* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/FRK.Rcheck’
* using R Under development (unstable) (2025-02-14 r87716)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘FRK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FRK’ version ‘2.3.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘dggrids’
* 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 ‘FRK’ can be installed ... [322s/464s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/FRK-00install.html' for details.
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 ... [10s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/11s] OK
* checking whether the package can be unloaded cleanly ... [8s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/12s] OK
* checking loading without being on the library search path ... [9s/11s] 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 ... [66s/83s] OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/23s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [31m/23m] ERROR
Running ‘testthat.R’ [31m/23m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> ops <- options("crayon.enabled" = FALSE)
> library(testthat)
> require("covr")
Loading required package: covr
>
> test_check("FRK")
Loading required package: FRK
Attaching package: 'FRK'
The following object is masked from 'package:stats':
simulate
NOTE: In FRK >2.0 simple_kriging_fixed = FALSE by default, and hence
universal kriging is done by default. However this is only the case when
method = 'TMB'. When method = 'EM', simple kriging is done, irrespective of
what the argument simple_kriging_fixed is set to.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Maximum EM iterations reached
Intercept
0.152395
Formula: z ~ 1
Assumed response distribution: gaussian
Specified link function: identity
Method of model fitting: EM
Number of datasets: 1
Number of basis functions: 18
Class of basis functions: Basis
Number of BAUs [extract using object@BAUs]: 138
Number of observations [extract using object@Z]: 50
Mean obs. variance at BAU level [extract using object@Ve]: 0.01
Fine-scale variance proportionality constant [extract using object@sigma2fshat]: 0.1172823
Dimensions of C in Z = C*Y + e [extract using object@Cmat]: c(50L, 138L)
Dimensions of S in Y = X*alpha + S*eta + delta [extract using object@S]: c(50L, 18L)
Number of covariates: 1
Formula: z ~ 1
Assumed response distribution: gaussian
Specified link function: identity
Method of model fitting: EM
Number of datasets: 1
Number of basis functions: 18
Class of basis functions: Basis
Number of BAUs [extract using object@BAUs]: 138
Number of observations [extract using object@Z]: 50
Mean obs. variance at BAU level [extract using object@Ve]: 0.01
Fine-scale variance proportionality constant [extract using object@sigma2fshat]: 0.1172823
Dimensions of C in Z = C*Y + e [extract using object@Cmat]: c(50L, 138L)
Dimensions of S in Y = X*alpha + S*eta + delta [extract using object@S]: c(50L, 18L)
Number of covariates: 1
NOTE: In FRK >2.0 simple_kriging_fixed = FALSE by default, and hence
universal kriging is done by default. However this is only the case when
method = 'TMB'. When method = 'EM', simple kriging is done, irrespective of
what the argument simple_kriging_fixed is set to.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Maximum EM iterations reached
Averaging over polygons...
NOTE: In FRK >2.0 simple_kriging_fixed = FALSE by default, and hence
universal kriging is done by default. However this is only the case when
method = 'TMB'. When method = 'EM', simple kriging is done, irrespective of
what the argument simple_kriging_fixed is set to.
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
Maximum EM iterations reached
Averaging over polygons...
NOTE: In FRK >2.0 simple_kriging_fixed = FALSE by default, and hence
universal kriging is done by default. However this is only the case when
method = 'TMB'. When method = 'EM', simple kriging is done, irrespective of
what the argument simple_kriging_fixed is set to.
|
| | 0%
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [33m/25m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘FRK_intro.Rnw’ using knitr
** Processing: figure/unnamed-chunk-27-1.png
600x600 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 99847 bytes
Input file size = 100849 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 98361
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 96990
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 96990
Output IDAT size = 96990 bytes (2857 bytes decrease)
Output file size = 97068 bytes (3781 bytes = 3.75% decrease)
** Processing: figure/unnamed-chunk-27-2.png
600x600 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 59981 bytes
Input file size = 60923 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 56451
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 56073
zc = 1 zm = 8 zs = 2 f = 0
zc = 9 zm = 8 zs = 3 f = 0
zc = 9 zm = 8 zs = 0 f = 5
zc = 9 zm = 8 zs = 1 f = 5
zc = 1 zm = 8 zs = 2 f = 5
zc = 9 zm = 8 zs = 3 f = 5
Selecting parameters:
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 56073
Output IDAT size = 56073 bytes (3908 bytes decrease)
Output file size = 56151 bytes (4772 bytes = 7.83% decrease)
--- re-building ‘FRK_non-Gaussian.Rnw’ using knitr
--- finished re-building ‘FRK_non-Gaussian.Rnw’
SUMMARY: processing the following file failed:
‘FRK_intro.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [9s/13s] 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: 2 ERRORs