Last updated on 2026-08-04 12:50:56 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 | 285.73 | 136.45 | 422.18 | 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 | 372.00 | 198.00 | 570.00 | 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 | 484.00 | 277.00 | 761.00 | 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/Rtmp0ChDkO’ ‘~/tmp/scratch/Rtmp0OWFOk’
‘~/tmp/scratch/Rtmp0WvVGM’ ‘~/tmp/scratch/Rtmp0bX09a’
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‘~/tmp/scratch/Rtmp248DWu’ ‘~/tmp/scratch/Rtmp2Q530b’
‘~/tmp/scratch/Rtmp3ixqXm’ ‘~/tmp/scratch/Rtmp40xEqg’
‘~/tmp/scratch/Rtmp4F0KZx’ ‘~/tmp/scratch/Rtmp5E2ARi’
‘~/tmp/scratch/Rtmp5R4fo1’ ‘~/tmp/scratch/Rtmp5zWXHN’
‘~/tmp/scratch/Rtmp70O7ST’ ‘~/tmp/scratch/Rtmp7JamC0’
‘~/tmp/scratch/Rtmp7mm46A’ ‘~/tmp/scratch/Rtmp7pnUJg’
‘~/tmp/scratch/Rtmp8OfMPY’ ‘~/tmp/scratch/Rtmp8SJ2d5’
‘~/tmp/scratch/RtmpAHeHn1’ ‘~/tmp/scratch/RtmpASvfxl’
‘~/tmp/scratch/RtmpAieasU’ ‘~/tmp/scratch/RtmpAz9FI2’
‘~/tmp/scratch/RtmpCIPAvP’ ‘~/tmp/scratch/RtmpCNI64d’
‘~/tmp/scratch/RtmpD7kaBE’ ‘~/tmp/scratch/RtmpDSohZl’
‘~/tmp/scratch/RtmpDVlaFI’ ‘~/tmp/scratch/RtmpDh4BMW’
‘~/tmp/scratch/RtmpDjeBnT’ ‘~/tmp/scratch/RtmpE3XYvX’
‘~/tmp/scratch/RtmpE6ybRc’ ‘~/tmp/scratch/RtmpEFGotk’
‘~/tmp/scratch/RtmpELXmi1’ ‘~/tmp/scratch/RtmpEMcpjG’
‘~/tmp/scratch/RtmpEVSnzf’ ‘~/tmp/scratch/RtmpEscGsF’
‘~/tmp/scratch/RtmpEv52rr’ ‘~/tmp/scratch/RtmpFMkKro’
‘~/tmp/scratch/RtmpG6qa7B’ ‘~/tmp/scratch/RtmpGLJcKn’
‘~/tmp/scratch/RtmpGbn9Le’ ‘~/tmp/scratch/RtmpGp7Va2’
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‘~/tmp/scratch/RtmpKqT6bm’ ‘~/tmp/scratch/RtmpKxvToh’
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‘~/tmp/scratch/RtmpO3cYIP’ ‘~/tmp/scratch/RtmpOoawZs’
‘~/tmp/scratch/RtmpOxq4oW’ ‘~/tmp/scratch/RtmpP033tL’
‘~/tmp/scratch/RtmpPItaxv’ ‘~/tmp/scratch/RtmpPfPXFL’
‘~/tmp/scratch/RtmpQC3jAn’ ‘~/tmp/scratch/RtmpQeDybN’
‘~/tmp/scratch/RtmpReYfLx’ ‘~/tmp/scratch/RtmpS57QnO’
‘~/tmp/scratch/RtmpSDEMFA’ ‘~/tmp/scratch/RtmpT2yScc’
‘~/tmp/scratch/RtmpT99tY7’ ‘~/tmp/scratch/RtmpU0PsKO’
‘~/tmp/scratch/RtmpUI0YBI’ ‘~/tmp/scratch/RtmpULrU4r’
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‘~/tmp/scratch/RtmpUj31BU’ ‘~/tmp/scratch/RtmpUja6it’
‘~/tmp/scratch/RtmpVWOUjr’ ‘~/tmp/scratch/RtmpVjILIH’
‘~/tmp/scratch/RtmpWNW9hd’ ‘~/tmp/scratch/RtmpWSs8WA’
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‘~/tmp/scratch/RtmpYF5AiZ’ ‘~/tmp/scratch/RtmpYJja2l’
‘~/tmp/scratch/RtmpZYhuZT’ ‘~/tmp/scratch/Rtmpa0FXfl’
‘~/tmp/scratch/RtmpaQROWU’ ‘~/tmp/scratch/Rtmpawat1A’
‘~/tmp/scratch/RtmpbVf20V’ ‘~/tmp/scratch/Rtmpbeup18’
‘~/tmp/scratch/RtmpblbiB5’ ‘~/tmp/scratch/RtmpcFgFG3’
‘~/tmp/scratch/RtmpcuwuSp’ ‘~/tmp/scratch/RtmpdU6wEx’
‘~/tmp/scratch/RtmpdZS4vr’ ‘~/tmp/scratch/RtmpdbjDFX’
‘~/tmp/scratch/RtmpeetZgY’ ‘~/tmp/scratch/RtmpevBT3V’
‘~/tmp/scratch/RtmpfbZDi4’ ‘~/tmp/scratch/Rtmpfsfr7u’
‘~/tmp/scratch/RtmpfxAVtE’ ‘~/tmp/scratch/RtmpgGG2Vt’
‘~/tmp/scratch/Rtmpgg0sMv’ ‘~/tmp/scratch/Rtmph33GXT’
‘~/tmp/scratch/Rtmph47Obc’ ‘~/tmp/scratch/Rtmph5nLiO’
‘~/tmp/scratch/RtmphLGYmc’ ‘~/tmp/scratch/RtmpiYGxBL’
‘~/tmp/scratch/RtmpiepPkj’ ‘~/tmp/scratch/RtmpizBpPf’
‘~/tmp/scratch/Rtmpj93MkE’ ‘~/tmp/scratch/RtmpjPOJzp’
‘~/tmp/scratch/RtmpjoYK6U’ ‘~/tmp/scratch/Rtmpk2hmEn’
‘~/tmp/scratch/RtmpkvlaXE’ ‘~/tmp/scratch/Rtmpl87Mt6’
‘~/tmp/scratch/RtmplRNTSa’ ‘~/tmp/scratch/RtmplSMGLt’
‘~/tmp/scratch/RtmplkL4Qt’ ‘~/tmp/scratch/RtmpmaPPK9’
‘~/tmp/scratch/RtmpnVhShk’ ‘~/tmp/scratch/RtmpnxwR37’
‘~/tmp/scratch/RtmppJ0Dj3’ ‘~/tmp/scratch/RtmppoUSNn’
‘~/tmp/scratch/RtmpppVlRl’ ‘~/tmp/scratch/Rtmpq3br0N’
‘~/tmp/scratch/Rtmpqfhb7i’ ‘~/tmp/scratch/RtmprIXgaL’
‘~/tmp/scratch/RtmpsAKVK7’ ‘~/tmp/scratch/RtmpsO4WOm’
‘~/tmp/scratch/RtmpsX8RGZ’ ‘~/tmp/scratch/Rtmpseurdx’
‘~/tmp/scratch/RtmpsjOjWW’ ‘~/tmp/scratch/Rtmpsryriq’
‘~/tmp/scratch/RtmptRMhyx’ ‘~/tmp/scratch/RtmptSlLwF’
‘~/tmp/scratch/Rtmptyat4H’ ‘~/tmp/scratch/Rtmpu343fN’
‘~/tmp/scratch/RtmpuDjNVV’ ‘~/tmp/scratch/RtmpuLx6fR’
‘~/tmp/scratch/RtmpucYuHa’ ‘~/tmp/scratch/Rtmpue1aJK’
‘~/tmp/scratch/RtmpuhdnLQ’ ‘~/tmp/scratch/Rtmpuz01Ck’
‘~/tmp/scratch/RtmpvBHOQ1’ ‘~/tmp/scratch/RtmpvcSDgO’
‘~/tmp/scratch/RtmpwSGpFo’ ‘~/tmp/scratch/RtmpwtWQGU’
‘~/tmp/scratch/Rtmpx5dadV’ ‘~/tmp/scratch/RtmpxKWCPT’
‘~/tmp/scratch/RtmpxWPJ86’ ‘~/tmp/scratch/RtmpxXXMhO’
‘~/tmp/scratch/Rtmpxh8plR’ ‘~/tmp/scratch/Rtmpy1tWsf’
‘~/tmp/scratch/RtmpyjVmSb’ ‘~/tmp/scratch/RtmpykSsR9’
‘~/tmp/scratch/Rtmpzo0cwB’ ‘~/tmp/scratch/arHz_ne2’
‘~/tmp/scratch/ccLIAp10.s’ ‘~/tmp/scratch/xvfb-run.0IONNO’
‘~/tmp/scratch/xvfb-run.0Q6XhO’ ‘~/tmp/scratch/xvfb-run.1MvdM6’
‘~/tmp/scratch/xvfb-run.1eINMP’ ‘~/tmp/scratch/xvfb-run.2IGGuX’
‘~/tmp/scratch/xvfb-run.2PohPP’ ‘~/tmp/scratch/xvfb-run.4HKQ5h’
‘~/tmp/scratch/xvfb-run.5CRSyl’ ‘~/tmp/scratch/xvfb-run.5PrrE0’
‘~/tmp/scratch/xvfb-run.9hz4Lh’ ‘~/tmp/scratch/xvfb-run.AFqjOO’
‘~/tmp/scratch/xvfb-run.BH71Ir’ ‘~/tmp/scratch/xvfb-run.BRIw31’
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‘~/tmp/scratch/xvfb-run.DbzM2M’ ‘~/tmp/scratch/xvfb-run.DqCOZb’
‘~/tmp/scratch/xvfb-run.EBOENK’ ‘~/tmp/scratch/xvfb-run.GxNVhw’
‘~/tmp/scratch/xvfb-run.Hgirpp’ ‘~/tmp/scratch/xvfb-run.I2w2gV’
‘~/tmp/scratch/xvfb-run.JQr7vr’ ‘~/tmp/scratch/xvfb-run.LowiDv’
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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