• using R Under development (unstable) (2025-02-15 r87723)
• 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 ‘palaeoSig/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘palaeoSig’ version ‘2.1-3’
• 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 ‘palaeoSig’ can be installed ... [19s/27s] OK See the install log for details.
• 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 ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... 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 ... [25s/35s] OK
• checking Rd files ... NOTE checkRd: (-1) jointsig.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:44-45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) jointsig.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) obs.cor.Rd:114-118: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) obs.cor.Rd:119-122: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) obs.cor.Rd:123-124: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) predict.agelme.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:100-103: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:106-107: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) randomTF.Rd:108: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) rne.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) rne.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
• 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 data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [21s/25s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... OK   Running ‘testthat.R’
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [32m/23m] ERROR Error(s) in re-building vignettes: --- re-building ‘h-block-crossvalidation.Rmd’ using rmarkdown # A tibble: 1 × 1    RMSE   <dbl> 1 1.28 ** Processing: /data/gannet/ripley/R/packages/tests-devel/palaeoSig.Rcheck/vign_test/palaeoSig/vignettes/h-block-crossvalidation_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12132 bytes Input file size = 12222 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8860   zc = 9 zm = 8 zs = 1 f = 0   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 = 0 f = 0 IDAT size = 8860 Output IDAT size = 8860 bytes (3272 bytes decrease) Output file size = 8938 bytes (3284 bytes = 26.87% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/palaeoSig.Rcheck/vign_test/palaeoSig/vignettes/h-block-crossvalidation_files/figure-html/unnamed-chunk-5-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11367 bytes Input file size = 11457 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8721   zc = 9 zm = 8 zs = 1 f = 0   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 = 0 f = 0 IDAT size = 8721 Output IDAT size = 8721 bytes (2646 bytes decrease) Output file size = 8799 bytes (2658 bytes = 23.20% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/palaeoSig.Rcheck/vign_test/palaeoSig/vignettes/h-block-crossvalidation_files/figure-html/unnamed-chunk-6-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 12477 bytes Input file size = 12567 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9348   zc = 9 zm = 8 zs = 1 f = 0   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 = 0 f = 0 IDAT size = 9348 Output IDAT size = 9348 bytes (3129 bytes decrease) Output file size = 9426 bytes (3141 bytes = 24.99% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/palaeoSig.Rcheck/vign_test/palaeoSig/vignettes/h-block-crossvalidation_files/figure-html/unnamed-chunk-8-1.png 288x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 16021 bytes Input file size = 16891 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15557   zc = 9 zm = 8 zs = 1 f = 0   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 = 0 f = 0 IDAT size = 15557 Output IDAT size = 15557 bytes (464 bytes decrease) Output file size = 15635 bytes (1256 bytes = 7.44% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-devel/palaeoSig.Rcheck/vign_test/palaeoSig/vignettes/h-block-crossvalidation_files/figure-html/unnamed-chunk-9-1.png 288x288 pixels, 8 bits/pixel, 243 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 3314 bytes Input file size = 4133 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2944   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2936   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 = 2936 Output IDAT size = 2936 bytes (378 bytes decrease) Output file size = 3014 bytes (1119 bytes = 27.07% decrease) Warning in so_squares < (min(so_squares) + 0.1 * range(so_squares)) :   longer object length is not a multiple of shorter object length # A tibble: 1 × 1       h   <dbl> 1 900 Warning in so_squares < (min(so_squares) + 0.1 * range(so_squares)) :   longer object length is not a multiple of shorter object length # A tibble: 1 × 1       h   <dbl> 1 900 --- finished re-building ‘h-block-crossvalidation.Rmd’ --- re-building ‘randomTF-spatial.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-devel/palaeoSig.Rcheck/vign_test/palaeoSig/vignettes/randomTF-spatial_files/figure-html/unnamed-chunk-4-1.png 288x288 pixels, 3x8 bits/pixel, RGB Input IDAT size = 11918 bytes Input file size = 12008 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9212   zc = 9 zm = 8 zs = 1 f = 0   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 = 0 f = 0 IDAT size = 9212 Output IDAT size = 9212 bytes (2706 bytes decrease) Output file size = 9290 bytes (2718 bytes = 22.63% decrease) SUMMARY: processing the following file failed:   ‘randomTF-spatial.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [10s/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: 1 ERROR, 1 NOTE