- using R version 4.4.2 (2024-10-31)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-14 (Debian 14.2.0-6) 14.2.0
GNU Fortran (Debian 14.2.0-6) 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 ... NOTE
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 ... [2s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [2s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
- checking loading without being on the library search path ... [2s/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 ... [13s/17s] OK
- checking Rd files ... [0s/1s] 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 ... [8s/10s] ERROR
Running ‘testthat.R’ [7s/9s]
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 ... [69s/88s] ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘diagnostics.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-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-release-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-release-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-release-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-release-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-release-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-release-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-release-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 = 21007 bytes
Input file size = 21109 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16924
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 = 16924
Output IDAT size = 16924 bytes (4083 bytes decrease)
Output file size = 17002 bytes (4107 bytes = 19.46% decrease)
--- finished re-building ‘diagnostics.Rmd’
--- re-building ‘user_guide.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-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 ... [5s/7s] OK
- checking HTML version of manual ... [1s/1s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs, 1 NOTE