• using R version 4.5.1 (2025-06-13)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.3.0-5) 14.3.0     GNU Fortran (Debian 14.3.0-5) 14.3.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘econullnetr/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘econullnetr’ version ‘0.2.1’
• 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 serialization versions ... OK
• checking whether package ‘econullnetr’ 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 ... [0s/0s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the package can be unloaded cleanly ... [0s/0s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
• checking loading without being on the library search path ... [0s/0s] 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 ... [7s/9s] OK
• checking Rd files ... [0s/0s] 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 ... [11s/17s] ERROR Running examples in ‘econullnetr-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plot_bipartite > ### Title: Plot a bipartite network, colour coding individual links > ### according to whether they are stronger or weaker than expected under > ### the null model > ### Aliases: plot_bipartite > > ### ** Examples > > > # Run the null model > set.seed(1234) > sil.null <- generate_null_net(Silene[, 2:7], Silene.plants[, 2:6], sims = 10, + c.samples = Silene[, 1], + r.samples = Silene.plants[, 1]) [1] 1 [1] 2 [1] 3 [1] 4 [1] 5 [1] 6 [1] 7 [1] 8 [1] 9 [1] 10 > > # Basic plot > plot_bipartite(sil.null) Error in bipartite::plotweb(obs.web, method = "normal", empty = FALSE, :   unused arguments (method = "normal", col.interaction = select.vector) Calls: plot_bipartite Execution halted Examples with CPU (user + system) or elapsed time > 5s                    user system elapsed generate_edgelist 5.001 0.027 6.275 bipartite_stats 4.237 0.132 7.026
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [7s/9s] OK   Running ‘testthat.R’ [6s/8s]
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [9s/17s] ERROR Error(s) in re-building vignettes:   ... --- re-building ‘econullnetr-intro.Rmd’ using rmarkdown Quitting from econullnetr-intro.Rmd:105-115 [unnamed-chunk-6] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `bipartite::plotweb()`: ! unused arguments (method = "normal", col.interaction = select.vector, low.abun = c(8.45454545454546, 12, 38, 43.0909090909091, 3.27272727272727), abuns.type = "independent", low.abun.col = "black", high.abun.col = "black", high.lablength = 5, low.lablength = 5) --- Backtrace:     ▆  1. └─econullnetr::plot_bipartite(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'econullnetr-intro.Rmd' failed with diagnostics: unused arguments (method = "normal", col.interaction = select.vector, low.abun = c(8.45454545454546, 12, 38, 43.0909090909091, 3.27272727272727), abuns.type = "independent", low.abun.col = "black", high.abun.col = "black", high.lablength = 5, low.lablength = 5) --- failed re-building ‘econullnetr-intro.Rmd’ SUMMARY: processing the following file failed:   ‘econullnetr-intro.Rmd’ Error: Vignette re-building failed. Execution halted
• checking PDF version of manual ... [6s/8s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs