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* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-tests --as-cran’
* checking for file ‘mkin/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mkin’ version ‘0.9.49.10’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* 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 serialization versions ... OK
* checking whether package ‘mkin’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... 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 ... NOTE
nlme.mmkin: no visible binding for global variable ‘na.fail’
nlme.mmkin: no visible binding for global variable ‘f’
Undefined global functions or variables:
f na.fail
Consider adding
importFrom("stats", "na.fail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘mkin-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nlme_function
> ### Title: Estimation of parameter distributions from mmkin row objects
> ### Aliases: nlme_function mean_degparms nlme_data
>
> ### ** Examples
>
> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
> m_SFO <- mkinmod(parent = mkinsub("SFO"))
> d_SFO_1 <- mkinpredict(m_SFO,
+ c(k_parent_sink = 0.1),
+ c(parent = 98), sampling_times)
> d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
> d_SFO_2 <- mkinpredict(m_SFO,
+ c(k_parent_sink = 0.05),
+ c(parent = 102), sampling_times)
> d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
> d_SFO_3 <- mkinpredict(m_SFO,
+ c(k_parent_sink = 0.02),
+ c(parent = 103), sampling_times)
> d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
>
> d1 <- add_err(d_SFO_1, function(value) 3, n = 1)
> d2 <- add_err(d_SFO_2, function(value) 2, n = 1)
> d3 <- add_err(d_SFO_3, function(value) 4, n = 1)
> ds <- c(d1 = d1, d2 = d2, d3 = d3)
>
> f <- mmkin("SFO", ds, cores = 1, quiet = TRUE)
> mean_dp <- mean_degparms(f)
> grouped_data <- nlme_data(f)
> nlme_f <- nlme_function(f)
> # These assignments are necessary for these objects to be
> # visible to nlme and augPred when evaluation is done by
> # pkgdown to generated the html docs.
> assign("nlme_f", nlme_f, globalenv())
> assign("grouped_data", grouped_data, globalenv())
>
> library(nlme)
> m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),
+ data = grouped_data,
+ fixed = parent_0 + log_k_parent_sink ~ 1,
+ random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+ start = mean_dp)
> summary(m_nlme)
Nonlinear mixed-effects model fit by maximum likelihood
Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink)
Data: grouped_data
AIC BIC logLik
253.6377 262.9937 -121.8188
Random effects:
Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
Level: ds
Structure: Diagonal
parent_0 log_k_parent_sink Residual
StdDev: 2.486822 0.6481355 2.368137
Fixed effects: parent_0 + log_k_parent_sink ~ 1
Value Std.Error DF t-value p-value
parent_0 101.43096 1.5960157 44 63.55261 0
log_k_parent_sink -3.07614 0.3827294 44 -8.03737 0
Correlation:
prnt_0
log_k_parent_sink 0.011
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-1.9643731 -0.5430765 0.1659516 0.6160408 1.8082871
Number of Observations: 48
Number of Groups: 3
> plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))
>
> m_nlme <- nlme(nlme_formula,
+ data = grouped_data,
+ fixed = parent_0 + log_k_parent_sink ~ 1,
+ random = pdDiag(parent_0 + log_k_parent_sink ~ 1),
+ start = mean_dp)
Error in nlme(nlme_formula, data = grouped_data, fixed = parent_0 + log_k_parent_sink ~ :
object 'nlme_formula' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
for details.
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