Last updated on 2024-12-22 10:50:25 CET.
| Package | ERROR | OK |
|---|---|---|
| heemod | 1 | 12 |
| rgho | 1 | 12 |
Current CRAN status: ERROR: 1, OK: 12
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘heemod-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apply_shift
> ### Title: Apply a time shift to a survival distribution
> ### Aliases: apply_shift
>
> ### ** Examples
>
>
> dist1 <- define_surv_dist(distribution = "gamma", rate = 0.25, shape = 3)
> shift_dist <- apply_shift(dist1, 4)
> compute_surv(dist1, 1:10)
Loading required namespace: flexsurv
Failed with error: ‘there is no package called ‘flexsurv’’
Error in eval_surv.surv_dist(x, cycle_length * time_, ...) :
'flexsurv' package required.
Calls: compute_surv -> eval_surv -> eval_surv.surv_dist
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [40s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(heemod)
>
> test_check("heemod")
I: detected use of 'state_time', expanding states: A, B.
I: detected use of 'state_time', expanding states: A, B.
I: detected use of 'state_time', expanding states: A, B.
I: detected use of 'state_time', expanding states: A, B.
I: detected use of 'state_time', expanding states: A, B.
I: detected use of 'state_time', expanding state: A.
I: detected use of 'state_time', expanding state: B.
I: detected use of 'state_time', expanding state: C.
Updating strategy 'I'...
Updating strategy 'II'...
Updating strategy 'I'...
Updating strategy 'II'...
No weights specified in update, using equal weights.
Updating strategy 'I'...
Updating strategy 'II'...
Loading required namespace: diagram
I: detected use of 'state_time', expanding state: A.
I: detected use of 'state_time', expanding state: A.
Updating strategy 'standard'...
Updating strategy 'new'...
Updating strategy 'standard'...
Updating strategy 'new'...
Cluster closed.
Resampling strategy 'I'...
Resampling strategy 'II'...
Resampling strategy 'I'...
Resampling strategy 'II'...
Resampling strategy 'I'...
Resampling strategy 'II'...
Loading required namespace: logitnorm
I: detected use of 'state_time', expanding state: X2.
II: detected use of 'state_time', expanding state: X2.
Resampling strategy 'I'...
Resampling strategy 'II'...
Loading required namespace: flexsurv
Failed with error: 'there is no package called 'flexsurv''
Resampling strategy 'standard'...
Resampling strategy 'new'...
Updating strategy 'standard'...
Updating strategy 'new'...
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 393 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_starting_values.R:200:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_part_surv.R:1:1'): (code run outside of `test_that()`) ─────────
<packageNotFoundError/error/condition>
Error in `library(flexsurv)`: there is no package called 'flexsurv'
Backtrace:
▆
1. └─base::library(flexsurv) at test_part_surv.R:1:1
── Error ('test_surv_eval.R:1:1'): (code run outside of `test_that()`) ─────────
<packageNotFoundError/error/condition>
Error in `library(flexsurv)`: there is no package called 'flexsurv'
Backtrace:
▆
1. └─base::library(flexsurv) at test_surv_eval.R:1:1
── Error ('test_surv_psa.R:7:1'): (code run outside of `test_that()`) ──────────
Error in `define_surv_dist(distribution = "weibullPH", shape = 1)`: 'flexsurv' package required.
Backtrace:
▆
1. └─heemod::define_surv_dist(distribution = "weibullPH", shape = 1) at test_surv_psa.R:7:1
[ FAIL 3 | WARN 0 | SKIP 1 | PASS 393 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a_introduction.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/a_introduction_files/figure-html/unnamed-chunk-6-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21412 bytes
Input file size = 21514 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17718
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 = 17718
Output IDAT size = 17718 bytes (3694 bytes decrease)
Output file size = 17796 bytes (3718 bytes = 17.28% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/a_introduction_files/figure-html/unnamed-chunk-7-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 19843 bytes
Input file size = 19945 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 16075
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 = 16075
Output IDAT size = 16075 bytes (3768 bytes decrease)
Output file size = 16153 bytes (3792 bytes = 19.01% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/a_introduction_files/figure-html/unnamed-chunk-8-1.png
576x384 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10735 bytes
Input file size = 11605 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9810
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 = 9810
Output IDAT size = 9810 bytes (925 bytes decrease)
Output file size = 9888 bytes (1717 bytes = 14.80% decrease)
--- finished re-building ‘a_introduction.Rmd’
--- re-building ‘b_time_dependency.Rmd’ using rmarkdown
--- finished re-building ‘b_time_dependency.Rmd’
--- re-building ‘c_homogeneous.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/c_homogeneous_files/figure-html/unnamed-chunk-4-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17372 bytes
Input file size = 18254 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15863
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 15829
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 = 15829
Output IDAT size = 15829 bytes (1543 bytes decrease)
Output file size = 15907 bytes (2347 bytes = 12.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/c_homogeneous_files/figure-html/unnamed-chunk-5-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 17262 bytes
Input file size = 18144 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 15782
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 15769
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 = 15769
Output IDAT size = 15769 bytes (1493 bytes decrease)
Output file size = 15847 bytes (2297 bytes = 12.66% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/c_homogeneous_files/figure-html/unnamed-chunk-13-1.png
576x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 64775 bytes
Input file size = 64937 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 49997
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 = 49997
Output IDAT size = 49997 bytes (14778 bytes decrease)
Output file size = 50075 bytes (14862 bytes = 22.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/c_homogeneous_files/figure-html/unnamed-chunk-14-1.png
576x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 78187 bytes
Input file size = 78373 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 57365
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 = 57365
Output IDAT size = 57365 bytes (20822 bytes decrease)
Output file size = 57443 bytes (20930 bytes = 26.71% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/c_homogeneous_files/figure-html/unnamed-chunk-15-1.png
576x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 86798 bytes
Input file size = 86996 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 63864
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 = 63864
Output IDAT size = 63864 bytes (22934 bytes decrease)
Output file size = 63942 bytes (23054 bytes = 26.50% decrease)
--- finished re-building ‘c_homogeneous.Rmd’
--- re-building ‘d_non_homogeneous.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/d_non_homogeneous_files/figure-html/unnamed-chunk-4-1.png
576x576 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 19274 bytes
Input file size = 20156 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17654
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 17605
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 = 17605
Output IDAT size = 17605 bytes (1669 bytes decrease)
Output file size = 17683 bytes (2473 bytes = 12.27% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/d_non_homogeneous_files/figure-html/unnamed-chunk-8-1.png
576x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 83935 bytes
Input file size = 84133 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 61718
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 = 61718
Output IDAT size = 61718 bytes (22217 bytes decrease)
Output file size = 61796 bytes (22337 bytes = 26.55% decrease)
--- finished re-building ‘d_non_homogeneous.Rmd’
--- re-building ‘e_probabilistic.Rmd’ using rmarkdown
--- finished re-building ‘e_probabilistic.Rmd’
--- re-building ‘f_sensitivity.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/f_sensitivity_files/figure-html/unnamed-chunk-5-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14243 bytes
Input file size = 14333 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11894
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 = 11894
Output IDAT size = 11894 bytes (2349 bytes decrease)
Output file size = 11972 bytes (2361 bytes = 16.47% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/f_sensitivity_files/figure-html/unnamed-chunk-6-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13381 bytes
Input file size = 13471 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11563
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 = 11563
Output IDAT size = 11563 bytes (1818 bytes decrease)
Output file size = 11641 bytes (1830 bytes = 13.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/f_sensitivity_files/figure-html/unnamed-chunk-7-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12337 bytes
Input file size = 12427 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10536
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 = 10536
Output IDAT size = 10536 bytes (1801 bytes decrease)
Output file size = 10614 bytes (1813 bytes = 14.59% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/f_sensitivity_files/figure-html/unnamed-chunk-8-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 14883 bytes
Input file size = 14973 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12748
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 = 12748
Output IDAT size = 12748 bytes (2135 bytes decrease)
Output file size = 12826 bytes (2147 bytes = 14.34% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/f_sensitivity_files/figure-html/unnamed-chunk-8-2.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 13738 bytes
Input file size = 13828 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 11962
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 = 11962
Output IDAT size = 11962 bytes (1776 bytes decrease)
Output file size = 12040 bytes (1788 bytes = 12.93% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/f_sensitivity_files/figure-html/unnamed-chunk-9-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 9716 bytes
Input file size = 9806 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 8297
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 = 8297
Output IDAT size = 8297 bytes (1419 bytes decrease)
Output file size = 8375 bytes (1431 bytes = 14.59% decrease)
--- finished re-building ‘f_sensitivity.Rmd’
--- re-building ‘g_heterogeneity.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/g_heterogeneity_files/figure-html/unnamed-chunk-5-1.png
576x384 pixels, 8 bits/pixel, 227 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4391 bytes
Input file size = 5162 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3415
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3406
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 = 3406
Output IDAT size = 3406 bytes (985 bytes decrease)
Output file size = 3484 bytes (1678 bytes = 32.51% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/g_heterogeneity_files/figure-html/unnamed-chunk-8-1.png
576x384 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5556 bytes
Input file size = 6384 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4657
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 = 4657
Output IDAT size = 4657 bytes (899 bytes decrease)
Output file size = 4735 bytes (1649 bytes = 25.83% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/g_heterogeneity_files/figure-html/unnamed-chunk-8-2.png
576x384 pixels, 8 bits/pixel, 243 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 5886 bytes
Input file size = 6705 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5088
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 = 5088
Output IDAT size = 5088 bytes (798 bytes decrease)
Output file size = 5166 bytes (1539 bytes = 22.95% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/g_heterogeneity_files/figure-html/unnamed-chunk-9-1.png
576x384 pixels, 8 bits/pixel, 226 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4180 bytes
Input file size = 4948 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3328
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 = 3328
Output IDAT size = 3328 bytes (852 bytes decrease)
Output file size = 3406 bytes (1542 bytes = 31.16% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/g_heterogeneity_files/figure-html/unnamed-chunk-9-2.png
576x384 pixels, 8 bits/pixel, 240 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4854 bytes
Input file size = 5664 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3926
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 = 3926
Output IDAT size = 3926 bytes (928 bytes decrease)
Output file size = 4004 bytes (1660 bytes = 29.31% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/g_heterogeneity_files/figure-html/unnamed-chunk-9-3.png
576x384 pixels, 8 bits/pixel, 239 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4610 bytes
Input file size = 5417 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3803
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 = 3803
Output IDAT size = 3803 bytes (807 bytes decrease)
Output file size = 3881 bytes (1536 bytes = 28.36% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/g_heterogeneity_files/figure-html/unnamed-chunk-10-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 61401 bytes
Input file size = 61563 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46758
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 = 46758
Output IDAT size = 46758 bytes (14643 bytes decrease)
Output file size = 46836 bytes (14727 bytes = 23.92% decrease)
--- finished re-building ‘g_heterogeneity.Rmd’
--- re-building ‘h_tabular.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/h_tabular_files/figure-html/unnamed-chunk-8-1.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 12953 bytes
Input file size = 13043 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10803
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 = 10803
Output IDAT size = 10803 bytes (2150 bytes decrease)
Output file size = 10881 bytes (2162 bytes = 16.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/heemod.Rcheck/vign_test/heemod/vignettes/h_tabular_files/figure-html/unnamed-chunk-8-2.png
576x288 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24897 bytes
Input file size = 25011 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20268
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 = 20268
Output IDAT size = 20268 bytes (4629 bytes decrease)
Output file size = 20346 bytes (4665 bytes = 18.65% decrease)
--- finished re-building ‘h_tabular.Rmd’
--- re-building ‘i_reproduction.Rmd’ using rmarkdown
--- finished re-building ‘i_reproduction.Rmd’
--- re-building ‘j_survival.Rmd’ using rmarkdown
Failed with error: 'there is no package called 'flexsurv''
Quitting from lines 29-39 [unnamed-chunk-1] (j_survival.Rmd)
Error: processing vignette 'j_survival.Rmd' failed with diagnostics:
'flexsurv' package required.
--- failed re-building ‘j_survival.Rmd’
--- re-building ‘j_survival_2_psa.Rmd’ using rmarkdown
Quitting from lines 14-16 [setup] (j_survival_2_psa.Rmd)
Error: processing vignette 'j_survival_2_psa.Rmd' failed with diagnostics:
there is no package called 'flexsurv'
--- failed re-building ‘j_survival_2_psa.Rmd’
--- re-building ‘k_calibration.Rmd’ using rmarkdown
--- finished re-building ‘k_calibration.Rmd’
SUMMARY: processing the following files failed:
‘j_survival.Rmd’ ‘j_survival_2_psa.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Current CRAN status: ERROR: 1, OK: 12
Version: 3.0.2
Check: tests
Result: ERROR
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(rgho)
>
> test_check("rgho")
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 2 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-data.R:5:1', 'test-search.R:5:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-get_gho.R:37:5'): Connection errors ──────────────────────────
`get_gho_values(dimension = "COUNTRY")` produced unexpected messages.
Expected match: [45]04
Actual values:
* Server error: (502) Bad Gateway
[ FAIL 1 | WARN 0 | SKIP 2 | PASS 2 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64