- using R Under development (unstable) (2026-05-06 r90009)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-15 (Debian 15.2.0-17) 15.2.0
GNU Fortran (Debian 15.2.0-17) 15.2.0
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-05-07 18:04:07 UTC
- checking for file ‘voluModel/DESCRIPTION’ ... OK
- this is package ‘voluModel’ version ‘0.2.3’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [1s/2s] OK
- 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 ‘voluModel’ can be installed ... OK
See the install log for details.
- 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [6s/9s] OK
- checking whether the package can be loaded with stated dependencies ... [6s/8s] OK
- checking whether the package can be unloaded cleanly ... [6s/6s] OK
- checking whether the namespace can be loaded with stated dependencies ... [6s/7s] OK
- checking whether the namespace can be unloaded cleanly ... [6s/9s] OK
- checking loading without being on the library search path ... [8s/10s] 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 ... [29s/36s] OK
- checking Rd files ... [0s/1s] 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 installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [8s/10s] ERROR
Running examples in ‘voluModel-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MESS3D
> ### Title: Calculate MESS
> ### Aliases: MESS3D
> ### Keywords: modelDiagnostics
>
> ### ** Examples
>
> library(terra)
terra 1.9.25
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:terra’:
intersect, union
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
>
> # Create sample rasterBricks
> r1 <- rast(ncol=10, nrow=10)
> values(r1) <- 1:100
> r2 <- rast(ncol=10, nrow=10)
> values(r2) <- c(rep(20, times = 50), rep(60, times = 50))
> r3 <- rast(ncol=10, nrow=10)
> values(r3) <- 8
> envBrick1 <- c(r1, r2, r3)
> names(envBrick1) <- c(0, 10, 30)
>
> r1 <- rast(ncol=10, nrow=10)
> values(r1) <- 100:1
> r2 <- rast(ncol=10, nrow=10)
> values(r2) <- c(rep(10, times = 50), rep(20, times = 50))
> r3 <- rast(ncol=10, nrow=10)
> values(r3) <- c(rep(c(10,20,30,25), times = 25))
> envBrick2 <- c(r1, r2, r3)
> names(envBrick2) <- c(0, 10, 30)
>
> rastList <- list("temperature" = envBrick1, "salinity" = envBrick2)
>
> # Create test reference set
> set.seed(0)
> longitude <- sample(ext(envBrick1)[1]:ext(envBrick1)[2],
+ size = 10, replace = FALSE)
> set.seed(0)
> latitude <- sample(ext(envBrick1)[3]:ext(envBrick1)[4],
+ size = 10, replace = FALSE)
> set.seed(0)
> depth <- sample(0:35, size = 10, replace = TRUE)
> occurrences <- as.data.frame(cbind(longitude,latitude,depth))
>
> # Calibration
> calibration <- lapply(rastList, FUN = function(x) xyzSample(occurrences, x)) %>% bind_rows
Using longitude, latitude, and depth
as x, y, and z coordinates, respectively.
Using longitude, latitude, and depth
as x, y, and z coordinates, respectively.
>
> # Run the function
> messStack <- MESS3D(calibration = calibration, projection = rastList)
Error in MESS(P = projVals, V = cal, verbosity = 0) :
The number of variables in V and P does not match.
Calls: MESS3D -> MESS
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [21s/29s] ERROR
Running ‘testthat.R’ [21s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(voluModel)
>
> test_check("voluModel")
terra 1.9.25
Attaching package: 'terra'
The following objects are masked from 'package:testthat':
compare, describe
Could not parse
spam, eggs, NA
into x and/or y coordinates.
Using longitude and latitude
as x and y coordinates, respectively.
Could not parse
spam, eggs, cheese
into x and/or y coordinates.
Using longitude, latitude, and depth
as x, y, and z coordinates, respectively.
Input SpatRaster vector names inappropriate:
a, b, c
Names must follow the format 'X' followed by a number corresponding to the starting depth of the layer.
Could not parse
into x and/or y coordinates.
Could not parse
into x and/or y coordinates.
Could not parse
cheese, eggs, NA
into x and/or y coordinates.
Could not parse
longitude, longitude, NA
into x and/or y coordinates.
Could not parse
latitude, latitude, NA
into x and/or y coordinates.
Could not parse
yak, yak, yak
into x and/or y coordinates.
Could not parse
xebu, xebu, xebu
into x and/or y coordinates.
Could not parse
xebu, xebu, xebu
into x and/or y coordinates.
Could not parse
xebu, xebu, xebu
into x and/or y coordinates.
Could not parse
xebu, xebu, xebu
into x and/or y coordinates.
Could not parse
cheese, eggs, spam
into x and/or y coordinates.
Could not parse
longitude, longitude, depth
into x and/or y coordinates.
Could not parse
latitude, latitude, depth
into x and/or y coordinates.
Could not parse
longitude, depth, depth
into x and/or y coordinates.
Could not parse
y, yum, X
into x, y, and/or z coordinates.
Could not parse
x, exlax, depth
into x and/or y coordinates.
Could not parse
z, z, sneeze
into x and/or y coordinates.
Could not parse
z, z, sneeze
into x and/or y coordinates.
Argument 'verbose' is not of type 'logical'.
Could not parse
spam, eggs
into x and/or y coordinates.
Using longitude and latitude
as x and y coordinates, respectively.
Using longitude and latitude
as x and y coordinates, respectively.
Loading required package: spam
Spam version 2.11-3 (2026-01-05) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following objects are masked from 'package:base':
backsolve, forwardsolve
Loading required package: viridisLite
Loading required package: RColorBrewer
Try help(fields) to get started.
Attaching package: 'fields'
The following object is masked from 'package:terra':
describe
The following object is masked from 'package:testthat':
describe
Could not parse
eggs, spam, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
into x and/or y coordinates.
Argument 'clipToOcean' is not of type 'logical'.
Argument 'clipToOcean' is not of type 'logical'.
Argument 'clipToOcean' is not of type 'logical'.
Argument 'clipToOcean' is not of type 'logical'.
Argument 'clipToOcean' is not of type 'logical'.
Argument 'clipToOcean' is not of type 'logical'.
Argument 'clipToOcean' is not of type 'logical'.
Argument 'clipToOcean' is not of type 'logical'.
Attaching package: 'dplyr'
The following objects are masked from 'package:terra':
intersect, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Using longitude, latitude, and depth
as x, y, and z coordinates, respectively.
Using longitude, latitude, and depth
as x, y, and z coordinates, respectively.
Saving _problems/test-modelDiagnostics-51.R
Could not parse
scientificName, decimalLongitude
into x and/or y coordinates.
Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Argument 'verbose' is not of type 'logical'.
Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Could not parse
scientificName, decimalLongitude
into x and/or y coordinates.
First set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Could not parse
scientificName, decimalLongitude
into x and/or y coordinates.
Argument 'verbose' is not of type 'logical'.
First set of occurrences: Using decimalLongitude and y
as x and y coordinates, respectively.
Second set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
First set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Second set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
First set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Second set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
First set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Second set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
First set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Second set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
First set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
Second set of occurrences: Using decimalLongitude and decimalLatitude
as x and y coordinates, respectively.
'rast2' was null. Replaced with blank raster.
'rast1' was null. Replaced with blank raster.
Both 'rast1' and 'rast2' were null.
They were replaced with blank rasters.
'rast2' was null. Replaced with blank raster.
'rast1' was null. Replaced with blank raster.
Both 'rast1' and 'rast2' were null.
They were replaced with blank rasters.
Argument 'graticule' is not of type 'logical'.
Argument 'verbose' is not of type 'logical'.
Argument 'graticule' is not of type 'logical'.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Input extremes exceed specified scale range.
Using input max and min instead.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Scale for y is already present.
Adding another scale for y, which will replace the existing scale.
Scale for x is already present.
Adding another scale for x, which will replace the existing scale.
Argument 'verbose' is not of type 'logical'.
Could not parse
cheese, eggs, spam
into x and/or y coordinates.
Input RasterBrick names inappropriate:
a, b, c
Names must be numeric.
Using longitude, latitude, and depth
as x, y, and z coordinates, respectively.
Using longitude, latitude, and depth
as x, y, and z coordinates, respectively.
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 243 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-marineBackground.R:48:3', 'test-marineBackground.R:61:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-modelDiagnostics.R:51:3'): MESS3D outputs as expected ──────────
Error in `MESS(P = projVals, V = cal, verbosity = 0)`: The number of variables in V and P does not match.
Backtrace:
▆
1. └─voluModel::MESS3D(calibration = calibration, projection = rastList) at test-modelDiagnostics.R:51:3
2. └─modEvA::MESS(P = projVals, V = cal, verbosity = 0)
[ FAIL 1 | WARN 1 | SKIP 2 | PASS 243 ]
Error:
! Test failures.
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [135s/185s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a_Introduction.Rmd’ using rmarkdown
--- finished re-building ‘a_Introduction.Rmd’
--- re-building ‘b_RasterProcessing.Rmd’ using rmarkdown
--- finished re-building ‘b_RasterProcessing.Rmd’
--- re-building ‘c_DataSampling.Rmd’ using rmarkdown
--- finished re-building ‘c_DataSampling.Rmd’
--- re-building ‘d_Visualization.Rmd’ using rmarkdown
--- finished re-building ‘d_Visualization.Rmd’
--- re-building ‘e_GLMWorkflow.Rmd’ using rmarkdown
Quitting from e_GLMWorkflow.Rmd:264-275 [calculate MESS]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `MESS()`:
! The number of variables in V and P does not match.
---
Backtrace:
▆
1. └─voluModel::MESS3D(calibration = datForMod, projection = projList)
2. └─modEvA::MESS(P = projVals, V = cal, verbosity = 0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'e_GLMWorkflow.Rmd' failed with diagnostics:
The number of variables in V and P does not match.
--- failed re-building ‘e_GLMWorkflow.Rmd’
SUMMARY: processing the following file failed:
‘e_GLMWorkflow.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [5s/8s] OK
- checking HTML version of manual ... [1s/2s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 3 ERRORs