* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/MatchIt.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 ‘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 ... [219s/249s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/MatchIt-00install.html' for details.
* used C++ compiler: ‘clang version 20.1.0-rc3’
* 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 ... [41s/62s] 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 ... [22s/25s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [90s/114s] 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 = 22286 bytes
Input file size = 23168 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21516
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 21225
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 = 21225
Output IDAT size = 21225 bytes (1061 bytes decrease)
Output file size = 21303 bytes (1865 bytes = 8.05% 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 = 25435 bytes
Input file size = 26329 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23399
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 23353
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 = 23353
Output IDAT size = 23353 bytes (2082 bytes decrease)
Output file size = 23431 bytes (2898 bytes = 11.01% 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/24s] 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