Last updated on 2026-10-21 11:59:02 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 4.0.2 | 10.78 | 313.81 | 324.59 | OK | |
| r-devel-linux-x86_64-debian-gcc | 4.0.2 | 9.15 | 208.33 | 217.48 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 4.0.2 | 214.44 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 4.0.2 | 208.05 | ERROR | |||
| r-devel-windows-x86_64 | 4.0.2 | 14.00 | 313.00 | 327.00 | OK | |
| r-patched-linux-x86_64 | 4.0.2 | 10.92 | 306.23 | 317.15 | OK | |
| r-release-linux-x86_64 | 4.0.2 | 10.17 | 308.65 | 318.82 | OK | |
| r-release-macos-arm64 | 4.0.2 | 3.00 | 80.00 | 83.00 | OK | |
| r-release-macos-x86_64 | 4.0.2 | 8.00 | 393.00 | 401.00 | OK | |
| r-release-windows-x86_64 | 4.0.2 | 14.00 | 303.00 | 317.00 | OK | |
| r-oldrel-macos-arm64 | 4.0.2 | 3.00 | 102.00 | 105.00 | OK | |
| r-oldrel-macos-x86_64 | 4.0.2 | 9.00 | 680.00 | 689.00 | OK | |
| r-oldrel-windows-x86_64 | 4.0.2 | 19.00 | 371.00 | 390.00 | OK |
Version: 4.0.2
Check: examples
Result: ERROR
Running examples in ‘ApplyPolygenicScore-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create.pgs.rank.plot
> ### Title: Plot PGS Rank
> ### Aliases: create.pgs.rank.plot
>
> ### ** Examples
>
> set.seed(200);
> percentiles <- get.pgs.percentiles(rnorm(200, 0, 1));
> pgs.data <- data.frame(
+ Indiv = paste0('sample', 1:200),
+ percentile = percentiles$percentile,
+ decile = percentiles$decile,
+ quartile = percentiles$quartile,
+ n.missing.genotypes = sample(1:10, 200, replace = TRUE),
+ percent.missing.genotypes = sample(1:10, 200, replace = TRUE) / 100,
+ continuous.pheno = rnorm(200, 1, 1),
+ categorical.pheno = sample(letters[1:5], 200, replace = TRUE),
+ binary.pheno = sample(c(0,1), 200, replace = TRUE)
+ );
>
> temp.dir <- tempdir();
>
> create.pgs.rank.plot(
+ pgs.data,
+ phenotype.columns = c('continuous.pheno', 'categorical.pheno', 'binary.pheno'),
+ missing.genotype.style = 'percent',
+ output.dir = temp.dir,
+ filename.prefix = 'example-rank-plot'
+ );
[1] "springgreen3"
[1] "darkturquoise"
Error: index out of bounds ("unit" subsetting)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [116s/150s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat);
> library(ApplyPolygenicScore);
>
> test_check('ApplyPolygenicScore');
Input data passed validation
Input data passed validation
Skipping test for >12 PGS columns as 'scales' package is available and will be used.
[1] "springgreen3"
[1] "darkturquoise"
Saving _problems/test-plotting-793.R
Saving _problems/test-plotting-802.R
Saving _problems/test-plotting-822.R
Saving _problems/test-plotting-831.R
[1] "springgreen3"
[1] "darkturquoise"
Saving _problems/test-plotting-849.R
Saving _problems/test-plotting-858.R
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 649 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotting.R:786:9'): create.pgs.rank.plot correctly switches between large and small sample size modes ──
Expected `create.pgs.rank.plot(...)` not to throw any errors.
Actually got a <simpleError> with message:
index out of bounds ("unit" subsetting)
── Failure ('test-plotting.R:800:9'): create.pgs.rank.plot correctly switches between large and small sample size modes ──
Expected `file.exists(file.path(temp.dir, test.filename))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-plotting.R:813:9'): create.pgs.rank.plot correctly handles user-provided color palette ──
Expected `create.pgs.rank.plot(...)` not to throw any errors.
Actually got a <simpleError> with message:
index out of bounds ("unit" subsetting)
── Failure ('test-plotting.R:829:9'): create.pgs.rank.plot correctly handles user-provided color palette ──
Expected `file.exists(file.path(temp.dir, test.filename))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-plotting.R:842:9'): create.pgs.rank.plot runs correctly with user provided phenotypes ──
Expected `create.pgs.rank.plot(...)` not to throw any errors.
Actually got a <simpleError> with message:
index out of bounds ("unit" subsetting)
── Failure ('test-plotting.R:856:9'): create.pgs.rank.plot runs correctly with user provided phenotypes ──
Expected `file.exists(file.path(temp.dir, test.filename))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 649 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘UserGuide.Rmd’ using rmarkdown
Quitting from UserGuide.Rmd:756-768 [pgs-rank-phenotype]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! index out of bounds ("unit" subsetting)
---
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.rank.plot(...)
2. ├─base::suppressWarnings(...)
3. │ └─base::withCallingHandlers(...)
4. └─BoutrosLab.plotting.general::legend.grob(cov.legends, title.just = "left")
5. └─grid::packGrob(...)
6. └─grid:::mod.dims(...)
7. ├─grid::unit.c(...)
8. ├─dims[(index + 1):(nindex - 1)]
9. └─grid:::`[.unit`(dims, (index + 1):(nindex - 1))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'UserGuide.Rmd' failed with diagnostics:
index out of bounds ("unit" subsetting)
--- failed re-building ‘UserGuide.Rmd’
SUMMARY: processing the following file failed:
‘UserGuide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 4.0.2
Check: examples
Result: ERROR
Running examples in ‘ApplyPolygenicScore-Ex.R’ failed
The error most likely occurred in:
> ### Name: create.pgs.rank.plot
> ### Title: Plot PGS Rank
> ### Aliases: create.pgs.rank.plot
>
> ### ** Examples
>
> set.seed(200);
> percentiles <- get.pgs.percentiles(rnorm(200, 0, 1));
> pgs.data <- data.frame(
+ Indiv = paste0('sample', 1:200),
+ percentile = percentiles$percentile,
+ decile = percentiles$decile,
+ quartile = percentiles$quartile,
+ n.missing.genotypes = sample(1:10, 200, replace = TRUE),
+ percent.missing.genotypes = sample(1:10, 200, replace = TRUE) / 100,
+ continuous.pheno = rnorm(200, 1, 1),
+ categorical.pheno = sample(letters[1:5], 200, replace = TRUE),
+ binary.pheno = sample(c(0,1), 200, replace = TRUE)
+ );
>
> temp.dir <- tempdir();
>
> create.pgs.rank.plot(
+ pgs.data,
+ phenotype.columns = c('continuous.pheno', 'categorical.pheno', 'binary.pheno'),
+ missing.genotype.style = 'percent',
+ output.dir = temp.dir,
+ filename.prefix = 'example-rank-plot'
+ );
[1] "springgreen3"
[1] "darkturquoise"
Error: index out of bounds ("unit" subsetting)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 4.0.2
Check: tests
Result: ERROR
Running ‘testthat.R’ [115s/115s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat);
> library(ApplyPolygenicScore);
>
> test_check('ApplyPolygenicScore');
Input data passed validation
Input data passed validation
Skipping test for >12 PGS columns as 'scales' package is available and will be used.
[1] "springgreen3"
[1] "darkturquoise"
Saving _problems/test-plotting-793.R
Saving _problems/test-plotting-802.R
Saving _problems/test-plotting-822.R
Saving _problems/test-plotting-831.R
[1] "springgreen3"
[1] "darkturquoise"
Saving _problems/test-plotting-849.R
Saving _problems/test-plotting-858.R
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 649 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotting.R:786:9'): create.pgs.rank.plot correctly switches between large and small sample size modes ──
Expected `create.pgs.rank.plot(...)` not to throw any errors.
Actually got a <simpleError> with message:
index out of bounds ("unit" subsetting)
── Failure ('test-plotting.R:800:9'): create.pgs.rank.plot correctly switches between large and small sample size modes ──
Expected `file.exists(file.path(temp.dir, test.filename))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-plotting.R:813:9'): create.pgs.rank.plot correctly handles user-provided color palette ──
Expected `create.pgs.rank.plot(...)` not to throw any errors.
Actually got a <simpleError> with message:
index out of bounds ("unit" subsetting)
── Failure ('test-plotting.R:829:9'): create.pgs.rank.plot correctly handles user-provided color palette ──
Expected `file.exists(file.path(temp.dir, test.filename))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
── Failure ('test-plotting.R:842:9'): create.pgs.rank.plot runs correctly with user provided phenotypes ──
Expected `create.pgs.rank.plot(...)` not to throw any errors.
Actually got a <simpleError> with message:
index out of bounds ("unit" subsetting)
── Failure ('test-plotting.R:856:9'): create.pgs.rank.plot runs correctly with user provided phenotypes ──
Expected `file.exists(file.path(temp.dir, test.filename))` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
[ FAIL 6 | WARN 87 | SKIP 0 | PASS 649 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 4.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘UserGuide.Rmd’ using rmarkdown
Quitting from UserGuide.Rmd:756-768 [pgs-rank-phenotype]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! index out of bounds ("unit" subsetting)
---
Backtrace:
▆
1. └─ApplyPolygenicScore::create.pgs.rank.plot(...)
2. ├─base::suppressWarnings(...)
3. │ └─base::withCallingHandlers(...)
4. └─BoutrosLab.plotting.general::legend.grob(cov.legends, title.just = "left")
5. └─grid::packGrob(...)
6. └─grid:::mod.dims(...)
7. ├─grid::unit.c(...)
8. ├─dims[(index + 1):(nindex - 1)]
9. └─grid:::`[.unit`(dims, (index + 1):(nindex - 1))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'UserGuide.Rmd' failed with diagnostics:
index out of bounds ("unit" subsetting)
--- failed re-building ‘UserGuide.Rmd’
SUMMARY: processing the following file failed:
‘UserGuide.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc