Last updated on 2025-06-07 06:50:32 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| betaper | 5 | 1 | 7 |
| rareNMtests | 13 |
Current CRAN status: ERROR: 5, NOTE: 1, OK: 7
Version: 1.1-2
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Luis Cayuela <luis.cayuela@urjc.es>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Luis",
family = "Cayuela",
role = c("aut", "cre"),
email = "luis.cayuela@urjc.es"),
person(given = "Marcelino",
family = "de la Cruz",
role = "aut"))
as necessary.
Found the following URLs which should use \doi (with the DOI name only):
File ‘adonis_pertables.Rd’:
http://dx.doi.org/10.1111/j.1600-0587.2009.05899.x
File ‘cca_pertables.Rd’:
http://dx.doi.org/10.1111/j.1600-0587.2009.05899.x
File ‘mantel_pertables.Rd’:
http://dx.doi.org/10.1111/j.1600-0587.2009.05899.x
File ‘pertables.Rd’:
http://dx.doi.org/10.1111/j.1600-0587.2009.05899.x
File ‘rda_pertables.Rd’:
http://dx.doi.org/10.1111/j.1600-0587.2009.05899.x
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.1-2
Check: examples
Result: ERROR
Running examples in ‘betaper-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adonis_pertables
> ### Title: Function to assess the efects of taxonomic uncertainty on
> ### permutational multivariate analysis of variance using distance
> ### matrices
> ### Aliases: adonis_pertables print.adonis_pertables plot.adonis_pertables
> ### Keywords: multivariate
>
> ### ** Examples
>
>
>
>
> data(Amazonia)
> data(soils)
>
> # Define a new index that includes the terms used in the \code{Amazonia} dataset to define
> # undetermined taxa at different taxonomic levels
>
> index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")
>
> # Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic
> # uncertainty)
> ## Not run:
> ##D Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100)
> ##D
> ##D # Assess the effects of taxonomic uncertainty on a PERMANOVA (i.e., adonis) test:
> ##D
> ##D Amazonia.adonis <- adonis_pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils)
> ##D
> ##D Amazonia.adonis
> ##D
> ##D plot(Amazonia.adonis)
> ## End(Not run)
> # Fast example for Rcheck
>
> Amazonia4.p2 <- pertables.p2(Amazonia[1:50,], index=index.Amazon, nsim=4, ncl=2, iseed=4)
> set.seed(2)
> Amazonia.adonis <- adonis_pertables(Amazonia4.p2 ~ Ca + K + Mg + Na, data=soils)
Error in adonis(formula = fmla, data = data, permutations = permutations, :
'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis_pertables -> adonis -> .Defunct
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.1-2
Check: examples
Result: ERROR
Running examples in ‘betaper-Ex.R’ failed
The error most likely occurred in:
> ### Name: adonis_pertables
> ### Title: Function to assess the efects of taxonomic uncertainty on
> ### permutational multivariate analysis of variance using distance
> ### matrices
> ### Aliases: adonis_pertables print.adonis_pertables plot.adonis_pertables
> ### Keywords: multivariate
>
> ### ** Examples
>
>
>
>
> data(Amazonia)
> data(soils)
>
> # Define a new index that includes the terms used in the \code{Amazonia} dataset to define
> # undetermined taxa at different taxonomic levels
>
> index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")
>
> # Generate a pertables object (i.e. a list of biological data tables simulated from taxonomic
> # uncertainty)
> ## Not run:
> ##D Amazonia100 <- pertables(Amazonia, index=index.Amazon, nsim=100)
> ##D
> ##D # Assess the effects of taxonomic uncertainty on a PERMANOVA (i.e., adonis) test:
> ##D
> ##D Amazonia.adonis <- adonis_pertables(Amazonia100 ~ Ca + K + Mg + Na, data=soils)
> ##D
> ##D Amazonia.adonis
> ##D
> ##D plot(Amazonia.adonis)
> ## End(Not run)
> # Fast example for Rcheck
>
> Amazonia4.p2 <- pertables.p2(Amazonia[1:50,], index=index.Amazon, nsim=4, ncl=2, iseed=4)
> set.seed(2)
> Amazonia.adonis <- adonis_pertables(Amazonia4.p2 ~ Ca + K + Mg + Na, data=soils)
Error in adonis(formula = fmla, data = data, permutations = permutations, :
'adonis' is defunct.
Use 'adonis2' instead.
See help("Defunct") and help("vegan-defunct").
Calls: adonis_pertables -> adonis -> .Defunct
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-windows-x86_64, r-oldrel-windows-x86_64
Current CRAN status: NOTE: 13
Version: 1.2
Check: CRAN incoming feasibility
Result: NOTE
Maintainer: ‘Luis Cayuela <luis.cayuela@urjc.es>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Luis",
family = "Cayuela",
role = c("aut", "cre"),
email = "luis.cayuela@urjc.es"),
person(given = c("Nicholas", "J."),
family = "Gotelli",
role = "aut"))
as necessary.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 1.2
Check: Rd files
Result: NOTE
checkRd: (-1) BiogTest.individual.Rd:25: Lost braces
25 | \item{powerfun}{ By default rarefied richness is estimated for all subsample sizes, from 1 to \emph{n}, where \emph{n} is the total number of individuals in the sample. If \code{powerfun} is less than 1, it decreases the total number of subsamples as a power function of \{h{n}. }
| ^
checkRd: (-1) BiogTest.individual.Rd:66: Lost braces
66 | Chao, A., Gotelli, N.J., Hsieh, T.C., Sander, E.L., Ma, K.H., Colwell, R.K. & Ellison, A.M. (2014). Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. emph{Ecological Monographs} 84: 45-67.
| ^
checkRd: (-1) BiogTest.individual.Rd:68: Lost braces
68 | Limpert, E., Stahel, W.A. & Abbt, M. (2001). Log-normal distributions across the sciences: keys and clues. emph{BioScience} 51: 341-352.
| ^
checkRd: (-1) BiogTest.individual.Rd:70: Lost braces
70 | O'Hara, R.B. (2005). Species richness estimators: how many species can dance on the head of a pin? emph{Journal of Animal Ecology} 74: 375-386.
| ^
checkRd: (-1) EcoTest.individual.Rd:57: Lost braces
57 | Chao, A., Gotelli, N.J., Hsieh, T.C., Sander, E.L., Ma, K.H., Colwell, R.K. & Ellison, A.M. (2014). Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. emph{Ecological Monographs} 84: 45-67.
| ^
checkRd: (-1) rarefaction.individual.Rd:37: Lost braces
37 | Chao, A., Gotelli, N.J., Hsieh, T.C., Sander, E.L., Ma, K.H., Colwell, R.K. & Ellison, A.M. (2014). Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. emph{Ecological Monographs} 84: 45-67.
| ^
checkRd: (-1) rarefaction.individual.Rd:39: Lost braces
39 | Chao, A. & Jost, J. (2012). Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size. emph{Ecology} 93: 2533-2547.
| ^
checkRd: (-1) rarefaction.individual.Rd:41: Lost braces
41 | Hill, M.O. (1973). Diversity and evenness: a unifying notation and its consequences. emph{Ecology} 54: 427-432.
| ^
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