* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/PNC.Rcheck’
* using R Under development (unstable) (2025-11-16 r89026)
* 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
* checking for file ‘PNC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PNC’ version ‘0.1.0’
* 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 ‘PNC’ can be installed ... [13s/14s] OK
* checking package 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 ... [19s/19s] OK
* checking Rd files ... 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 ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [30m/31m] ERROR
Running examples in ‘PNC-Ex.R’ failed
The error most likely occurred in:

> ### Name: pnc_robustness
> ### Title: Test Robustness of Phylogenetic Niche Conservatism Analysis
> ### Aliases: pnc_robustness
> 
> ### ** Examples
> 
> ## No test: 
> # Load example data
> data(BCI)
> data(TRY)
> 
> # Extract trait data
> sp <- colnames(BCI$com)
> subtraits <- extract_traits(sp, TRY, rank = "species",
+                           traits = c("LA", "LMA", "LeafN", "PlantHeight"))
The missing species in the dataset: ( 41 ):
 [1] "Abarema macradenia"         "Appunia seibertii"         
 [3] "Ardisia bartlettii"         "Aspidosperma cruentum"     
 [5] "Beilschmiedia tovarensis"   "Capparidastrum frondosum"  
 [7] "Casearia commersoniana"     "Cassipourea elliptica"     
 [9] "Cinnamomum triplinerve"     "Clidemia dentata"          
[11] "Conostegia bracteata"       "Conostegia cinnamomea"     
[13] "Coussarea curvigemmia"      "Eugenia coloradoensis"     
[15] "Garcinia recondita"         "Guapira standleyana"       
[17] "Guarea grandifolia"         "Leandra dichotoma"         
[19] "Maytenus longipes"          "Miconia septuplinervia"    
[21] "Mosannona garwoodii"        "Nectandra fuzzy"           
[23] "Ocotea cernua"              "Piper albopunctulatissimum"
[25] "Piper cabagranum"           "Piper culebranum"          
[27] "Piper longispicum"          "Piper paulowniifolium"     
[29] "Piper playablancanum"       "Piper subnudispicum"       
[31] "Pochota quinata"            "Psychotria graciliflora"   
[33] "Pterocarpus hayesii"        "Rinorea sylvatica"         
[35] "Sapium broadleaf"           "Staphylea occidentalis"    
[37] "Tachigali panamensis"       "Talisia croatii"           
[39] "Trema integerrima"          "Virola nobilis"            
[41] "Zuelania guidonia"         
> 
> # Test robustness of phylogenetic signal analysis
> # This function's runtime is long
> pnc_robustness(subtraits, BCI$phy_species, methods = "lambda", n_simulations = 5)

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* checking PDF version of manual ... 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: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/PNC.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 32:38.17, 1893.96 + 21.32