* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘RSDA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RSDA’ version ‘3.2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘RSDA’ can be installed ... [38s/55s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/RSDA-00install.html' for details.
* checking installed package size ... INFO
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 4.2Mb
* 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 ... [7s/10s] OK
* checking whether startup messages can be suppressed ... 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/89s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/36s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [9s/11s] OK
Running ‘testthat.R’ [8s/11s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [31m/40m] ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 36617 bytes
Input file size = 36743 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26166
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 = 26166
Output IDAT size = 26166 bytes (10451 bytes decrease)
Output file size = 26244 bytes (10499 bytes = 28.57% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-2.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38887 bytes
Input file size = 39013 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27823
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 = 27823
Output IDAT size = 27823 bytes (11064 bytes decrease)
Output file size = 27901 bytes (11112 bytes = 28.48% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-3.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 8914 bytes
Input file size = 9004 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8136
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 IDAT size = 7598
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 = 5 IDAT size = 7598
Output IDAT size = 7598 bytes (1316 bytes decrease)
Output file size = 7676 bytes (1328 bytes = 14.75% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-28-4.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11328 bytes
Input file size = 11418 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9791
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 IDAT size = 9777
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 = 5 IDAT size = 9777
Output IDAT size = 9777 bytes (1551 bytes decrease)
Output file size = 9855 bytes (1563 bytes = 13.69% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-29-1.png
576x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7076 bytes
Input file size = 7934 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6165
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6165
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 = 6165
Output IDAT size = 6165 bytes (911 bytes decrease)
Output file size = 6243 bytes (1691 bytes = 21.31% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-30-1.png
576x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7750 bytes
Input file size = 8608 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6714
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 6699
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 = 6699
Output IDAT size = 6699 bytes (1051 bytes decrease)
Output file size = 6777 bytes (1831 bytes = 21.27% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-31-1.png
576x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7391 bytes
Input file size = 8249 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 6110
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 = 6110
Output IDAT size = 6110 bytes (1281 bytes decrease)
Output file size = 6188 bytes (2061 bytes = 24.98% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-38-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 29484 bytes
Input file size = 29598 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21370
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 = 21370
Output IDAT size = 21370 bytes (8114 bytes decrease)
Output file size = 21448 bytes (8150 bytes = 27.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-38-2.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31562 bytes
Input file size = 31676 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24683
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 = 24683
Output IDAT size = 24683 bytes (6879 bytes decrease)
Output file size = 24761 bytes (6915 bytes = 21.83% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-42-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31444 bytes
Input file size = 31558 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22932
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 = 22932
Output IDAT size = 22932 bytes (8512 bytes decrease)
Output file size = 23010 bytes (8548 bytes = 27.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-42-2.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32103 bytes
Input file size = 32217 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25854
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 = 25854
Output IDAT size = 25854 bytes (6249 bytes decrease)
Output file size = 25932 bytes (6285 bytes = 19.51% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-43-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 10465 bytes
Input file size = 10555 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8652
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 = 8652
Output IDAT size = 8652 bytes (1813 bytes decrease)
Output file size = 8730 bytes (1825 bytes = 17.29% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-43-2.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 27297 bytes
Input file size = 27411 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21070
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 = 21070
Output IDAT size = 21070 bytes (6227 bytes decrease)
Output file size = 21148 bytes (6263 bytes = 22.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-44-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11365 bytes
Input file size = 11455 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9410
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 = 9410
Output IDAT size = 9410 bytes (1955 bytes decrease)
Output file size = 9488 bytes (1967 bytes = 17.17% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/RSDA.Rcheck/vign_test/RSDA/vignettes/introduction_files/figure-html/unnamed-chunk-45-1.png
576x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 15761 bytes
Input file size = 15851 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12690
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 = 12690
Output IDAT size = 12690 bytes (3071 bytes decrease)
Output file size = 12768 bytes (3083 bytes = 19.45% decrease)
* checking PDF version of manual ... [13s/17s] OK
* checking HTML version of manual ... [7s/13s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR