* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/dyngen.Rcheck’
* using R Under development (unstable) (2026-02-08 r89382)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* current time: 2026-02-09 03:15:04 UTC
* checking for file ‘dyngen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dyngen’ version ‘1.0.5’
* package encoding: UTF-8
* 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 ‘dyngen’ can be installed ... [30s/32s] OK
* checking package directory ... 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [37s/40s] OK
* checking Rd files ... NOTE
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
* 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 ... 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 ... [13s/14s] ERROR
Running examples in ‘dyngen-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_timings
> ### Title: Return the timings of each of the dyngen steps
> ### Aliases: get_timings
> 
> ### ** Examples
> 
> data("example_model")
> timings <- get_timings(example_model)
Error in `summarise()`:
ℹ In argument: `task = .data$task[-length(.data$task)]`.
ℹ In group 2: `group = "2_tf_network"`.
Caused by error:
! `task` must be size 1, not 2.
ℹ To return more or less than 1 row per group, use `reframe()`.
Backtrace:
     ▆
  1. ├─dyngen::get_timings(example_model)
  2. │ └─model$timings %>% group_by(.data$group) %>% ...
  3. ├─dplyr::summarise(...)
  4. ├─dplyr:::summarise.grouped_df(...)
  5. │ └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
  6. │   └─base::withCallingHandlers(...)
  7. ├─dplyr:::dplyr_internal_error(...)
  8. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data)
  9. │   └─rlang:::signal_abort(cnd, .file)
 10. │     └─base::signalCondition(cnd)
 11. └─dplyr (local) `<fn>`(`<dpl:::__>`)
 12.   └─dplyr (local) handler(cnd)
 13.     └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
Execution halted
* checking examples with --run-donttest ... [36s/37s] ERROR
Running examples in ‘dyngen-Ex.R’ failed
The error most likely occurred in:

> ### Name: as_dyno
> ### Title: Convert simulation output to different formats.
> ### Aliases: as_dyno as_anndata as_sce as_seurat as_list wrap_dataset
> 
> ### ** Examples
> 
> data("example_model")
> dataset <- wrap_dataset(example_model, format = "list")
> ## No test: 
> dataset <- wrap_dataset(example_model, format = "dyno")
Loading required namespace: dynwrap
> dataset <- wrap_dataset(example_model, format = "sce")
Loading required namespace: SingleCellExperiment
> dataset <- wrap_dataset(example_model, format = "seurat")
Loading required namespace: Seurat
> dataset <- wrap_dataset(example_model, format = "anndata")
Loading required namespace: anndata
Error in py_module_import(module, convert = convert) : 
  ModuleNotFoundError: No module named 'anndata'
Run `reticulate::py_last_error()` for details.
Calls: wrap_dataset ... do.call -> <Anonymous> -> <Anonymous> -> py_module_import
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [79s/88s]
 [80s/88s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [12s/13s] OK
* checking PDF version of manual ... [9s/11s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/dyngen.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 7:21.25, 338.55 + 67.83