Last updated on 2026-06-04 11:54:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.6.0 | 11.14 | 91.53 | 102.67 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.6.0 | 8.09 | 75.58 | 83.67 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.6.0 | 21.00 | 144.95 | 165.95 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.6.0 | 20.00 | 154.42 | 174.42 | OK | |
| r-devel-windows-x86_64 | 0.6.0 | 12.00 | 176.00 | 188.00 | OK | |
| r-patched-linux-x86_64 | 0.6.0 | 14.77 | 83.58 | 98.35 | OK | |
| r-release-linux-x86_64 | 0.6.0 | 9.48 | 84.00 | 93.48 | OK | |
| r-release-macos-arm64 | 0.6.0 | 3.00 | 25.00 | 28.00 | OK | |
| r-release-macos-x86_64 | 0.6.0 | 8.00 | 89.00 | 97.00 | OK | |
| r-release-windows-x86_64 | 0.6.0 | 14.00 | 119.00 | 133.00 | OK | |
| r-oldrel-macos-arm64 | 0.6.0 | OK | ||||
| r-oldrel-macos-x86_64 | 0.6.0 | 8.00 | 146.00 | 154.00 | OK | |
| r-oldrel-windows-x86_64 | 0.6.0 | 19.00 | 151.00 | 170.00 | OK |
Version: 0.6.0
Check: examples
Result: ERROR
Running examples in ‘nexus-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barplot
> ### Title: Barplot of Compositional Data
> ### Aliases: barplot barplot,CompositionMatrix-method
>
> ### ** Examples
>
> ## Data from Aitchison 1986
> data("hongite")
>
> ## Coerce to compositional data
> coda <- as_composition(hongite)
>
> ## Bar plot
> barplot(coda)
>
> ## Data from Day et al. 2011
> data("kommos", package = "folio")
> kommos <- remove_NA(kommos, margin = 1) # Remove cases with missing values
> coda <- as_composition(kommos, groups = 1) # Coerce to compositional data
>
> ## Use ceramic types for grouping
> barplot(coda, order_columns = TRUE)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': assignment of an object of class “numeric” is not valid for @‘.Data’ in an object of class “CompositionMatrix”; is(value, "matrix") is not TRUE
Calls: barplot ... prepare_barplot -> t -> apply -> FUN -> FUN -> <Anonymous>
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.0
Check: tests
Result: ERROR
Running ‘tinytest.R’ [4s/6s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
> if (requireNamespace("tinytest", quietly = TRUE)) {
+ ## Force tests to be executed if in dev release
+ ## (which we define as having a sub-release)
+ NOT_CRAN <- length(unclass(packageVersion("nexus"))[[1]]) == 4
+
+ tinytest::test_package("nexus", at_home = NOT_CRAN)
+ }
Loading required package: dimensio
test_chemistry.R.............. 0 tests
test_chemistry.R.............. 0 tests
test_chemistry.R.............. 0 tests
test_chemistry.R.............. 1 tests OK
test_chemistry.R.............. 2 tests OK
test_chemistry.R.............. 3 tests OK
test_chemistry.R.............. 4 tests OK
test_chemistry.R.............. 5 tests OK
test_chemistry.R.............. 5 tests OK
test_chemistry.R.............. 6 tests OK
test_chemistry.R.............. 7 tests OK 0.1s
test_coerce.R................. 0 tests
test_coerce.R................. 0 tests
test_coerce.R................. 0 tests
test_coerce.R................. 0 tests
test_coerce.R................. 1 tests OK 89ms
test_condense.R............... 0 tests
test_condense.R............... 0 tests
test_condense.R............... 0 tests
test_condense.R............... 0 tests
test_condense.R............... 1 tests OK
test_condense.R............... 2 tests OK
test_condense.R............... 2 tests OK
test_condense.R............... 2 tests OK
test_condense.R............... 3 tests OK
test_condense.R............... 3 tests OK
test_condense.R............... 4 tests OK
test_condense.R............... 5 tests OK
test_condense.R............... 6 tests OK
test_condense.R............... 6 tests OK
test_condense.R............... 6 tests OK
test_condense.R............... 6 tests OK
test_condense.R............... 6 tests OK
test_condense.R............... 6 tests OK
test_condense.R............... 7 tests OK 1.0s
test_describe.R............... 0 tests
test_describe.R............... 0 tests
test_describe.R............... 0 tests
test_describe.R............... 0 tests
test_describe.R............... 1 tests OK
test_describe.R............... 2 tests OK
test_describe.R............... 2 tests OK
test_describe.R............... 3 tests OK
test_describe.R............... 4 tests OK 1.0s
test_dist.R................... 0 tests
test_dist.R................... 0 tests
test_dist.R................... 0 tests
test_dist.R................... 1 tests OK
test_dist.R................... 2 tests OK 24ms
test_group.R.................. 0 tests
test_group.R.................. 0 tests
test_group.R.................. 0 tests
test_group.R.................. 1 tests OK
test_group.R.................. 1 tests OK
test_group.R.................. 2 tests OK
test_group.R.................. 3 tests OK
test_group.R.................. 4 tests OK
test_group.R.................. 5 tests OK
test_group.R.................. 6 tests OK
test_group.R.................. 7 tests OK
test_group.R.................. 8 tests OK
test_group.R.................. 9 tests OK
test_group.R.................. 10 tests OK
test_group.R.................. 11 tests OK
test_group.R.................. 12 tests OK
test_group.R.................. 13 tests OK
test_group.R.................. 14 tests OK
test_group.R.................. 15 tests OK
test_group.R.................. 16 tests OK
test_group.R.................. 17 tests OK 0.1s
test_mutators.R............... 0 tests
test_mutators.R............... 0 tests
test_mutators.R............... 0 tests
test_mutators.R............... 1 tests OK
test_mutators.R............... 1 tests OK
test_mutators.R............... 2 tests OK
test_mutators.R............... 3 tests OK
test_mutators.R............... 4 tests OK 6ms
test_outliers.R............... 0 tests
test_outliers.R............... 0 tests
test_outliers.R............... 0 tests
test_outliers.R............... 0 tests
test_outliers.R............... 1 tests OK
test_outliers.R............... 2 tests OK
test_outliers.R............... 2 tests OK 9ms
test_packages.R............... 0 tests 2ms
test_pca.R.................... 0 tests
test_pca.R.................... 0 tests
test_pca.R.................... 0 tests
test_pca.R.................... 1 tests OK 12ms
test_plot.R................... 0 tests
test_plot.R................... 0 tests 2ms
test_replace.R................ 0 tests
test_replace.R................ 0 tests
test_replace.R................ 0 tests
test_replace.R................ 1 tests OK
test_replace.R................ 2 tests OK
test_replace.R................ 3 tests OK
test_replace.R................ 4 tests OK
test_replace.R................ 5 tests OK
test_replace.R................ 6 tests OK
test_replace.R................ 7 tests OK
test_replace.R................ 7 tests OK
test_replace.R................ 8 tests 1 fails
test_replace.R................ 8 tests 1 fails
test_replace.R................ 8 tests 1 fails
test_replace.R................ 9 tests 1 fails
test_replace.R................ 10 tests 1 fails
test_replace.R................ 11 tests 1 fails
test_replace.R................ 12 tests 1 fails
test_replace.R................ 13 tests 1 fails
test_replace.R................ 14 tests 1 fails
test_replace.R................ 15 tests 1 fails
test_replace.R................ 15 tests 1 fails
test_replace.R................ 16 tests 2 fails
test_replace.R................ 16 tests 2 fails
test_replace.R................ 17 tests 3 fails 0.2s
test_simplex.R................ 0 tests
test_simplex.R................ 0 tests
test_simplex.R................ 0 tests
test_simplex.R................ 1 tests OK
test_simplex.R................ 2 tests OK
test_simplex.R................ 3 tests OK
test_simplex.R................ 4 tests OK
test_simplex.R................ 5 tests OK
test_simplex.R................ 6 tests OK
test_simplex.R................ 7 tests OK
test_simplex.R................ 7 tests OK
test_simplex.R................ 7 tests OK
test_simplex.R................ 7 tests OK
test_simplex.R................ 8 tests OK
test_simplex.R................ 9 tests OK
test_simplex.R................ 10 tests OK
test_simplex.R................ 11 tests OK
test_simplex.R................ 12 tests OK
test_simplex.R................ 13 tests OK
test_simplex.R................ 13 tests OK
test_simplex.R................ 13 tests OK
test_simplex.R................ 14 tests OK 97ms
test_statistics.R............. 0 tests
test_statistics.R............. 0 tests
test_statistics.R............. 0 tests
test_statistics.R............. 1 tests OK
test_statistics.R............. 2 tests OK
test_statistics.R............. 3 tests OK
test_statistics.R............. 4 tests OK
test_statistics.R............. 5 tests OK
test_statistics.R............. 5 tests OK
test_statistics.R............. 5 tests OK
test_statistics.R............. 6 tests OK Error: <NumericMatrix> instance initialization:
* node stack overflow
In addition: Warning message:
In sprintf(tr_("<%s> instance initialization:\n%s"), class(object), :
restarting interrupted promise evaluation
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.6.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘groups.Rmd’ using knitr
Quitting from groups.Rmd:71-77 [barplot]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'x' in selecting a method for function 't': assignment of an object of class "numeric" is not valid for @'.Data' in an object of class "CompositionMatrix"; is(value, "matrix") is not TRUE
---
Backtrace:
▆
1. ├─graphics::barplot(major, order_rows = "Cu", space = 0)
2. ├─nexus::barplot(major, order_rows = "Cu", space = 0)
3. │ └─nexus (local) .local(height, ...)
4. │ └─nexus:::prepare_barplot(...)
5. │ ├─base::t(apply(X = z, MARGIN = 1, FUN = cumsum))
6. │ └─base::apply(X = z, MARGIN = 1, FUN = cumsum)
7. │ ├─methods (local) FUN(newX[, i], ...)
8. │ └─methods (local) FUN(newX[, i], ...)
9. │ └─methods (local) `<fn>`(`<chr>`, ".Data", "numeric")
10. │ └─base::stop(...)
11. └─base::.handleSimpleError(...)
12. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'groups.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 't': assignment of an object of class "numeric" is not valid for @'.Data' in an object of class "CompositionMatrix"; is(value, "matrix") is not TRUE
--- failed re-building ‘groups.Rmd’
--- re-building ‘nexus.Rmd’ using knitr
Quitting from nexus.Rmd:142-146 [histogram]
Error: processing vignette 'nexus.Rmd' failed with diagnostics:
evaluation nested too deeply: infinite recursion / options(expressions=)?
--- failed re-building ‘nexus.Rmd’
SUMMARY: processing the following files failed:
‘groups.Rmd’ ‘nexus.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc