- using R Under development (unstable) (2024-11-22 r87365)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘soilassessment/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘soilassessment’ version ‘0.2.6’
- 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 ‘soilassessment’ can be installed ... [113s/366s] OK
See the install log for details.
- 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 ... [24s/68s] OK
- checking whether the package can be loaded with stated dependencies ... [22s/65s] OK
- checking whether the package can be unloaded cleanly ... [23s/75s] OK
- checking whether the namespace can be loaded with stated dependencies ... [23s/38s] OK
- checking whether the namespace can be unloaded cleanly ... [24s/39s] OK
- checking loading without being on the library search path ... [25s/38s] 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 ... [171s/185s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
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- 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 LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [31s/35s] ERROR
Running examples in ‘soilassessment-Ex.R’ failed
The error most likely occurred in:
> ### Name: depthharm
> ### Title: A function for harmonizing soil property between uniform depth
> ### intervals in observation pits
> ### Aliases: depthharm
>
> ### ** Examples
>
> library(aqp)
This is aqp 2.1.0
> library(plyr)
> library(sp)
Attaching package: ‘sp’
The following objects are masked from ‘package:aqp’:
coordinates, coordinates<-, proj4string, proj4string<-
> x=c(rep(2.12,4),rep(2.05,4))
> y=c(rep(9.34,4),rep(8.17,4))
> pit=c(rep(1,4),rep(2,4))
> depthcode=c(1,2,3,4,1,2,3,4)
> upper=c(0,18,25,35,0,12,33,50)
> lower=c(10,25,35,67,12,33,50,100)
> pH=c(6.7,5.5,5.1,6.7,6.4,5.8,5.3,5.0)
> df=data.frame(pit,x,y,upper,lower,depthcode,pH)
> lat=df$x;lon=df$y;id=df$pit;top=df$upper;
> bottom=df$lower;horizon=df$depthcode;Varn=df$pH
>
> soildata <- join(data.frame(id, top, bottom, Varn, horizon),
+ data.frame(id, lat, lon), type='inner')
Joining by: id
> depths(soildata) <- id ~ top + bottom
> site(soildata) <- ~ lat + lon
> coordinates(soildata) <- ~ lat + lon
Error: unable to find an inherited method for function ‘coordinates<-’ for signature ‘object = "SoilProfileCollection"’
Execution halted
- checking PDF version of manual ... [10s/11s] OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR