- using R version 4.4.1 (2024-06-14)
- using platform: aarch64-apple-darwin20
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘embryogrowth/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘embryogrowth’ version ‘10.3’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘embryogrowth’ can be installed ... [10s/11s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [1s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the package can be unloaded cleanly ... [1s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
- checking loading without being on the library search path ... [1s/1s] OK
- checking whether startup messages can be suppressed ... [1s/2s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [9s/10s] OK
- checking Rd files ... [2s/2s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'HeterogeneityNests.Rd':
HeterogeneityNests
Code: function(nests = stop("An object of class Nests2, NestsResult,
or mcmcComposite."), probs = c(0.025, 0.975),
control.legend.total = list(),
control.legend.metabolicheating = list(),
show.full.incubation = TRUE,
show.first.half.incubation = TRUE,
col.absolute.difference.full = rgb(blue = 0.1, green =
0.1, red = 1, alpha = 0.01),
pch.absolute.difference.full = 19,
col.absolute.difference.first = rgb(blue = 1, green =
0.1, red = 0.1, alpha = 0.01),
pch.absolute.difference.first = 19, show.se = TRUE,
show.sd = TRUE, n.iter = 10000, n.adapt = 1000, thin =
5, adaptive = TRUE, return.mcmc = FALSE, trace =
FALSE, rules = rbind(data.frame(Name = "min", Min = 0,
Max = 2), data.frame(Name = "max", Min = 0, Max = 20),
data.frame(Name = "S", Min = 0, Max = 10),
data.frame(Name = "P", Min = 0, Max = 50),
data.frame(Name = "asd", Min = 0, Max = 2),
data.frame(Name = "bsd", Min = 0, Max = 1)),
fitted.parameters = c(min = 1, max = 3.94384206319577,
S = 0.621279598124434, P = 5.69863056154756, asd =
0.0139849297499185, bsd = 1.19025174327629),
fixed.parameters = NULL, ...)
Docs: function(nests = stop("An object of class Nests2, NestsResult,
or mcmcComposite."), probs = c(0.025, 0.975),
control.legend.total = list(),
control.legend.metabolicheating = list(),
show.full.incubation = TRUE,
show.first.half.incubation = TRUE,
col.absolute.difference.full = rgb(blue = 0.1, green =
0.1, red = 1, alpha = 0.01),
pch.absolute.difference.full = 19,
col.absolute.difference.first = rgb(blue = 1, green =
0.1, red = 0.1, alpha = 0.01),
pch.absolute.difference.first = 19, show.se = TRUE,
show.sd = TRUE, n.iter = 10000, n.adapt = 1000, thin =
5, adaptive = TRUE, return.mcmc = FALSE, trace =
FALSE, rules = rbind(data.frame(Name = "min", Min = 0,
Max = 2), data.frame(Name = "max", Min = 0, Max = 20),
data.frame(Name = "S", Min = 0, Max = 10),
data.frame(Name = "P", Min = 0, Max = 50),
data.frame(Name = "asd", Min = 0, Max = 2),
data.frame(Name = "bsd", Min = 0, Max = 1)),
fitted.parameters = c(min = 1, max = 3.94384206319577,
S = 0.621279598124434, P = 5.69863056154757, asd =
0.0139849297499185, bsd = 1.19025174327629),
fixed.parameters = NULL, ...)
Mismatches in argument default values:
Name: 'fitted.parameters'
Code: c(min = 1, max = 3.94384206319577, S = 0.621279598124434, P = 5.69863056154756,
asd = 0.0139849297499185, bsd = 1.19025174327629)
Docs: c(min = 1, max = 3.94384206319577, S = 0.621279598124434, P = 5.69863056154757,
asd = 0.0139849297499185, bsd = 1.19025174327629)
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [2s/2s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [1s/1s] OK
- checking PDF version of manual ... [6s/8s] OK
- DONE
Status: 1 WARNING
- using check arguments '--no-clean-on-error '