- using R version 4.4.1 (2024-06-14)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.3.0-1) 13.3.0
GNU Fortran (Debian 13.3.0-1) 13.3.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘isotracer/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘isotracer’ version ‘1.1.6’
- 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 ‘isotracer’ can be installed ... OK
See the install log for details.
- used C++ compiler: ‘g++-13 (Debian 13.3.0-1) 13.3.0’
- checking C++ specification ... OK
Not all R platforms support C++17
- 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 ... [5s/6s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
- checking whether the package can be unloaded cleanly ... [4s/6s] OK
- checking whether the namespace can be loaded with stated dependencies ... [4s/5s] OK
- checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
- checking loading without being on the library search path ... [10s/11s] OK
- checking whether startup messages can be suppressed ... [5s/5s] 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 ... [54s/59s] OK
- checking Rd files ... [1s/1s] 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 ... [11s/11s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in shell scripts ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [33s/38s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tidy_flows 5.550 0.382 4.106
sankey 4.745 0.012 6.149
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [158s/158s] ERROR
Running ‘testthat.R’ [158s/157s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(isotracer)
To automatically run isotracer in parallel on a multicore CPU, you can call:
options(mc.cores = parallel::detectCores())
Attaching package: 'isotracer'
The following object is masked from 'package:stats':
filter
>
> test_check("isotracer")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 503 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-steady-states-flows-pred.R:328:3'): Predictions for open network, multiple units, one steady, one split ──
<purrr_error_indexed/rlang_error/error/condition>
Error in `purrr::map(seq_len(nrow(nm)), function(k) {
nmRow <- nm[k, ]
sizes <- list()
for (i in seq_len(nrow(to))) {
nmRow <- set_params(nmRow, to$mcmc.parameters[[i]], force = TRUE)
sizes[[i]] <- calculate_steady_state_one_row(nmRow)
}
out <- to
out$stable_sizes <- sizes
return(out)
})`: ℹ In index: 2.
Caused by error in `calculate_steady_state_one_row()`:
! Eigenvector incompatible with steady state compartments.
Backtrace:
▆
1. ├─isotracer::tidy_steady_states(m, r) at test-steady-states-flows-pred.R:328:3
2. │ └─purrr::map(...)
3. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
4. │ ├─purrr:::with_indexed_errors(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ ├─purrr:::call_with_cleanup(...)
7. │ └─isotracer (local) .f(.x[[i]], ...)
8. │ └─isotracer:::calculate_steady_state_one_row(nmRow)
9. │ └─base::stop("Eigenvector incompatible with steady state compartments.")
10. └─base::.handleSimpleError(...)
11. └─purrr (local) h(simpleError(msg, call))
12. └─cli::cli_abort(...)
13. └─rlang::abort(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 503 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [26s/32s] OK
- checking PDF version of manual ... [8s/11s] OK
- checking HTML version of manual ... [3s/6s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE