- using R Under development (unstable) (2025-10-13 r88918)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘rbmiUtils/DESCRIPTION’ ... OK
- this is package ‘rbmiUtils’ version ‘0.1.6’
- 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 ‘rbmiUtils’ can be installed ... [6s/11s] OK
See the install log 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 ... 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 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 ... 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 ... [17s/36s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [21s/42s] ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [20s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(rbmiUtils)
>
> test_check("rbmiUtils")
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 62 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-utils.R:39:3'): positive test get_imputed_data (from vignettes) ──
Error in `fit_mcmc(designmat = model_df_scaled[, -1, drop = FALSE], outcome = model_df_scaled[,
1, drop = TRUE], group = data2[[vars$group]], visit = data2[[vars$visit]],
subjid = data2[[vars$subjid]], method = method, quiet = quiet)`: unable to load shared object '/tmp/Rtmp3OBhSe/working_dir/Rtmp7dDa8z/file35f74b5029332.so':
libunwind.so.1: cannot open shared object file: No such file or directory
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method, quiet = TRUE) at test-utils.R:39:3
2. └─rbmi:::draws.bayes(...)
3. └─rbmi:::fit_mcmc(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 62 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [31s/67s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘analyse2.Rmd’ using rmarkdown
Quitting from analyse2.Rmd:90-99 [impute]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `fit_mcmc()`:
! unable to load shared object '/tmp/Rtmp3OBhSe/working_dir/RtmpG4dQqf/file360ef95ff06858.so':
libunwind.so.1: cannot open shared object file: No such file or directory
---
Backtrace:
▆
1. ├─rbmi::draws(data = dat, vars = vars, method = method)
2. └─rbmi:::draws.bayes(data = dat, vars = vars, method = method)
3. └─rbmi:::fit_mcmc(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'analyse2.Rmd' failed with diagnostics:
unable to load shared object '/tmp/Rtmp3OBhSe/working_dir/RtmpG4dQqf/file360ef95ff06858.so':
libunwind.so.1: cannot open shared object file: No such file or directory
--- failed re-building ‘analyse2.Rmd’
SUMMARY: processing the following file failed:
‘analyse2.Rmd’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [7s/12s] 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: 2 ERRORs