Last updated on 2024-11-27 10:49:39 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.8.1 | 8.04 | 1206.04 | 1214.08 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.8.1 | 4.51 | 803.56 | 808.07 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.8.1 | 2011.90 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.8.1 | 1878.22 | ERROR | |||
| r-devel-windows-x86_64 | 0.8.1 | 8.00 | 732.00 | 740.00 | ERROR | |
| r-patched-linux-x86_64 | 0.8.1 | 7.61 | 1155.59 | 1163.20 | ERROR | |
| r-release-linux-x86_64 | 0.8.1 | 7.10 | 1196.65 | 1203.75 | OK | |
| r-release-macos-arm64 | 0.8.1 | 305.00 | OK | |||
| r-release-macos-x86_64 | 0.8.1 | 491.00 | OK | |||
| r-release-windows-x86_64 | 0.8.1 | 9.00 | 748.00 | 757.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.8.1 | 388.00 | OK | |||
| r-oldrel-macos-x86_64 | 0.8.1 | 543.00 | OK | |||
| r-oldrel-windows-x86_64 | 0.8.1 | 11.00 | 1096.00 | 1107.00 | ERROR |
Version: 0.8.1
Check: dependencies in R code
Result: WARN
Missing or unexported object: ‘visOmopResults::optionsVisOmopTable’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-oldrel-windows-x86_64
Version: 0.8.1
Check: examples
Result: ERROR
Running examples in ‘IncidencePrevalence-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optionsTableIncidence
> ### Title: Additional arguments for the functions tableIncidence.
> ### Aliases: optionsTableIncidence
>
> ### ** Examples
>
> {
+ optionsTableIncidence()
+ }
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [598s/337s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
══ Skipped tests (71) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Error ('test-tables.R:13:3'): test tables ───────────────────────────────────
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3
2. └─IncidencePrevalence:::tableInternal(...)
3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...)
── Failure ('test-tables.R:73:3'): test importing results ──────────────────────
Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:91:3'): test importing results ──────────────────────
Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:98:3'): test importing results ──────────────────────
Expected `tableIncidence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:99:3'): test importing results ──────────────────────
Expected `tablePrevalence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.8.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31155 bytes
Input file size = 31269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26287
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 = 26287
Output IDAT size = 26287 bytes (4868 bytes decrease)
Output file size = 26365 bytes (4904 bytes = 15.68% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25820 bytes
Input file size = 25934 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21650
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 = 21650
Output IDAT size = 21650 bytes (4170 bytes decrease)
Output file size = 21728 bytes (4206 bytes = 16.22% decrease)
--- finished re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
--- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 236 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6463 bytes
Input file size = 7261 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5226
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190
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 = 5190
Output IDAT size = 5190 bytes (1273 bytes decrease)
Output file size = 5268 bytes (1993 bytes = 27.45% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6802 bytes
Input file size = 7657 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541
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 = 5541
Output IDAT size = 5541 bytes (1261 bytes decrease)
Output file size = 5619 bytes (2038 bytes = 26.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6892 bytes
Input file size = 7744 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599
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 = 5599
Output IDAT size = 5599 bytes (1293 bytes decrease)
Output file size = 5677 bytes (2067 bytes = 26.69% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7218 bytes
Input file size = 8073 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890
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 = 5890
Output IDAT size = 5890 bytes (1328 bytes decrease)
Output file size = 5968 bytes (2105 bytes = 26.07% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6563 bytes
Input file size = 7418 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333
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 = 5333
Output IDAT size = 5333 bytes (1230 bytes decrease)
Output file size = 5411 bytes (2007 bytes = 27.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-17-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35692 bytes
Input file size = 35818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947
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 = 27947
Output IDAT size = 27947 bytes (7745 bytes decrease)
Output file size = 28025 bytes (7793 bytes = 21.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-18-1.png
672x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47934 bytes
Input file size = 48072 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761
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 = 37761
Output IDAT size = 37761 bytes (10173 bytes decrease)
Output file size = 37839 bytes (10233 bytes = 21.29% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-19-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 71868 bytes
Input file size = 72042 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52951
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 = 52951
Output IDAT size = 52951 bytes (18917 bytes decrease)
Output file size = 53029 bytes (19013 bytes = 26.39% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-20-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38083 bytes
Input file size = 38209 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31650
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 = 31650
Output IDAT size = 31650 bytes (6433 bytes decrease)
Output file size = 31728 bytes (6481 bytes = 16.96% decrease)
--- finished re-building ‘a02_Creating_denominator_populations.Rmd’
--- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 8 bits/pixel, 244 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3203 bytes
Input file size = 4025 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769
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 = 2769
Output IDAT size = 2769 bytes (434 bytes decrease)
Output file size = 2847 bytes (1178 bytes = 29.27% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 239 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3471 bytes
Input file size = 4278 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027
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 = 3027
Output IDAT size = 3027 bytes (444 bytes decrease)
Output file size = 3105 bytes (1173 bytes = 27.42% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3037 bytes
Input file size = 3865 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2562
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555
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 = 2555
Output IDAT size = 2555 bytes (482 bytes decrease)
Output file size = 2633 bytes (1232 bytes = 31.88% decrease)
--- finished re-building ‘a03_Creating_target_denominator_populations.Rmd’
--- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9180 bytes
Input file size = 10047 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7626
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 = 7626
Output IDAT size = 7626 bytes (1554 bytes decrease)
Output file size = 7704 bytes (2343 bytes = 23.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21563 bytes
Input file size = 22445 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20002
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 = 20002
Output IDAT size = 20002 bytes (1561 bytes decrease)
Output file size = 20080 bytes (2365 bytes = 10.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9773 bytes
Input file size = 10640 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7812
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 = 7812
Output IDAT size = 7812 bytes (1961 bytes decrease)
Output file size = 7890 bytes (2750 bytes = 25.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8600 bytes
Input file size = 9461 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7051
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 = 7051
Output IDAT size = 7051 bytes (1549 bytes decrease)
Output file size = 7129 bytes (2332 bytes = 24.65% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15267 bytes
Input file size = 16137 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13390
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 = 13390
Output IDAT size = 13390 bytes (1877 bytes decrease)
Output file size = 13468 bytes (2669 bytes = 16.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15894 bytes
Input file size = 16764 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14157
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 = 14157
Output IDAT size = 14157 bytes (1737 bytes decrease)
Output file size = 14235 bytes (2529 bytes = 15.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 28455 bytes
Input file size = 29349 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26399
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 = 26399
Output IDAT size = 26399 bytes (2056 bytes decrease)
Output file size = 26477 bytes (2872 bytes = 9.79% decrease)
--- finished re-building ‘a04_Calculating_prevalence.Rmd’
--- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8760 bytes
Input file size = 9630 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7247
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 = 7247
Output IDAT size = 7247 bytes (1513 bytes decrease)
Output file size = 7325 bytes (2305 bytes = 23.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8731 bytes
Input file size = 9601 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7238
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 = 7238
Output IDAT size = 7238 bytes (1493 bytes decrease)
Output file size = 7316 bytes (2285 bytes = 23.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8764 bytes
Input file size = 9628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7250
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 = 7250
Output IDAT size = 7250 bytes (1514 bytes decrease)
Output file size = 7328 bytes (2300 bytes = 23.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8565 bytes
Input file size = 9432 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7096
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 = 7096
Output IDAT size = 7096 bytes (1469 bytes decrease)
Output file size = 7174 bytes (2258 bytes = 23.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15082 bytes
Input file size = 15952 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13092
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 = 13092
Output IDAT size = 13092 bytes (1990 bytes decrease)
Output file size = 13170 bytes (2782 bytes = 17.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15219 bytes
Input file size = 16089 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13313
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 = 13313
Output IDAT size = 13313 bytes (1906 bytes decrease)
Output file size = 13391 bytes (2698 bytes = 16.77% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-2.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 27339 bytes
Input file size = 28233 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25241
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 = 25241
Output IDAT size = 25241 bytes (2098 bytes decrease)
Output file size = 25319 bytes (2914 bytes = 10.32% decrease)
Quitting from lines 249-258 [unnamed-chunk-14] (a05_Calculating_incidence.Rmd)
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
ℹ In argument: `min_cell_count = paste0(...)`.
Caused by error in `.data$min_cell_count`:
! Column `min_cell_count` not found in `.data`.
--- failed re-building ‘a05_Calculating_incidence.Rmd’
--- re-building ‘a06_Plotting_options.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/facetplot-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8622 bytes
Input file size = 9486 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7145
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 = 7145
Output IDAT size = 7145 bytes (1477 bytes decrease)
Output file size = 7223 bytes (2263 bytes = 23.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/linesplot-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11872 bytes
Input file size = 12739 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10222
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 = 10222
Output IDAT size = 10222 bytes (1650 bytes decrease)
Output file size = 10300 bytes (2439 bytes = 19.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/noconfplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10960 bytes
Input file size = 11830 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9324
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 = 9324
Output IDAT size = 9324 bytes (1636 bytes decrease)
Output file size = 9402 bytes (2428 bytes = 20.52% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/stackedplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11257 bytes
Input file size = 12127 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9844
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 = 9844
Output IDAT size = 9844 bytes (1413 bytes decrease)
Output file size = 9922 bytes (2205 bytes = 18.18% decrease)
--- finished re-building ‘a06_Plotting_options.Rmd’
SUMMARY: processing the following file failed:
‘a05_Calculating_incidence.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [405s/266s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
══ Skipped tests (71) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Error ('test-tables.R:13:3'): test tables ───────────────────────────────────
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3
2. └─IncidencePrevalence:::tableInternal(...)
3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...)
── Failure ('test-tables.R:73:3'): test importing results ──────────────────────
Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:91:3'): test importing results ──────────────────────
Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:98:3'): test importing results ──────────────────────
Expected `tableIncidence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:99:3'): test importing results ──────────────────────
Expected `tablePrevalence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.8.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31155 bytes
Input file size = 31269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26287
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 = 26287
Output IDAT size = 26287 bytes (4868 bytes decrease)
Output file size = 26365 bytes (4904 bytes = 15.68% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25820 bytes
Input file size = 25934 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21650
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 = 21650
Output IDAT size = 21650 bytes (4170 bytes decrease)
Output file size = 21728 bytes (4206 bytes = 16.22% decrease)
--- finished re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
--- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 236 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6463 bytes
Input file size = 7261 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5226
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190
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 = 5190
Output IDAT size = 5190 bytes (1273 bytes decrease)
Output file size = 5268 bytes (1993 bytes = 27.45% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6802 bytes
Input file size = 7657 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541
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 = 5541
Output IDAT size = 5541 bytes (1261 bytes decrease)
Output file size = 5619 bytes (2038 bytes = 26.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6892 bytes
Input file size = 7744 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599
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 = 5599
Output IDAT size = 5599 bytes (1293 bytes decrease)
Output file size = 5677 bytes (2067 bytes = 26.69% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7218 bytes
Input file size = 8073 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890
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 = 5890
Output IDAT size = 5890 bytes (1328 bytes decrease)
Output file size = 5968 bytes (2105 bytes = 26.07% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6563 bytes
Input file size = 7418 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333
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 = 5333
Output IDAT size = 5333 bytes (1230 bytes decrease)
Output file size = 5411 bytes (2007 bytes = 27.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-17-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35692 bytes
Input file size = 35818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947
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 = 27947
Output IDAT size = 27947 bytes (7745 bytes decrease)
Output file size = 28025 bytes (7793 bytes = 21.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-18-1.png
672x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47934 bytes
Input file size = 48072 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761
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 = 37761
Output IDAT size = 37761 bytes (10173 bytes decrease)
Output file size = 37839 bytes (10233 bytes = 21.29% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-19-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 71868 bytes
Input file size = 72042 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52951
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 = 52951
Output IDAT size = 52951 bytes (18917 bytes decrease)
Output file size = 53029 bytes (19013 bytes = 26.39% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-20-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38083 bytes
Input file size = 38209 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31650
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 = 31650
Output IDAT size = 31650 bytes (6433 bytes decrease)
Output file size = 31728 bytes (6481 bytes = 16.96% decrease)
--- finished re-building ‘a02_Creating_denominator_populations.Rmd’
--- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 8 bits/pixel, 244 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3203 bytes
Input file size = 4025 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769
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 = 2769
Output IDAT size = 2769 bytes (434 bytes decrease)
Output file size = 2847 bytes (1178 bytes = 29.27% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 239 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3471 bytes
Input file size = 4278 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027
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 = 3027
Output IDAT size = 3027 bytes (444 bytes decrease)
Output file size = 3105 bytes (1173 bytes = 27.42% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3037 bytes
Input file size = 3865 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2562
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555
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 = 2555
Output IDAT size = 2555 bytes (482 bytes decrease)
Output file size = 2633 bytes (1232 bytes = 31.88% decrease)
--- finished re-building ‘a03_Creating_target_denominator_populations.Rmd’
--- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9180 bytes
Input file size = 10047 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7626
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 = 7626
Output IDAT size = 7626 bytes (1554 bytes decrease)
Output file size = 7704 bytes (2343 bytes = 23.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21563 bytes
Input file size = 22445 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20002
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 = 20002
Output IDAT size = 20002 bytes (1561 bytes decrease)
Output file size = 20080 bytes (2365 bytes = 10.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9773 bytes
Input file size = 10640 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7812
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 = 7812
Output IDAT size = 7812 bytes (1961 bytes decrease)
Output file size = 7890 bytes (2750 bytes = 25.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8600 bytes
Input file size = 9461 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7051
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 = 7051
Output IDAT size = 7051 bytes (1549 bytes decrease)
Output file size = 7129 bytes (2332 bytes = 24.65% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15267 bytes
Input file size = 16137 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13390
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 = 13390
Output IDAT size = 13390 bytes (1877 bytes decrease)
Output file size = 13468 bytes (2669 bytes = 16.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15894 bytes
Input file size = 16764 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14157
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 = 14157
Output IDAT size = 14157 bytes (1737 bytes decrease)
Output file size = 14235 bytes (2529 bytes = 15.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 28455 bytes
Input file size = 29349 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26399
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 = 26399
Output IDAT size = 26399 bytes (2056 bytes decrease)
Output file size = 26477 bytes (2872 bytes = 9.79% decrease)
--- finished re-building ‘a04_Calculating_prevalence.Rmd’
--- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8760 bytes
Input file size = 9630 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7247
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 = 7247
Output IDAT size = 7247 bytes (1513 bytes decrease)
Output file size = 7325 bytes (2305 bytes = 23.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8731 bytes
Input file size = 9601 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7238
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 = 7238
Output IDAT size = 7238 bytes (1493 bytes decrease)
Output file size = 7316 bytes (2285 bytes = 23.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8764 bytes
Input file size = 9628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7250
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 = 7250
Output IDAT size = 7250 bytes (1514 bytes decrease)
Output file size = 7328 bytes (2300 bytes = 23.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8565 bytes
Input file size = 9432 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7096
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 = 7096
Output IDAT size = 7096 bytes (1469 bytes decrease)
Output file size = 7174 bytes (2258 bytes = 23.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15082 bytes
Input file size = 15952 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13092
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 = 13092
Output IDAT size = 13092 bytes (1990 bytes decrease)
Output file size = 13170 bytes (2782 bytes = 17.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15219 bytes
Input file size = 16089 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13313
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 = 13313
Output IDAT size = 13313 bytes (1906 bytes decrease)
Output file size = 13391 bytes (2698 bytes = 16.77% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-2.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 27339 bytes
Input file size = 28233 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25241
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 = 25241
Output IDAT size = 25241 bytes (2098 bytes decrease)
Output file size = 25319 bytes (2914 bytes = 10.32% decrease)
Quitting from lines 249-258 [unnamed-chunk-14] (a05_Calculating_incidence.Rmd)
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
ℹ In argument: `min_cell_count = paste0(...)`.
Caused by error in `.data$min_cell_count`:
! Column `min_cell_count` not found in `.data`.
--- failed re-building ‘a05_Calculating_incidence.Rmd’
--- re-building ‘a06_Plotting_options.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/facetplot-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8622 bytes
Input file size = 9486 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7145
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 = 7145
Output IDAT size = 7145 bytes (1477 bytes decrease)
Output file size = 7223 bytes (2263 bytes = 23.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/linesplot-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11872 bytes
Input file size = 12739 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10222
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 = 10222
Output IDAT size = 10222 bytes (1650 bytes decrease)
Output file size = 10300 bytes (2439 bytes = 19.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/noconfplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10960 bytes
Input file size = 11830 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9324
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 = 9324
Output IDAT size = 9324 bytes (1636 bytes decrease)
Output file size = 9402 bytes (2428 bytes = 20.52% decrease)
** Processing: /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/stackedplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11257 bytes
Input file size = 12127 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9844
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 = 9844
Output IDAT size = 9844 bytes (1413 bytes decrease)
Output file size = 9922 bytes (2205 bytes = 18.18% decrease)
--- finished re-building ‘a06_Plotting_options.Rmd’
SUMMARY: processing the following file failed:
‘a05_Calculating_incidence.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.8.1
Check: examples
Result: ERROR
Running examples in ‘IncidencePrevalence-Ex.R’ failed
The error most likely occurred in:
> ### Name: optionsTableIncidence
> ### Title: Additional arguments for the functions tableIncidence.
> ### Aliases: optionsTableIncidence
>
> ### ** Examples
>
> {
+ optionsTableIncidence()
+ }
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [969s/571s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
══ Skipped tests (71) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Error ('test-tables.R:13:3'): test tables ───────────────────────────────────
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3
2. └─IncidencePrevalence:::tableInternal(...)
3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...)
── Failure ('test-tables.R:73:3'): test importing results ──────────────────────
Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:91:3'): test importing results ──────────────────────
Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:98:3'): test importing results ──────────────────────
Expected `tableIncidence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:99:3'): test importing results ──────────────────────
Expected `tablePrevalence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31155 bytes
Input file size = 31269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26287
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 = 26287
Output IDAT size = 26287 bytes (4868 bytes decrease)
Output file size = 26365 bytes (4904 bytes = 15.68% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25820 bytes
Input file size = 25934 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21650
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 = 21650
Output IDAT size = 21650 bytes (4170 bytes decrease)
Output file size = 21728 bytes (4206 bytes = 16.22% decrease)
--- finished re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
--- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 236 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6463 bytes
Input file size = 7261 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5226
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190
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 = 5190
Output IDAT size = 5190 bytes (1273 bytes decrease)
Output file size = 5268 bytes (1993 bytes = 27.45% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6802 bytes
Input file size = 7657 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541
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 = 5541
Output IDAT size = 5541 bytes (1261 bytes decrease)
Output file size = 5619 bytes (2038 bytes = 26.62% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6892 bytes
Input file size = 7744 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599
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 = 5599
Output IDAT size = 5599 bytes (1293 bytes decrease)
Output file size = 5677 bytes (2067 bytes = 26.69% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7218 bytes
Input file size = 8073 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890
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 = 5890
Output IDAT size = 5890 bytes (1328 bytes decrease)
Output file size = 5968 bytes (2105 bytes = 26.07% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6563 bytes
Input file size = 7418 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333
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 = 5333
Output IDAT size = 5333 bytes (1230 bytes decrease)
Output file size = 5411 bytes (2007 bytes = 27.06% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-17-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35692 bytes
Input file size = 35818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947
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 = 27947
Output IDAT size = 27947 bytes (7745 bytes decrease)
Output file size = 28025 bytes (7793 bytes = 21.76% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-18-1.png
672x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47934 bytes
Input file size = 48072 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761
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 = 37761
Output IDAT size = 37761 bytes (10173 bytes decrease)
Output file size = 37839 bytes (10233 bytes = 21.29% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-19-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 71868 bytes
Input file size = 72042 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52951
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 = 52951
Output IDAT size = 52951 bytes (18917 bytes decrease)
Output file size = 53029 bytes (19013 bytes = 26.39% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-20-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38083 bytes
Input file size = 38209 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31650
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 = 31650
Output IDAT size = 31650 bytes (6433 bytes decrease)
Output file size = 31728 bytes (6481 bytes = 16.96% decrease)
--- finished re-building ‘a02_Creating_denominator_populations.Rmd’
--- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 8 bits/pixel, 244 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3203 bytes
Input file size = 4025 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769
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 = 2769
Output IDAT size = 2769 bytes (434 bytes decrease)
Output file size = 2847 bytes (1178 bytes = 29.27% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 239 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3471 bytes
Input file size = 4278 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027
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 = 3027
Output IDAT size = 3027 bytes (444 bytes decrease)
Output file size = 3105 bytes (1173 bytes = 27.42% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3037 bytes
Input file size = 3865 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2562
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555
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 = 2555
Output IDAT size = 2555 bytes (482 bytes decrease)
Output file size = 2633 bytes (1232 bytes = 31.88% decrease)
--- finished re-building ‘a03_Creating_target_denominator_populations.Rmd’
--- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9180 bytes
Input file size = 10047 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7626
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 = 7626
Output IDAT size = 7626 bytes (1554 bytes decrease)
Output file size = 7704 bytes (2343 bytes = 23.32% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21563 bytes
Input file size = 22445 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20002
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 = 20002
Output IDAT size = 20002 bytes (1561 bytes decrease)
Output file size = 20080 bytes (2365 bytes = 10.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9773 bytes
Input file size = 10640 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7812
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 = 7812
Output IDAT size = 7812 bytes (1961 bytes decrease)
Output file size = 7890 bytes (2750 bytes = 25.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8600 bytes
Input file size = 9461 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7051
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 = 7051
Output IDAT size = 7051 bytes (1549 bytes decrease)
Output file size = 7129 bytes (2332 bytes = 24.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15267 bytes
Input file size = 16137 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13390
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 = 13390
Output IDAT size = 13390 bytes (1877 bytes decrease)
Output file size = 13468 bytes (2669 bytes = 16.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15894 bytes
Input file size = 16764 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14157
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 = 14157
Output IDAT size = 14157 bytes (1737 bytes decrease)
Output file size = 14235 bytes (2529 bytes = 15.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 28455 bytes
Input file size = 29349 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26399
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 = 26399
Output IDAT size = 26399 bytes (2056 bytes decrease)
Output file size = 26477 bytes (2872 bytes = 9.79% decrease)
--- finished re-building ‘a04_Calculating_prevalence.Rmd’
--- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8760 bytes
Input file size = 9630 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7247
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 = 7247
Output IDAT size = 7247 bytes (1513 bytes decrease)
Output file size = 7325 bytes (2305 bytes = 23.94% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8731 bytes
Input file size = 9601 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7238
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 = 7238
Output IDAT size = 7238 bytes (1493 bytes decrease)
Output file size = 7316 bytes (2285 bytes = 23.80% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8764 bytes
Input file size = 9628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7250
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 = 7250
Output IDAT size = 7250 bytes (1514 bytes decrease)
Output file size = 7328 bytes (2300 bytes = 23.89% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8565 bytes
Input file size = 9432 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7096
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 = 7096
Output IDAT size = 7096 bytes (1469 bytes decrease)
Output file size = 7174 bytes (2258 bytes = 23.94% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15082 bytes
Input file size = 15952 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13092
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 = 13092
Output IDAT size = 13092 bytes (1990 bytes decrease)
Output file size = 13170 bytes (2782 bytes = 17.44% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15219 bytes
Input file size = 16089 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13313
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 = 13313
Output IDAT size = 13313 bytes (1906 bytes decrease)
Output file size = 13391 bytes (2698 bytes = 16.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-2.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 27339 bytes
Input file size = 28233 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25241
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 = 25241
Output IDAT size = 25241 bytes (2098 bytes decrease)
Output file size = 25319 bytes (2914 bytes = 10.32% decrease)
Quitting from lines 249-258 [unnamed-chunk-14] (a05_Calculating_incidence.Rmd)
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
ℹ In argument: `min_cell_count = paste0(...)`.
Caused by error in `.data$min_cell_count`:
! Column `min_cell_count` not found in `.data`.
--- failed re-building ‘a05_Calculating_incidence.Rmd’
--- re-building ‘a06_Plotting_options.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/facetplot-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8622 bytes
Input file size = 9486 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7145
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 = 7145
Output IDAT size = 7145 bytes (1477 bytes decrease)
Output file size = 7223 bytes (2263 bytes = 23.86% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/linesplot-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11872 bytes
Input file size = 12739 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10222
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 = 10222
Output IDAT size = 10222 bytes (1650 bytes decrease)
Output file size = 10300 bytes (2439 bytes = 19.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/noconfplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10960 bytes
Input file size = 11830 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9324
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 = 9324
Output IDAT size = 9324 bytes (1636 bytes decrease)
Output file size = 9402 bytes (2428 bytes = 20.52% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-clang/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/stackedplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11257 bytes
Input file size = 12127 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9844
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 = 9844
Output IDAT size = 9844 bytes (1413 bytes decrease)
Output file size = 9922 bytes (2205 bytes = 18.18% decrease)
--- finished re-building ‘a06_Plotting_options.Rmd’
SUMMARY: processing the following file failed:
‘a05_Calculating_incidence.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [893s/507s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
══ Skipped tests (71) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Error ('test-tables.R:13:3'): test tables ───────────────────────────────────
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3
2. └─IncidencePrevalence:::tableInternal(...)
3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...)
── Failure ('test-tables.R:73:3'): test importing results ──────────────────────
Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:91:3'): test importing results ──────────────────────
Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:98:3'): test importing results ──────────────────────
Expected `tableIncidence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:99:3'): test importing results ──────────────────────
Expected `tablePrevalence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.8.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31155 bytes
Input file size = 31269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26287
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 = 26287
Output IDAT size = 26287 bytes (4868 bytes decrease)
Output file size = 26365 bytes (4904 bytes = 15.68% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25820 bytes
Input file size = 25934 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21650
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 = 21650
Output IDAT size = 21650 bytes (4170 bytes decrease)
Output file size = 21728 bytes (4206 bytes = 16.22% decrease)
--- finished re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
--- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 236 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6463 bytes
Input file size = 7261 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5226
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190
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 = 5190
Output IDAT size = 5190 bytes (1273 bytes decrease)
Output file size = 5268 bytes (1993 bytes = 27.45% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6802 bytes
Input file size = 7657 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541
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 = 5541
Output IDAT size = 5541 bytes (1261 bytes decrease)
Output file size = 5619 bytes (2038 bytes = 26.62% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6892 bytes
Input file size = 7744 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599
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 = 5599
Output IDAT size = 5599 bytes (1293 bytes decrease)
Output file size = 5677 bytes (2067 bytes = 26.69% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7218 bytes
Input file size = 8073 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890
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 = 5890
Output IDAT size = 5890 bytes (1328 bytes decrease)
Output file size = 5968 bytes (2105 bytes = 26.07% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6563 bytes
Input file size = 7418 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333
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 = 5333
Output IDAT size = 5333 bytes (1230 bytes decrease)
Output file size = 5411 bytes (2007 bytes = 27.06% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-17-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35692 bytes
Input file size = 35818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947
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 = 27947
Output IDAT size = 27947 bytes (7745 bytes decrease)
Output file size = 28025 bytes (7793 bytes = 21.76% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-18-1.png
672x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47934 bytes
Input file size = 48072 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761
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 = 37761
Output IDAT size = 37761 bytes (10173 bytes decrease)
Output file size = 37839 bytes (10233 bytes = 21.29% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-19-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 71868 bytes
Input file size = 72042 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52951
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 = 52951
Output IDAT size = 52951 bytes (18917 bytes decrease)
Output file size = 53029 bytes (19013 bytes = 26.39% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-20-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38083 bytes
Input file size = 38209 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31650
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 = 31650
Output IDAT size = 31650 bytes (6433 bytes decrease)
Output file size = 31728 bytes (6481 bytes = 16.96% decrease)
--- finished re-building ‘a02_Creating_denominator_populations.Rmd’
--- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 8 bits/pixel, 244 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3203 bytes
Input file size = 4025 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769
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 = 2769
Output IDAT size = 2769 bytes (434 bytes decrease)
Output file size = 2847 bytes (1178 bytes = 29.27% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 239 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3471 bytes
Input file size = 4278 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027
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 = 3027
Output IDAT size = 3027 bytes (444 bytes decrease)
Output file size = 3105 bytes (1173 bytes = 27.42% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3037 bytes
Input file size = 3865 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2562
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555
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 = 2555
Output IDAT size = 2555 bytes (482 bytes decrease)
Output file size = 2633 bytes (1232 bytes = 31.88% decrease)
--- finished re-building ‘a03_Creating_target_denominator_populations.Rmd’
--- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9180 bytes
Input file size = 10047 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7626
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 = 7626
Output IDAT size = 7626 bytes (1554 bytes decrease)
Output file size = 7704 bytes (2343 bytes = 23.32% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21563 bytes
Input file size = 22445 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20002
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 = 20002
Output IDAT size = 20002 bytes (1561 bytes decrease)
Output file size = 20080 bytes (2365 bytes = 10.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9773 bytes
Input file size = 10640 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7812
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 = 7812
Output IDAT size = 7812 bytes (1961 bytes decrease)
Output file size = 7890 bytes (2750 bytes = 25.85% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8600 bytes
Input file size = 9461 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7051
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 = 7051
Output IDAT size = 7051 bytes (1549 bytes decrease)
Output file size = 7129 bytes (2332 bytes = 24.65% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15267 bytes
Input file size = 16137 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13390
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 = 13390
Output IDAT size = 13390 bytes (1877 bytes decrease)
Output file size = 13468 bytes (2669 bytes = 16.54% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15894 bytes
Input file size = 16764 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14157
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 = 14157
Output IDAT size = 14157 bytes (1737 bytes decrease)
Output file size = 14235 bytes (2529 bytes = 15.09% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 28455 bytes
Input file size = 29349 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26399
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 = 26399
Output IDAT size = 26399 bytes (2056 bytes decrease)
Output file size = 26477 bytes (2872 bytes = 9.79% decrease)
--- finished re-building ‘a04_Calculating_prevalence.Rmd’
--- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8760 bytes
Input file size = 9630 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7247
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 = 7247
Output IDAT size = 7247 bytes (1513 bytes decrease)
Output file size = 7325 bytes (2305 bytes = 23.94% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8731 bytes
Input file size = 9601 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7238
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 = 7238
Output IDAT size = 7238 bytes (1493 bytes decrease)
Output file size = 7316 bytes (2285 bytes = 23.80% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8764 bytes
Input file size = 9628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7250
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 = 7250
Output IDAT size = 7250 bytes (1514 bytes decrease)
Output file size = 7328 bytes (2300 bytes = 23.89% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8565 bytes
Input file size = 9432 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7096
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 = 7096
Output IDAT size = 7096 bytes (1469 bytes decrease)
Output file size = 7174 bytes (2258 bytes = 23.94% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15082 bytes
Input file size = 15952 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13092
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 = 13092
Output IDAT size = 13092 bytes (1990 bytes decrease)
Output file size = 13170 bytes (2782 bytes = 17.44% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15219 bytes
Input file size = 16089 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13313
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 = 13313
Output IDAT size = 13313 bytes (1906 bytes decrease)
Output file size = 13391 bytes (2698 bytes = 16.77% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-2.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 27339 bytes
Input file size = 28233 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25241
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 = 25241
Output IDAT size = 25241 bytes (2098 bytes decrease)
Output file size = 25319 bytes (2914 bytes = 10.32% decrease)
Quitting from lines 249-258 [unnamed-chunk-14] (a05_Calculating_incidence.Rmd)
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
ℹ In argument: `min_cell_count = paste0(...)`.
Caused by error in `.data$min_cell_count`:
! Column `min_cell_count` not found in `.data`.
--- failed re-building ‘a05_Calculating_incidence.Rmd’
--- re-building ‘a06_Plotting_options.Rmd’ using rmarkdown
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/facetplot-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8622 bytes
Input file size = 9486 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7145
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 = 7145
Output IDAT size = 7145 bytes (1477 bytes decrease)
Output file size = 7223 bytes (2263 bytes = 23.86% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/linesplot-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11872 bytes
Input file size = 12739 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10222
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 = 10222
Output IDAT size = 10222 bytes (1650 bytes decrease)
Output file size = 10300 bytes (2439 bytes = 19.15% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/noconfplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10960 bytes
Input file size = 11830 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9324
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 = 9324
Output IDAT size = 9324 bytes (1636 bytes decrease)
Output file size = 9402 bytes (2428 bytes = 20.52% decrease)
** Processing: /data/gannet/ripley/R/packages/tests-devel/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/stackedplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11257 bytes
Input file size = 12127 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9844
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 = 9844
Output IDAT size = 9844 bytes (1413 bytes decrease)
Output file size = 9922 bytes (2205 bytes = 18.18% decrease)
--- finished re-building ‘a06_Plotting_options.Rmd’
SUMMARY: processing the following file failed:
‘a05_Calculating_incidence.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.8.1
Check: tests
Result: ERROR
Running 'testthat.R' [250s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
══ Skipped tests (71) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Error ('test-tables.R:13:3'): test tables ───────────────────────────────────
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3
2. └─IncidencePrevalence:::tableInternal(...)
3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...)
── Failure ('test-tables.R:73:3'): test importing results ──────────────────────
Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:91:3'): test importing results ──────────────────────
Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:98:3'): test importing results ──────────────────────
Expected `tableIncidence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:99:3'): test importing results ──────────────────────
Expected `tablePrevalence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.8.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building 'a01_Introduction_to_IncidencePrevalence.Rmd' using rmarkdown
--- finished re-building 'a01_Introduction_to_IncidencePrevalence.Rmd'
--- re-building 'a02_Creating_denominator_populations.Rmd' using rmarkdown
--- finished re-building 'a02_Creating_denominator_populations.Rmd'
--- re-building 'a03_Creating_target_denominator_populations.Rmd' using rmarkdown
--- finished re-building 'a03_Creating_target_denominator_populations.Rmd'
--- re-building 'a04_Calculating_prevalence.Rmd' using rmarkdown
--- finished re-building 'a04_Calculating_prevalence.Rmd'
--- re-building 'a05_Calculating_incidence.Rmd' using rmarkdown
Quitting from lines 249-258 [unnamed-chunk-14] (a05_Calculating_incidence.Rmd)
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
ℹ In argument: `min_cell_count = paste0(...)`.
Caused by error in `.data$min_cell_count`:
! Column `min_cell_count` not found in `.data`.
--- failed re-building 'a05_Calculating_incidence.Rmd'
--- re-building 'a06_Plotting_options.Rmd' using rmarkdown
--- finished re-building 'a06_Plotting_options.Rmd'
SUMMARY: processing the following file failed:
'a05_Calculating_incidence.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [578s/322s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
══ Skipped tests (71) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Error ('test-tables.R:13:3'): test tables ───────────────────────────────────
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3
2. └─IncidencePrevalence:::tableInternal(...)
3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...)
── Failure ('test-tables.R:73:3'): test importing results ──────────────────────
Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:91:3'): test importing results ──────────────────────
Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:98:3'): test importing results ──────────────────────
Expected `tableIncidence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:99:3'): test importing results ──────────────────────
Expected `tablePrevalence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.8.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 31155 bytes
Input file size = 31269 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26287
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 = 26287
Output IDAT size = 26287 bytes (4868 bytes decrease)
Output file size = 26365 bytes (4904 bytes = 15.68% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a01_Introduction_to_IncidencePrevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 25820 bytes
Input file size = 25934 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 21650
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 = 21650
Output IDAT size = 21650 bytes (4170 bytes decrease)
Output file size = 21728 bytes (4206 bytes = 16.22% decrease)
--- finished re-building ‘a01_Introduction_to_IncidencePrevalence.Rmd’
--- re-building ‘a02_Creating_denominator_populations.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 236 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6463 bytes
Input file size = 7261 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5226
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 5190
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 = 5190
Output IDAT size = 5190 bytes (1273 bytes decrease)
Output file size = 5268 bytes (1993 bytes = 27.45% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6802 bytes
Input file size = 7657 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5541
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 = 5541
Output IDAT size = 5541 bytes (1261 bytes decrease)
Output file size = 5619 bytes (2038 bytes = 26.62% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6892 bytes
Input file size = 7744 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5599
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 = 5599
Output IDAT size = 5599 bytes (1293 bytes decrease)
Output file size = 5677 bytes (2067 bytes = 26.69% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 7218 bytes
Input file size = 8073 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5890
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 = 5890
Output IDAT size = 5890 bytes (1328 bytes decrease)
Output file size = 5968 bytes (2105 bytes = 26.07% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 6563 bytes
Input file size = 7418 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 5333
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 = 5333
Output IDAT size = 5333 bytes (1230 bytes decrease)
Output file size = 5411 bytes (2007 bytes = 27.06% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-17-1.png
672x480 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 35692 bytes
Input file size = 35818 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27947
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 = 27947
Output IDAT size = 27947 bytes (7745 bytes decrease)
Output file size = 28025 bytes (7793 bytes = 21.76% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-18-1.png
672x768 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 47934 bytes
Input file size = 48072 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 37761
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 = 37761
Output IDAT size = 37761 bytes (10173 bytes decrease)
Output file size = 37839 bytes (10233 bytes = 21.29% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-19-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 71868 bytes
Input file size = 72042 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 52951
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 = 52951
Output IDAT size = 52951 bytes (18917 bytes decrease)
Output file size = 53029 bytes (19013 bytes = 26.39% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a02_Creating_denominator_populations_files/figure-html/unnamed-chunk-20-1.png
672x960 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 38083 bytes
Input file size = 38209 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 31650
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 = 31650
Output IDAT size = 31650 bytes (6433 bytes decrease)
Output file size = 31728 bytes (6481 bytes = 16.96% decrease)
--- finished re-building ‘a02_Creating_denominator_populations.Rmd’
--- re-building ‘a03_Creating_target_denominator_populations.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-4-1.png
288x288 pixels, 8 bits/pixel, 244 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3203 bytes
Input file size = 4025 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2769
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 = 2769
Output IDAT size = 2769 bytes (434 bytes decrease)
Output file size = 2847 bytes (1178 bytes = 29.27% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-6-1.png
288x288 pixels, 8 bits/pixel, 239 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3471 bytes
Input file size = 4278 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3027
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 = 3027
Output IDAT size = 3027 bytes (444 bytes decrease)
Output file size = 3105 bytes (1173 bytes = 27.42% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a03_Creating_target_denominator_populations_files/figure-html/unnamed-chunk-7-1.png
288x288 pixels, 8 bits/pixel, 246 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 3037 bytes
Input file size = 3865 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 2562
zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 2555
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 = 2555
Output IDAT size = 2555 bytes (482 bytes decrease)
Output file size = 2633 bytes (1232 bytes = 31.88% decrease)
--- finished re-building ‘a03_Creating_target_denominator_populations.Rmd’
--- re-building ‘a04_Calculating_prevalence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-6-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9180 bytes
Input file size = 10047 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7626
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 = 7626
Output IDAT size = 7626 bytes (1554 bytes decrease)
Output file size = 7704 bytes (2343 bytes = 23.32% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21563 bytes
Input file size = 22445 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20002
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 = 20002
Output IDAT size = 20002 bytes (1561 bytes decrease)
Output file size = 20080 bytes (2365 bytes = 10.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 9773 bytes
Input file size = 10640 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7812
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 = 7812
Output IDAT size = 7812 bytes (1961 bytes decrease)
Output file size = 7890 bytes (2750 bytes = 25.85% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 253 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8600 bytes
Input file size = 9461 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7051
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 = 7051
Output IDAT size = 7051 bytes (1549 bytes decrease)
Output file size = 7129 bytes (2332 bytes = 24.65% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 21112 bytes
Input file size = 21994 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 19579
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 = 19579
Output IDAT size = 19579 bytes (1533 bytes decrease)
Output file size = 19657 bytes (2337 bytes = 10.63% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15267 bytes
Input file size = 16137 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13390
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 = 13390
Output IDAT size = 13390 bytes (1877 bytes decrease)
Output file size = 13468 bytes (2669 bytes = 16.54% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-13-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15894 bytes
Input file size = 16764 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 14157
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 = 14157
Output IDAT size = 14157 bytes (1737 bytes decrease)
Output file size = 14235 bytes (2529 bytes = 15.09% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a04_Calculating_prevalence_files/figure-html/unnamed-chunk-14-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 28455 bytes
Input file size = 29349 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 26399
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 = 26399
Output IDAT size = 26399 bytes (2056 bytes decrease)
Output file size = 26477 bytes (2872 bytes = 9.79% decrease)
--- finished re-building ‘a04_Calculating_prevalence.Rmd’
--- re-building ‘a05_Calculating_incidence.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-7-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8760 bytes
Input file size = 9630 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7247
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 = 7247
Output IDAT size = 7247 bytes (1513 bytes decrease)
Output file size = 7325 bytes (2305 bytes = 23.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-8-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8731 bytes
Input file size = 9601 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7238
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 = 7238
Output IDAT size = 7238 bytes (1493 bytes decrease)
Output file size = 7316 bytes (2285 bytes = 23.80% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-9-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8764 bytes
Input file size = 9628 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7250
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 = 7250
Output IDAT size = 7250 bytes (1514 bytes decrease)
Output file size = 7328 bytes (2300 bytes = 23.89% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-10-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8565 bytes
Input file size = 9432 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7096
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 = 7096
Output IDAT size = 7096 bytes (1469 bytes decrease)
Output file size = 7174 bytes (2258 bytes = 23.94% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-11-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15082 bytes
Input file size = 15952 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13092
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 = 13092
Output IDAT size = 13092 bytes (1990 bytes decrease)
Output file size = 13170 bytes (2782 bytes = 17.44% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 15219 bytes
Input file size = 16089 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 13313
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 = 13313
Output IDAT size = 13313 bytes (1906 bytes decrease)
Output file size = 13391 bytes (2698 bytes = 16.77% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a05_Calculating_incidence_files/figure-html/unnamed-chunk-12-2.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 27339 bytes
Input file size = 28233 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 25241
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 = 25241
Output IDAT size = 25241 bytes (2098 bytes decrease)
Output file size = 25319 bytes (2914 bytes = 10.32% decrease)
Quitting from lines 249-258 [unnamed-chunk-14] (a05_Calculating_incidence.Rmd)
Error: processing vignette 'a05_Calculating_incidence.Rmd' failed with diagnostics:
ℹ In argument: `min_cell_count = paste0(...)`.
Caused by error in `.data$min_cell_count`:
! Column `min_cell_count` not found in `.data`.
--- failed re-building ‘a05_Calculating_incidence.Rmd’
--- re-building ‘a06_Plotting_options.Rmd’ using rmarkdown
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/facetplot-1.png
672x480 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 8622 bytes
Input file size = 9486 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 7145
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 = 7145
Output IDAT size = 7145 bytes (1477 bytes decrease)
Output file size = 7223 bytes (2263 bytes = 23.86% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/linesplot-1.png
672x480 pixels, 8 bits/pixel, 255 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11872 bytes
Input file size = 12739 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10222
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 = 10222
Output IDAT size = 10222 bytes (1650 bytes decrease)
Output file size = 10300 bytes (2439 bytes = 19.15% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/noconfplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 10960 bytes
Input file size = 11830 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9324
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 = 9324
Output IDAT size = 9324 bytes (1636 bytes decrease)
Output file size = 9402 bytes (2428 bytes = 20.52% decrease)
** Processing: /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/IncidencePrevalence.Rcheck/vign_test/IncidencePrevalence/vignettes/a06_Plotting_options_files/figure-html/stackedplot-1.png
672x480 pixels, 8 bits/pixel, 256 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 11257 bytes
Input file size = 12127 bytes
Trying:
zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 9844
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 = 9844
Output IDAT size = 9844 bytes (1413 bytes decrease)
Output file size = 9922 bytes (2205 bytes = 18.18% decrease)
--- finished re-building ‘a06_Plotting_options.Rmd’
SUMMARY: processing the following file failed:
‘a05_Calculating_incidence.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.8.1
Check: tests
Result: ERROR
Running 'testthat.R' [253s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 3 | WARN 40 | SKIP 72 | PASS 134 ]
══ Skipped tests (72) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
• empty test (1): 'test-tables.R:1:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
[ FAIL 3 | WARN 40 | SKIP 72 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.8.1
Check: tests
Result: ERROR
Running 'testthat.R' [415s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(IncidencePrevalence)
>
> test_check("IncidencePrevalence")
Starting 2 test processes
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
══ Skipped tests (71) ══════════════════════════════════════════════════════════
• On CRAN (71): 'test-benchmarkIncidencePrevalence.R:2:3',
'test-estimatePrevalence.R:67:3', 'test-estimatePrevalence.R:124:3',
'test-estimatePrevalence.R:244:3', 'test-estimatePrevalence.R:380:3',
'test-estimatePrevalence.R:462:3', 'test-estimatePrevalence.R:607:3',
'test-estimatePrevalence.R:658:3', 'test-estimatePrevalence.R:715:3',
'test-estimatePrevalence.R:763:3', 'test-estimatePrevalence.R:787:3',
'test-estimatePrevalence.R:812:3', 'test-estimatePrevalence.R:945:3',
'test-estimatePrevalence.R:987:3', 'test-estimatePrevalence.R:1017:3',
'test-estimatePrevalence.R:1098:3', 'test-estimatePrevalence.R:1150:3',
'test-estimateIncidence.R:91:3', 'test-estimateIncidence.R:201:3',
'test-estimateIncidence.R:273:3', 'test-estimateIncidence.R:374:3',
'test-estimateIncidence.R:479:3', 'test-estimateIncidence.R:576:3',
'test-estimateIncidence.R:744:3', 'test-estimateIncidence.R:853:3',
'test-estimateIncidence.R:1008:3', 'test-estimateIncidence.R:1074:3',
'test-estimateIncidence.R:1130:3', 'test-estimateIncidence.R:1219:3',
'test-estimateIncidence.R:1394:3', 'test-estimateIncidence.R:1512:3',
'test-estimateIncidence.R:1593:3', 'test-estimateIncidence.R:1703:3',
'test-estimateIncidence.R:1809:3', 'test-estimateIncidence.R:1962:3',
'test-estimateIncidence.R:2019:3', 'test-estimateIncidence.R:2209:3',
'test-estimateIncidence.R:2407:3', 'test-estimateIncidence.R:2485:3',
'test-estimateIncidence.R:2899:3', 'test-estimateIncidence.R:2940:3',
'test-estimateIncidence.R:2989:3', 'test-estimateIncidence.R:3047:3',
'test-mockIncidencePrevalenceRef.R:2:3',
'test-mockIncidencePrevalenceRef.R:39:3',
'test-mockIncidencePrevalenceRef.R:67:3',
'test-mockIncidencePrevalenceRef.R:118:3',
'test-mockIncidencePrevalenceRef.R:220:3', 'test-plotting.R:2:3',
'test-plotting.R:105:3', 'test-plotting.R:160:3', 'test-plotting.R:211:3',
'test-generateDenominatorCohortSet.R:138:3',
'test-generateDenominatorCohortSet.R:185:3',
'test-generateDenominatorCohortSet.R:289:3',
'test-generateDenominatorCohortSet.R:325:3',
'test-generateDenominatorCohortSet.R:581:3',
'test-generateDenominatorCohortSet.R:799:3',
'test-generateDenominatorCohortSet.R:842:3',
'test-generateDenominatorCohortSet.R:894:3',
'test-generateDenominatorCohortSet.R:978:3',
'test-generateDenominatorCohortSet.R:1101:3',
'test-generateDenominatorCohortSet.R:1165:3',
'test-generateDenominatorCohortSet.R:1218:3',
'test-generateDenominatorCohortSet.R:1276:3',
'test-generateDenominatorCohortSet.R:1352:3',
'test-generateDenominatorCohortSet.R:1473:3',
'test-generateDenominatorCohortSet.R:1572:3',
'test-generateDenominatorCohortSet.R:1623:3',
'test-generateDenominatorCohortSet.R:1686:3',
'test-generateDenominatorCohortSet.R:1905:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-benchmarkIncidencePrevalence.R:55:3'): check tables cleaned up ──
Error in `omopgenerics::newSummarisedResult(x = prs, settings = dplyr::mutate(dplyr::select(analysisSettings,
!c("denominator_cohort_name", "outcome_cohort_name")), dplyr::across(-"result_id",
as.character)))`: Each `result_id` must be unique and contain a unique set of settings.
Backtrace:
▆
1. └─IncidencePrevalence::benchmarkIncidencePrevalence(cdm) at test-benchmarkIncidencePrevalence.R:55:3
2. └─IncidencePrevalence::estimatePointPrevalence(...)
3. └─IncidencePrevalence:::estimatePrevalence(...)
4. └─omopgenerics::newSummarisedResult(...)
5. └─omopgenerics:::validateSummarisedResult(x)
6. └─omopgenerics:::validateResultSettings(attr(x, "settings"), call = call)
7. └─cli::cli_abort(...)
8. └─rlang::abort(...)
── Failure ('test-estimatePrevalence.R:1202:3'): mock db: prevalence using strata vars ──
visOmopResults::filterSettings(prev_orig, result_type == "prevalence") (`actual`) not equal to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Failure ('test-estimateIncidence.R:3154:3'): mock db: incidence using strata vars ──
visOmopResults::filterSettings(inc_orig, result_type == "incidence") (`actual`) not identical to ... %>% ... (`expected`).
attr(actual, 'settings') vs attr(expected, 'settings')
strata
- attr(actual, 'settings')[1, ]
+ attr(expected, 'settings')[1, ] my_strata
`attr(actual, 'settings')$strata`: ""
`attr(expected, 'settings')$strata`: "my_strata"
── Error ('test-tables.R:13:3'): test tables ───────────────────────────────────
Error: 'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
Backtrace:
▆
1. └─IncidencePrevalence::tablePrevalence(prev_period, type = "gt") at test-tables.R:13:3
2. └─IncidencePrevalence:::tableInternal(...)
3. └─IncidencePrevalence:::defaultTableIncidencePrevalence(...)
── Failure ('test-tables.R:73:3'): test importing results ──────────────────────
Expected `tablePrevalence(prev_period_imported, type = "gt")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:91:3'): test importing results ──────────────────────
Expected `tableIncidence(inc_imported, type = "tibble")` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:98:3'): test importing results ──────────────────────
Expected `tableIncidence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
── Failure ('test-tables.R:99:3'): test importing results ──────────────────────
Expected `tablePrevalence(results_imported)` to run without any errors.
i Actually got a <simpleError> with text:
'optionsVisOmopTable' is not an exported object from 'namespace:visOmopResults'
[ FAIL 8 | WARN 3 | SKIP 71 | PASS 134 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64