• using R Under development (unstable) (2026-06-02 r90096)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-16 (Debian 16.1.0-1) 16.1.0     GNU Fortran (Debian 16.1.0-1) 16.1.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8 * current time: 2026-06-03 16:11:15 UTC
• checking for file ‘nexus/DESCRIPTION’ ... OK
• this is package ‘nexus’ version ‘0.6.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/3s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘nexus’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [1s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the package can be unloaded cleanly ... [1s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
• checking loading without being on the library search path ... [1s/1s] OK
• checking whether startup messages can be suppressed ... [1s/1s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [9s/14s] OK
• checking Rd files ... [1s/2s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [2s/3s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [4s/6s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [17s/24s] 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
• checking PDF version of manual ... [6s/7s] OK
• checking HTML version of manual ... [5s/8s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs