* using log directory ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/nestedLogit.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-13 (Debian 13.2.0-25) 13.2.0 GNU Fortran (Debian 13.2.0-25) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘nestedLogit/DESCRIPTION’ ... OK * this is package ‘nestedLogit’ version ‘0.3.2’ * 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 ‘nestedLogit’ can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/nestedLogit-00install.html' 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 ... [5s/6s] OK * checking whether the package can be loaded with stated dependencies ... [4s/4s] OK * checking whether the package can be unloaded cleanly ... [4s/4s] OK * checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK * checking whether the namespace can be unloaded cleanly ... [5s/6s] OK * checking loading without being on the library search path ... [5s/6s] 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 ... [26s/31s] OK * checking Rd files ... [1s/1s] NOTE checkRd: (-1) GSS.Rd:17: Lost braces 17 | code{2016}.} | ^ * 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 ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [13s/16s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [8s/10s] OK Running ‘spelling.R’ [0s/1s] Running ‘testthat.R’ [8s/9s] * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [24s/32s] ERROR Error(s) in re-building vignettes: ... --- re-building ‘nestedLogit.Rmd’ using rmarkdown ** Processing: fig/wlf-plot-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38737 bytes Input file size = 38863 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29909 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 = 29909 Output IDAT size = 29909 bytes (8828 bytes decrease) Output file size = 29987 bytes (8876 bytes = 22.84% decrease) ** Processing: fig/wlf-effect-plot-1-1.png 672x576 pixels, 3x8 bits/pixel, RGB Input IDAT size = 55761 bytes Input file size = 55911 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 43999 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 = 43999 Output IDAT size = 43999 bytes (11762 bytes decrease) Output file size = 44077 bytes (11834 bytes = 21.17% decrease) ** Processing: fig/wlf-effect-plot-2-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 28568 bytes Input file size = 28682 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23984 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 = 23984 Output IDAT size = 23984 bytes (4584 bytes decrease) Output file size = 24062 bytes (4620 bytes = 16.11% decrease) ** Processing: fig/wlf-alt-plot-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 37411 bytes Input file size = 37537 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 29174 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 = 29174 Output IDAT size = 29174 bytes (8237 bytes decrease) Output file size = 29252 bytes (8285 bytes = 22.07% decrease) --- finished re-building ‘nestedLogit.Rmd’ --- re-building ‘plotting-ggplot.Rmd’ using rmarkdown ** Processing: fig/wlf-ggplot-p1-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 66096 bytes Input file size = 66270 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52263 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 = 52263 Output IDAT size = 52263 bytes (13833 bytes decrease) Output file size = 52341 bytes (13929 bytes = 21.02% decrease) Quitting from lines 150-156 [wlf-ggplot-p2] (plotting-ggplot.Rmd) Error: processing vignette 'plotting-ggplot.Rmd' failed with diagnostics: Problem while converting geom to grob. ℹ Error occurred in the 4th layer. Caused by error in `txt$shape[, shape_vars]`: ! Can't subset columns that don't exist. ✖ Column `x_midpoint` doesn't exist. --- failed re-building ‘plotting-ggplot.Rmd’ --- re-building ‘standard-errors.Rmd’ using rmarkdown --- finished re-building ‘standard-errors.Rmd’ SUMMARY: processing the following file failed: ‘plotting-ggplot.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... [8s/10s] OK * checking HTML version of manual ... [1s/2s] OK * checking for non-standard things in the check directory ... OK * DONE Status: 1 ERROR, 1 NOTE