/tmp/scratch/RtmpJWnWQc’
‘~/tmp/scratch/RtmpJc4ILM’ ‘~/tmp/scratch/RtmpJckpu3’
‘~/tmp/scratch/RtmpJxtuGt’ ‘~/tmp/scratch/RtmpJyiuOk’
‘~/tmp/scratch/RtmpK2Xy63’ ‘~/tmp/scratch/RtmpKqkMdg’
‘~/tmp/scratch/RtmpKrW5QU’ ‘~/tmp/scratch/RtmpL2ilzz’
‘~/tmp/scratch/RtmpLGp91T’ ‘~/tmp/scratch/RtmpLLpHwF’
‘~/tmp/scratch/RtmpLlBKYu’ ‘~/tmp/scratch/RtmpNO9edN’
‘~/tmp/scratch/RtmpO65UkA’ ‘~/tmp/scratch/RtmpOTddNN’
‘~/tmp/scratch/RtmpOgbqJM’ ‘~/tmp/scratch/RtmpOxgHb7’
‘~/tmp/scratch/RtmpPL8FCd’ ‘~/tmp/scratch/RtmpPPd5pt’
‘~/tmp/scratch/RtmpPdmAHp’ ‘~/tmp/scratch/RtmpPlfp20’
‘~/tmp/scratch/RtmpPx4Fbu’ ‘~/tmp/scratch/RtmpPxWpgu’
‘~/tmp/scratch/RtmpQgMpqt’ ‘~/tmp/scratch/RtmpR7241Y’
‘~/tmp/scratch/RtmpRBTckC’ ‘~/tmp/scratch/RtmpSWUuxX’
‘~/tmp/scratch/RtmpSo4h77’ ‘~/tmp/scratch/RtmpT72Ac2’
‘~/tmp/scratch/RtmpTClOhf’ ‘~/tmp/scratch/RtmpTH6VXv’
‘~/tmp/scratch/RtmpTg3YTG’ ‘~/tmp/scratch/RtmpV05cCy’
‘~/tmp/scratch/RtmpVaTJuD’ ‘~/tmp/scratch/RtmpVpLPpe’
‘~/tmp/scratch/RtmpWK96w4’ ‘~/tmp/scratch/RtmpWZDqBX’
‘~/tmp/scratch/RtmpX0S18Q’ ‘~/tmp/scratch/RtmpXK4Lhy’
‘~/tmp/scratch/RtmpY12rXU’ ‘~/tmp/scratch/RtmpYJEjCN’
‘~/tmp/scratch/RtmpYVWFR5’ ‘~/tmp/scratch/RtmpYgpJ4I’
‘~/tmp/scratch/RtmpZI9fBs’ ‘~/tmp/scratch/RtmparrXtd’
‘~/tmp/scratch/Rtmpay5HFP’ ‘~/tmp/scratch/RtmpbELvaY’
‘~/tmp/scratch/RtmpbYYpLd’ ‘~/tmp/scratch/Rtmpbct9UJ’
‘~/tmp/scratch/Rtmpc2Cb26’ ‘~/tmp/scratch/RtmpcIkuD5’
‘~/tmp/scratch/RtmpcXG5X7’ ‘~/tmp/scratch/RtmpcYmTVh’
‘~/tmp/scratch/Rtmpcb8skJ’ ‘~/tmp/scratch/RtmpcgC9F9’
‘~/tmp/scratch/Rtmpcndrjh’ ‘~/tmp/scratch/RtmpdgztaA’
‘~/tmp/scratch/Rtmpdn65mB’ ‘~/tmp/scratch/RtmpeQo0Xm’
‘~/tmp/scratch/RtmpelSIyP’ ‘~/tmp/scratch/RtmpfpeROz’
‘~/tmp/scratch/RtmpgCo012’ ‘~/tmp/scratch/RtmpgImaRd’
‘~/tmp/scratch/RtmpgfNhKb’ ‘~/tmp/scratch/RtmpgmpTzV’
‘~/tmp/scratch/RtmphP5Rzw’ ‘~/tmp/scratch/Rtmpiu3R0R’
‘~/tmp/scratch/RtmpjCduHV’ ‘~/tmp/scratch/RtmpjSNTqh’
‘~/tmp/scratch/RtmpjoCWNl’ ‘~/tmp/scratch/RtmpkhqGs1’
‘~/tmp/scratch/RtmpkqgZvF’ ‘~/tmp/scratch/RtmplECr7d’
‘~/tmp/scratch/RtmplQqJho’ ‘~/tmp/scratch/RtmpmPOFmn’
‘~/tmp/scratch/RtmpmblScj’ ‘~/tmp/scratch/RtmpnScfy2’
‘~/tmp/scratch/RtmpoVYHy2’ ‘~/tmp/scratch/RtmpoxmWW5’
‘~/tmp/scratch/RtmppDoHNr’ ‘~/tmp/scratch/Rtmppdxmra’
‘~/tmp/scratch/Rtmppfxcks’ ‘~/tmp/scratch/Rtmpq6kqbN’
‘~/tmp/scratch/RtmpqogKyH’ ‘~/tmp/scratch/RtmprNv9Ty’
‘~/tmp/scratch/RtmprrHb7V’ ‘~/tmp/scratch/Rtmps5rm0u’
‘~/tmp/scratch/RtmpsTQ8F8’ ‘~/tmp/scratch/RtmptQPMfk’
‘~/tmp/scratch/RtmptfgVoE’ ‘~/tmp/scratch/RtmpvmzjWg’
‘~/tmp/scratch/Rtmpw5L6fZ’ ‘~/tmp/scratch/Rtmpw9Pj1f’
‘~/tmp/scratch/Rtmpx1phZT’ ‘~/tmp/scratch/Rtmpx417uK’
‘~/tmp/scratch/RtmpxQkG5D’ ‘~/tmp/scratch/RtmpxYBEgk’
‘~/tmp/scratch/RtmpxcmORZ’ ‘~/tmp/scratch/RtmpyzFs6U’
‘~/tmp/scratch/Rtmpzvd34i’ ‘~/tmp/scratch/RtmpzxH0No’
‘~/tmp/scratch/RtmpzxPlz0’ ‘~/tmp/scratch/cctWtWBK.s’
‘~/tmp/scratch/xvfb-run.0UmrIW’ ‘~/tmp/scratch/xvfb-run.0uMQDx’
‘~/tmp/scratch/xvfb-run.1fIka1’ ‘~/tmp/scratch/xvfb-run.2otShc’
‘~/tmp/scratch/xvfb-run.3mm2vZ’ ‘~/tmp/scratch/xvfb-run.44MaRD’
‘~/tmp/scratch/xvfb-run.45G3Z0’ ‘~/tmp/scratch/xvfb-run.4CeHS8’
‘~/tmp/scratch/xvfb-run.532bee’ ‘~/tmp/scratch/xvfb-run.5eyrtZ’
‘~/tmp/scratch/xvfb-run.5slBWg’ ‘~/tmp/scratch/xvfb-run.6nXd76’
‘~/tmp/scratch/xvfb-run.7w80H0’ ‘~/tmp/scratch/xvfb-run.7yTm81’
‘~/tmp/scratch/xvfb-run.98wYjo’ ‘~/tmp/scratch/xvfb-run.9Vlj8n’
‘~/tmp/scratch/xvfb-run.9jWmy1’ ‘~/tmp/scratch/xvfb-run.9jcDKX’
‘~/tmp/scratch/xvfb-run.9ouVit’ ‘~/tmp/scratch/xvfb-run.9pdYjI’
‘~/tmp/scratch/xvfb-run.AOxyRC’ ‘~/tmp/scratch/xvfb-run.AQd7YD’
‘~/tmp/scratch/xvfb-run.AzsBSq’ ‘~/tmp/scratch/xvfb-run.BzrA5b’
‘~/tmp/scratch/xvfb-run.CSSzkl’ ‘~/tmp/scratch/xvfb-run.H8ftXz’
‘~/tmp/scratch/xvfb-run.HhDUYB’ ‘~/tmp/scratch/xvfb-run.HxOCDK’
‘~/tmp/scratch/xvfb-run.IY0aoo’ ‘~/tmp/scratch/xvfb-run.KphLN5’
‘~/tmp/scratch/xvfb-run.LK6s8A’ ‘~/tmp/scratch/xvfb-run.MjkTTM’
‘~/tmp/scratch/xvfb-run.N2RSPU’ ‘~/tmp/scratch/xvfb-run.OTRSN3’
‘~/tmp/scratch/xvfb-run.PORkIM’ ‘~/tmp/scratch/xvfb-run.PyHFM9’
‘~/tmp/scratch/xvfb-run.Q9yjWw’ ‘~/tmp/scratch/xvfb-run.QNzP9n’
‘~/tmp/scratch/xvfb-run.QzZ2OO’ ‘~/tmp/scratch/xvfb-run.R3nwKg’
‘~/tmp/scratch/xvfb-run.SdIPmM’ ‘~/tmp/scratch/xvfb-run.TxQarw’
‘~/tmp/scratch/xvfb-run.UC0br9’ ‘~/tmp/scratch/xvfb-run.ULHiPF’
‘~/tmp/scratch/xvfb-run.UUEeCe’ ‘~/tmp/scratch/xvfb-run.VZ0lM7’
‘~/tmp/scratch/xvfb-run.Vc832C’ ‘~/tmp/scratch/xvfb-run.WgmkYD’
‘~/tmp/scratch/xvfb-run.XIPUFe’ ‘~/tmp/scratch/xvfb-run.Xj5rjx’
‘~/tmp/scratch/xvfb-run.Xy82Sj’ ‘~/tmp/scratch/xvfb-run.atEpfM’
‘~/tmp/scratch/xvfb-run.cRCPbE’ ‘~/tmp/scratch/xvfb-run.cyMNGo’
‘~/tmp/scratch/xvfb-run.d8W5vE’ ‘~/tmp/scratch/xvfb-run.eix3t1’
‘~/tmp/scratch/xvfb-run.fOxdAP’ ‘~/tmp/scratch/xvfb-run.gEoB05’
‘~/tmp/scratch/xvfb-run.gSg7RE’ ‘~/tmp/scratch/xvfb-run.gpp08v’
‘~/tmp/scratch/xvfb-run.hP888c’ ‘~/tmp/scratch/xvfb-run.hdQBGQ’
‘~/tmp/scratch/xvfb-run.lBSY3Q’ ‘~/tmp/scratch/xvfb-run.m4uUXY’
‘~/tmp/scratch/xvfb-run.m9sJM5’ ‘~/tmp/scratch/xvfb-run.oaFeAu’
‘~/tmp/scratch/xvfb-run.pQIDNo’ ‘~/tmp/scratch/xvfb-run.rtqn2V’
‘~/tmp/scratch/xvfb-run.wXwJyL’ ‘~/tmp/scratch/xvfb-run.xe8dxi’
‘~/tmp/scratch/xvfb-run.z3lYci’ ‘~/tmp/scratch/xvfb-run.zSzVaA’
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