• 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 the install log 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