• using R Under development (unstable) (2025-02-19 r87749)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 20.1.0-rc2     flang version 20.1.0-rc2
• running under: Fedora Linux 40 (Workstation Edition)
• using session charset: UTF-8
• using option ‘--no-stop-on-test-error’
• checking for file ‘MatchIt/DESCRIPTION’ ... OK
• this is package ‘MatchIt’ version ‘4.7.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... INFO Package suggested but not available for checking: ‘gurobi’
• 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 ‘MatchIt’ can be installed ... [210s/217s] OK See the install log for details.
• used C++ compiler: ‘clang version 20.1.0-rc2’
• checking installed package size ... OK
• 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 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 ... [39s/54s] 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 line endings in Makefiles ... OK
• checking compilation flags in Makevars ... OK
• checking for GNU extensions in Makefiles ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
• checking compilation flags used ... OK
• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [21s/25s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [90s/124s] ERROR Error(s) in re-building vignettes: --- re-building ‘MatchIt.Rmd’ using rmarkdown_notangle ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/MatchIt_files/figure-html/unnamed-chunk-7-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 22102 bytes Input file size = 22984 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21325   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 21070   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 = 21070 Output IDAT size = 21070 bytes (1032 bytes decrease) Output file size = 21148 bytes (1836 bytes = 7.99% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/MatchIt_files/figure-html/unnamed-chunk-8-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 14986 bytes Input file size = 15856 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13276   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 = 13276 Output IDAT size = 13276 bytes (1710 bytes decrease) Output file size = 13354 bytes (2502 bytes = 15.78% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/MatchIt_files/figure-html/unnamed-chunk-12-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11831 bytes Input file size = 12701 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10710   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 10578   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 = 10578 Output IDAT size = 10578 bytes (1253 bytes decrease) Output file size = 10656 bytes (2045 bytes = 16.10% decrease) --- finished re-building ‘MatchIt.Rmd’ --- re-building ‘assessing-balance.Rmd’ using rmarkdown_notangle ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-3-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 16018 bytes Input file size = 16888 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14870   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 14684   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 = 14684 Output IDAT size = 14684 bytes (1334 bytes decrease) Output file size = 14762 bytes (2126 bytes = 12.59% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-4-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 25490 bytes Input file size = 26384 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23478   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 23438   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 = 23438 Output IDAT size = 23438 bytes (2052 bytes decrease) Output file size = 23516 bytes (2868 bytes = 10.87% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-5-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11666 bytes Input file size = 12536 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10322   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 = 10322 Output IDAT size = 10322 bytes (1344 bytes decrease) Output file size = 10400 bytes (2136 bytes = 17.04% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-6-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15727 bytes Input file size = 16597 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14072   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 = 14072 Output IDAT size = 14072 bytes (1655 bytes decrease) Output file size = 14150 bytes (2447 bytes = 14.74% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-10-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11959 bytes Input file size = 12829 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10962   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 10952   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 = 10952 Output IDAT size = 10952 bytes (1007 bytes decrease) Output file size = 11030 bytes (1799 bytes = 14.02% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-11-1.png 672x480 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 15017 bytes Input file size = 15887 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13363   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 = 13363 Output IDAT size = 13363 bytes (1654 bytes decrease) Output file size = 13441 bytes (2446 bytes = 15.40% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-16-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 21454 bytes Input file size = 21556 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17394   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 = 17394 Output IDAT size = 17394 bytes (4060 bytes decrease) Output file size = 17472 bytes (4084 bytes = 18.95% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-17-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 35854 bytes Input file size = 35980 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28142   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 = 28142 Output IDAT size = 28142 bytes (7712 bytes decrease) Output file size = 28220 bytes (7760 bytes = 21.57% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-18-1.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 42260 bytes Input file size = 42398 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 39985   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 = 37602   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 = 37602 Output IDAT size = 37602 bytes (4658 bytes decrease) Output file size = 37680 bytes (4718 bytes = 11.13% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-18-2.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 16181 bytes Input file size = 16271 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14594   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 = 14064   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 = 14064 Output IDAT size = 14064 bytes (2117 bytes decrease) Output file size = 14142 bytes (2129 bytes = 13.08% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-clang/MatchIt.Rcheck/vign_test/MatchIt/vignettes/assessing-balance_files/figure-html/unnamed-chunk-18-3.png 672x480 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20201 bytes Input file size = 20303 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17001   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 = 17001 Output IDAT size = 17001 bytes (3200 bytes decrease) Output file size = 17079 bytes (3224 bytes = 15.88% decrease) --- finished re-building ‘assessing-balance.Rmd’ --- re-building ‘estimating-effects.Rmd’ using rmarkdown_notangle Quitting from lines 583-589 [unnamed-chunk-23] (estimating-effects.Rmd) Error: processing vignette 'estimating-effects.Rmd' failed with diagnostics: Assertion failed. One of the following must apply:  * checkmate::check_character(hypothesis): Must comply to pattern '='  * checkmate::check_numeric(hypothesis): Must be of type 'numeric', not 'character'  * checkmate::check_formula(hypothesis): Must be a formula, not character  * checkmate::check_matrix(hypothesis): Must be of type 'matrix', not 'character'  * checkmate::check_function(hypothesis): Must be a function, not 'character'  * checkmate::check_null(hypothesis): Must be NULL --- failed re-building ‘estimating-effects.Rmd’ --- re-building ‘matching-methods.Rmd’ using rmarkdown_notangle --- finished re-building ‘matching-methods.Rmd’ --- re-building ‘sampling-weights.Rmd’ using rmarkdown_notangle --- finished re-building ‘sampling-weights.Rmd’ SUMMARY: processing the following file failed:   ‘estimating-effects.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [19s/27s] OK
• checking HTML version of manual ... [11s/19s] OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 1 ERROR