Last updated on 2024-09-13 00:50:01 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.5.4 | 235.39 | 320.94 | 556.33 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.5.4 | 185.61 | 252.13 | 437.74 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.5.4 | 1026.72 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.5.4 | 1108.99 | ERROR | |||
| r-devel-windows-x86_64 | 0.5.4 | 257.00 | 400.00 | 657.00 | NOTE | |
| r-patched-linux-x86_64 | 0.5.4 | 267.40 | 333.15 | 600.55 | ERROR | |
| r-release-linux-x86_64 | 0.5.4 | 264.64 | 321.22 | 585.86 | ERROR | |
| r-release-macos-arm64 | 0.5.4 | 247.00 | NOTE | |||
| r-release-macos-x86_64 | 0.5.4 | 376.00 | NOTE | |||
| r-release-windows-x86_64 | 0.5.4 | 266.00 | 410.00 | 676.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.5.4 | 265.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.5.4 | 509.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 0.5.4 | 315.00 | 506.00 | 821.00 | NOTE |
Version: 0.5.4
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
create_IndivCtstmTrans.Rd: R6Class
create_trans_dt.Rd: data.table
input_mats.Rd: data.table, print.data.table
partsurvfit.Rd: flexsurvreg, flexsurvspline
plot_ceac.Rd: ggplot2
plot_ceaf.Rd: ggplot2
plot_ceplane.Rd: ggplot2
plot_evpi.Rd: ggplot2
summary.eval_rng.Rd: data.table
summary.params.Rd: data.table
summary.tparams_transprobs.Rd: data.table
summary.tpmatrix.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64
Version: 0.5.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [39s/45s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
sample = 1
sample = 2
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tpmatrix.R:232:3'): qmatrix.msm() works with factor covariates and 'newdata' is one row ──
msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:242:3'): qmatrix.msm() works with factor covariates and 'newdata' is multiple rows ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:253:3'): qmatrix.msm() works with covariates that vary by transition ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:280:3'): qmatrix.msm() works with a hidden Markov model ──
msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none") not equal to ...[].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:302:3'): qmatrix.msm() does not require 'newdata' if no covariates are included in the model. ──
msm::qmatrix.msm(fit, ci = "none") not equal to qmatrix(fit, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.5.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [30s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
sample = 1
sample = 2
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tpmatrix.R:232:3'): qmatrix.msm() works with factor covariates and 'newdata' is one row ──
msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:242:3'): qmatrix.msm() works with factor covariates and 'newdata' is multiple rows ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:253:3'): qmatrix.msm() works with covariates that vary by transition ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:280:3'): qmatrix.msm() works with a hidden Markov model ──
msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none") not equal to ...[].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:302:3'): qmatrix.msm() does not require 'newdata' if no covariates are included in the model. ──
msm::qmatrix.msm(fit, ci = "none") not equal to qmatrix(fit, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.5.4
Check: installed package size
Result: NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
doc 2.2Mb
libs 2.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.5.4
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘R6’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.5.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [72s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
sample = 1
sample = 2
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tpmatrix.R:232:3'): qmatrix.msm() works with factor covariates and 'newdata' is one row ──
msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:242:3'): qmatrix.msm() works with factor covariates and 'newdata' is multiple rows ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:253:3'): qmatrix.msm() works with covariates that vary by transition ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:280:3'): qmatrix.msm() works with a hidden Markov model ──
msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none") not equal to ...[].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:302:3'): qmatrix.msm() does not require 'newdata' if no covariates are included in the model. ──
msm::qmatrix.msm(fit, ci = "none") not equal to qmatrix(fit, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.5.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [64s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
sample = 1
sample = 2
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tpmatrix.R:232:3'): qmatrix.msm() works with factor covariates and 'newdata' is one row ──
msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:242:3'): qmatrix.msm() works with factor covariates and 'newdata' is multiple rows ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:253:3'): qmatrix.msm() works with covariates that vary by transition ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:280:3'): qmatrix.msm() works with a hidden Markov model ──
msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none") not equal to ...[].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:302:3'): qmatrix.msm() does not require 'newdata' if no covariates are included in the model. ──
msm::qmatrix.msm(fit, ci = "none") not equal to qmatrix(fit, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.5.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [39s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
sample = 1
sample = 2
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tpmatrix.R:232:3'): qmatrix.msm() works with factor covariates and 'newdata' is one row ──
msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:242:3'): qmatrix.msm() works with factor covariates and 'newdata' is multiple rows ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:253:3'): qmatrix.msm() works with covariates that vary by transition ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:280:3'): qmatrix.msm() works with a hidden Markov model ──
msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none") not equal to ...[].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:302:3'): qmatrix.msm() does not require 'newdata' if no covariates are included in the model. ──
msm::qmatrix.msm(fit, ci = "none") not equal to qmatrix(fit, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.5.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [39s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(hesim)
>
> test_check("hesim")
sample = 1
sample = 2
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-tpmatrix.R:232:3'): qmatrix.msm() works with factor covariates and 'newdata' is one row ──
msm::qmatrix.msm(fit, newdata[1, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:242:3'): qmatrix.msm() works with factor covariates and 'newdata' is multiple rows ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:253:3'): qmatrix.msm() works with covariates that vary by transition ──
msm::qmatrix.msm(fit, newdata[2, , drop = FALSE], ci = "none") not equal to qmatrix(fit, newdata, uncertainty = "none")[, , 2].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:280:3'): qmatrix.msm() works with a hidden Markov model ──
msm::qmatrix.msm(fith, covariates = list(acute = 0), ci = "none") not equal to ...[].
target is msm.est, current is matrix
── Failure ('test-tpmatrix.R:302:3'): qmatrix.msm() does not require 'newdata' if no covariates are included in the model. ──
msm::qmatrix.msm(fit, ci = "none") not equal to qmatrix(fit, uncertainty = "none")[, , 1].
target is msm.est, current is matrix
[ FAIL 5 | WARN 0 | SKIP 0 | PASS 1120 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.5.4
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘cea.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/ceplane_plot-1.png
768x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 61204 bytes
Input file size = 61366 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 46126
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 = 46126
Output IDAT size = 46126 bytes (15078 bytes decrease)
Output file size = 46204 bytes (15162 bytes = 24.71% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/mce_plot-1.png
768x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 42015 bytes
Input file size = 42153 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 36352
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 = 36352
Output IDAT size = 36352 bytes (5663 bytes decrease)
Output file size = 36430 bytes (5723 bytes = 13.58% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/ceac_plot-1.png
768x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38110 bytes
Input file size = 38236 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 33890
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 = 33890
Output IDAT size = 33890 bytes (4220 bytes decrease)
Output file size = 33968 bytes (4268 bytes = 11.16% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/ceaf_plot-1.png
768x432 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 32803 bytes
Input file size = 32929 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 28394
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 = 28394
Output IDAT size = 28394 bytes (4409 bytes decrease)
Output file size = 28472 bytes (4457 bytes = 13.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/evpi_plot-1.png
768x432 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 14221 bytes
Input file size = 15091 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 12357
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 = 12357
Output IDAT size = 12357 bytes (1864 bytes decrease)
Output file size = 12435 bytes (2656 bytes = 17.60% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/cea_files/figure-html/totevpi-1.png
576x432 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8299 bytes
Input file size = 9169 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7238
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 7169
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 = 7169
Output IDAT size = 7169 bytes (1130 bytes decrease)
Output file size = 7247 bytes (1922 bytes = 20.96% decrease)
--- finished re-building ‘cea.Rmd’
--- re-building ‘intro.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/intro_files/figure-html/ceac_plot-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 24624 bytes
Input file size = 24738 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19836
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 = 19836
Output IDAT size = 19836 bytes (4788 bytes decrease)
Output file size = 19914 bytes (4824 bytes = 19.50% decrease)
--- finished re-building ‘intro.Rmd’
--- re-building ‘markov-cohort.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/markov-cohort_files/figure-html/simStateprobsPlot-1.png
672x576 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 77222 bytes
Input file size = 77408 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 65319
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 = 65319
Output IDAT size = 65319 bytes (11903 bytes decrease)
Output file size = 65397 bytes (12011 bytes = 15.52% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/markov-cohort_files/figure-html/ceac-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 23732 bytes
Input file size = 23834 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19696
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 = 19696
Output IDAT size = 19696 bytes (4036 bytes decrease)
Output file size = 19774 bytes (4060 bytes = 17.03% decrease)
--- finished re-building ‘markov-cohort.Rmd’
--- re-building ‘markov-inhomogeneous-cohort.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/markov-inhomogeneous-cohort_files/figure-html/simStateprobsPlot-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 46747 bytes
Input file size = 46885 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38027
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 = 38027
Output IDAT size = 38027 bytes (8720 bytes decrease)
Output file size = 38105 bytes (8780 bytes = 18.73% decrease)
*** caught segfault ***
address 0x30, cause 'memory not mapped'
Traceback:
1: fcase(outcome %in% c("Incremental costs", "Incremental NMB"), format_ci(estimate, lower, upper, costs = TRUE, digits = digits_costs), outcome == "Incremental QALYs", format_ci(estimate, lower, upper, costs = FALSE, digits = digits_qalys), outcome == "ICER" & icer_plane == "Dominates", "Dominates", outcome == "ICER" & icer_plane == "Dominated", "Dominated", outcome == "ICER" & !icer_plane %in% c("Dominates", "Dominated"), format_costs(estimate, digits = digits_costs))
2: eval(jsub, SDenv, parent.frame())
3: eval(jsub, SDenv, parent.frame())
4: `[.data.table`(y, , `:=`(value, fcase(outcome %in% c("Incremental costs", "Incremental NMB"), format_ci(estimate, lower, upper, costs = TRUE, digits = digits_costs), outcome == "Incremental QALYs", format_ci(estimate, lower, upper, costs = FALSE, digits = digits_qalys), outcome == "ICER" & icer_plane == "Dominates", "Dominates", outcome == "ICER" & icer_plane == "Dominated", "Dominated", outcome == "ICER" & !icer_plane %in% c("Dominates", "Dominated"), format_costs(estimate, digits = digits_costs))))
5: y[, `:=`(value, fcase(outcome %in% c("Incremental costs", "Incremental NMB"), format_ci(estimate, lower, upper, costs = TRUE, digits = digits_costs), outcome == "Incremental QALYs", format_ci(estimate, lower, upper, costs = FALSE, digits = digits_qalys), outcome == "ICER" & icer_plane == "Dominates", "Dominates", outcome == "ICER" & icer_plane == "Dominated", "Dominated", outcome == "ICER" & !icer_plane %in% c("Dominates", "Dominated"), format_costs(estimate, digits = digits_costs)))]
6: format.icer(., pivot_from = "outcome")
7: format(., pivot_from = "outcome")
8: icer(cea_pw_out) %>% format(pivot_from = "outcome")
9: eval(expr, envir, enclos)
10: eval(expr, envir, enclos)
11: eval_with_user_handlers(expr, envir, enclos, user_handlers)
12: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
13: withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)
14: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler))
15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers)), warning = wHandler, error = eHandler, message = mHandler)))
16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, log_echo = log_echo, log_warning = log_warning, output_handler = output_handler, include_timing = include_timing)
17: evaluate::evaluate(...)
18: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
19: in_dir(input_dir(), expr)
20: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
21: eng_r(options)
22: block_exec(params)
23: call_block(x)
24: process_group(group)
25: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
26: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from lines ", loc) }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
27: process_file(text, output)
28: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
29: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
30: vweave_rmarkdown(...)
31: engine$weave(file, quiet = quiet, encoding = enc)
32: doTryCatch(return(expr), name, parentenv, handler)
33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
34: tryCatchList(expr, classes, parentenv, handlers)
35: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
36: tools:::.buildOneVignette("markov-inhomogeneous-cohort.Rmd", "/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim", TRUE, FALSE, "markov-inhomogeneous-cohort", "UTF-8", "/home/hornik/tmp/scratch/RtmpKv2aB7/file3eac9443e66d28.rds")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
--- re-building ‘markov-inhomogeneous-indiv.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/markov-inhomogeneous-indiv_files/figure-html/unnamed-chunk-31-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 51727 bytes
Input file size = 51877 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 42220
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 = 42220
Output IDAT size = 42220 bytes (9507 bytes decrease)
Output file size = 42298 bytes (9579 bytes = 18.46% decrease)
--- finished re-building ‘markov-inhomogeneous-indiv.Rmd’
--- re-building ‘mlogit.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/mlogit_files/figure-html/stateprobs-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31756 bytes
Input file size = 31870 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27763
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 = 27763
Output IDAT size = 27763 bytes (3993 bytes decrease)
Output file size = 27841 bytes (4029 bytes = 12.64% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/mlogit_files/figure-html/icerHeterogeneity-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25343 bytes
Input file size = 25457 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20625
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 = 20625
Output IDAT size = 20625 bytes (4718 bytes decrease)
Output file size = 20703 bytes (4754 bytes = 18.67% decrease)
--- finished re-building ‘mlogit.Rmd’
--- re-building ‘mstate.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/predicted_hazards_plot-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45648 bytes
Input file size = 45786 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 35947
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 = 35947
Output IDAT size = 35947 bytes (9701 bytes decrease)
Output file size = 36025 bytes (9761 bytes = 21.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/stprobs_by_strategy_plot-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 37474 bytes
Input file size = 37600 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 30328
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 = 30328
Output IDAT size = 30328 bytes (7146 bytes decrease)
Output file size = 30406 bytes (7194 bytes = 19.13% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/stprobs_by_timescale_plot-1.png
672x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 33615 bytes
Input file size = 33741 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27450
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 = 27450
Output IDAT size = 27450 bytes (6165 bytes decrease)
Output file size = 27528 bytes (6213 bytes = 18.41% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/mstate_files/figure-html/qalys_plot-1.png
576x384 pixels, 8 bits/pixel, 255 colors in palette
Input IDAT size = 5464 bytes
Input file size = 6319 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4024
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 = 4024
Output IDAT size = 4024 bytes (1440 bytes decrease)
Output file size = 4879 bytes (1440 bytes = 22.79% decrease)
--- finished re-building ‘mstate.Rmd’
--- re-building ‘psm.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/psm_files/figure-html/survcurves-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 66250 bytes
Input file size = 66424 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 57820
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 = 57820
Output IDAT size = 57820 bytes (8430 bytes decrease)
Output file size = 57898 bytes (8526 bytes = 12.84% decrease)
** Processing: /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hesim.Rcheck/vign_test/hesim/vignettes/psm_files/figure-html/stateprobs-1.png
576x384 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 26707 bytes
Input file size = 26821 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 22317
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 = 22317
Output IDAT size = 22317 bytes (4390 bytes decrease)
Output file size = 22395 bytes (4426 bytes = 16.50% decrease)
--- finished re-building ‘psm.Rmd’
SUMMARY: processing the following file failed:
‘markov-inhomogeneous-cohort.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64