* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/siland.Rcheck’
* 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 ‘siland/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘siland’ version ‘3.0.2’
* 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 ‘siland’ can be installed ... [60s/84s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/siland-00install.html' 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 ... [19s/30s] OK
* checking whether the package can be loaded with stated dependencies ... [19s/28s] OK
* checking whether the package can be unloaded cleanly ... [20s/31s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/24s] OK
* checking whether the namespace can be unloaded cleanly ... [19s/27s] OK
* checking loading without being on the library search path ... [19s/23s] 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 ... [85s/116s] OK
* checking Rd files ... NOTE
checkRd: (-1) siland.Rd:64: Lost braces; missing escapes or markup?
64 | \item x_{l,i}, local variable l,
| ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
| ^
* 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 ... [19s/27s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [129s/153s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘siland.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/siland.Rcheck/vign_test/siland/vignettes/siland_files/figure-html/unnamed-chunk-5-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 189382 bytes
Input file size = 189736 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 116317
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 = 116317
Output IDAT size = 116317 bytes (73065 bytes decrease)
Output file size = 116395 bytes (73341 bytes = 38.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/siland.Rcheck/vign_test/siland/vignettes/siland_files/figure-html/unnamed-chunk-9-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21197 bytes
Input file size = 21299 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16939
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 = 16939
Output IDAT size = 16939 bytes (4258 bytes decrease)
Output file size = 17017 bytes (4282 bytes = 20.10% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/siland.Rcheck/vign_test/siland/vignettes/siland_files/figure-html/unnamed-chunk-11-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 74002 bytes
Input file size = 74188 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 66918
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 = 66918
Output IDAT size = 66918 bytes (7084 bytes decrease)
Output file size = 66996 bytes (7192 bytes = 9.69% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/siland.Rcheck/vign_test/siland/vignettes/siland_files/figure-html/unnamed-chunk-13-1.png
672x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21690 bytes
Input file size = 21792 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17387
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 = 17387
Output IDAT size = 17387 bytes (4303 bytes decrease)
Output file size = 17465 bytes (4327 bytes = 19.86% decrease)
Quitting from lines 161-162 [unnamed-chunk-14] (siland.Rmd)
Error: processing vignette 'siland.Rmd' failed with diagnostics:
function cannot be evaluated at initial parameters
--- failed re-building ‘siland.Rmd’
SUMMARY: processing the following file failed:
‘siland.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [9s/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, 1 NOTE