- using R Under development (unstable) (2025-09-03 r88788 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'MF.beta4/DESCRIPTION' ... OK
- checking extension type ... Package
- this is package 'MF.beta4' version '1.1.1'
- 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'MF.beta4' can be installed ... OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [4s] OK
- checking whether the package can be loaded with stated dependencies ... [3s] OK
- checking whether the package can be unloaded cleanly ... [4s] OK
- checking whether the namespace can be loaded with stated dependencies ... [3s] OK
- checking whether the namespace can be unloaded cleanly ... [3s] OK
- checking loading without being on the library search path ... [4s] 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 ... [11s] OK
- checking Rd files ... [1s] OK
- checking Rd metadata ... 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 ... [0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking sizes of PDF files under 'inst/doc' ... OK
- checking installed files from 'inst/doc' ... OK
- checking files in 'vignettes' ... OK
- checking examples ... [9s] ERROR
Running examples in 'MF.beta4-Ex.R' failed
The error most likely occurred in:
> ### Name: MFggplot
> ### Title: ggplot2 extension for a MF1_single or MF2_multiple object
> ### Aliases: MFggplot
>
> ### ** Examples
>
>
> library(dplyr)
Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> ### Use the entire of 209 plots data from six countries
>
>
>
>
> ### Use partial data to calculate multifunctionality based on 3 plots in each country, not by pairs
> ### (Take the first 3 plots in each country)
>
> data("forest_function_data_raw")
> data("forest_biodiversity_data")
>
> forest_function_data_raw_3plots <- forest_function_data_raw[c(1:3,29:31,67:69,103:105,
+ 146:148,174:176),]
> forest_function_data_normalized_3plots <-
+ function_normalization(data = forest_function_data_raw_3plots,
+ fun_cols = 6:31,
+ negative = c("soil_cn_ff_10","wue"),
+ by_group = "country")
> forest_biodiversity_data_3plots <-
+ forest_biodiversity_data[c(1:6,49:52,141:148,230:232,351:355,411:417),]
>
> output5 <- MF2_multiple(func_data = forest_function_data_normalized_3plots[,6:32],
+ species_data = forest_biodiversity_data_3plots,
+ weight = 1,
+ by_group = "country", by_pair = FALSE)
>
> ## BEF relationships: display fitted line of linear model
> figure_all_plots <- MFggplot(output5, model = "lm", caption = "slope")
Error in ll(object) : could not find function "ll"
Calls: MFggplot ... tibble_quos -> eval_tidy -> <Anonymous> -> AIC.default
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [13s] OK
- checking PDF version of manual ... [27s] OK
- checking HTML version of manual ... [2s] OK
- DONE
Status: 1 ERROR