• using R Under development (unstable) (2024-12-19 r87451)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-8) 14.2.0     GNU Fortran (Debian 14.2.0-8) 14.2.0
• running under: Debian GNU/Linux trixie/sid
• using session charset: UTF-8
• checking for file ‘rprev/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘rprev’ version ‘1.0.5’
• checking package namespace information ... OK
• checking package dependencies ... INFO Packages suggested but not available for checking:   'flexsurv', 'flexsurvcure'
• 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 serialization versions ... OK
• checking whether package ‘rprev’ can be installed ... OK See the install log 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 ... [1s/2s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [1s/2s] 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 ... [10s/13s] OK
• checking Rd files ... [0s/0s] 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 ... [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 ... [2s/2s] OK
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [7s/7s] ERROR   Running ‘testthat.R’ [6s/7s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library(testthat)   > library(rprev)   Loading required package: survival   >   > test_check("rprev")   [ FAIL 1 | WARN 0 | SKIP 0 | PASS 136 ]      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_survival_model.R:80:9'): predict_survival_probability produces correct survival estimates ──   <packageNotFoundError/error/condition>   Error in `loadNamespace(x)`: there is no package called 'flexsurv'   Backtrace:       ▆    1. ├─rprev (local) test_surv(Surv(time, status) ~ 1, "weibull", data.frame(), time = 500) at test_survival_model.R:93:5    2. └─base::loadNamespace(x) at test_survival_model.R:80:9    3. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)    4. └─base (local) withOneRestart(expr, restarts[[1L]])    5. └─base (local) doWithOneRestart(return(expr), restart)      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 136 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [50s/63s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘diagnostics.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/unnamed-chunk-3-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 32136 bytes Input file size = 32250 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25816   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 = 25816 Output IDAT size = 25816 bytes (6320 bytes decrease) Output file size = 25894 bytes (6356 bytes = 19.71% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/incidenceage-1.png 672x384 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 10174 bytes Input file size = 11044 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8346   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 8317   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 = 8317 Output IDAT size = 8317 bytes (1857 bytes decrease) Output file size = 8395 bytes (2649 bytes = 23.99% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/survivaldiag-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 22632 bytes Input file size = 22734 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17721   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 = 17721 Output IDAT size = 17721 bytes (4911 bytes decrease) Output file size = 17799 bytes (4935 bytes = 21.71% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/survivaldiag2-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 30731 bytes Input file size = 30845 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23109   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 = 23109 Output IDAT size = 23109 bytes (7622 bytes decrease) Output file size = 23187 bytes (7658 bytes = 24.83% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/survivaldiag4-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27542 bytes Input file size = 27656 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22064   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 = 22064 Output IDAT size = 22064 bytes (5478 bytes decrease) Output file size = 22142 bytes (5514 bytes = 19.94% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/survivaldiag3-1.png 672x384 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 38093 bytes Input file size = 38999 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36717   zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 36365   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 = 36365 Output IDAT size = 36365 bytes (1728 bytes decrease) Output file size = 36443 bytes (2556 bytes = 6.55% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/ageform3-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20595 bytes Input file size = 20697 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19705   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 = 18989   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 = 18989 Output IDAT size = 18989 bytes (1606 bytes decrease) Output file size = 19067 bytes (1630 bytes = 7.88% decrease) ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/diagnostics_files/figure-html/unnamed-chunk-9-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 20993 bytes Input file size = 21095 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16911   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 = 16911 Output IDAT size = 16911 bytes (4082 bytes decrease) Output file size = 16989 bytes (4106 bytes = 19.46% decrease) --- finished re-building ‘diagnostics.Rmd’ --- re-building ‘user_guide.Rmd’ using rmarkdown ** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rprev.Rcheck/vign_test/rprev/vignettes/user_guide_files/figure-html/basicsurvival-1.png 672x384 pixels, 3x8 bits/pixel, RGB Input IDAT size = 23071 bytes Input file size = 23173 bytes Trying:   zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19055   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 = 19055 Output IDAT size = 19055 bytes (4016 bytes decrease) Output file size = 19133 bytes (4040 bytes = 17.43% decrease) Quitting from lines 117-119 [unnamed-chunk-7] (user_guide.Rmd) Error: processing vignette 'user_guide.Rmd' failed with diagnostics: there is no package called 'flexsurv' --- failed re-building ‘user_guide.Rmd’ SUMMARY: processing the following file failed:   ‘user_guide.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [4s/5s] OK
• checking HTML version of manual ... [0s/1s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs