* using log directory ‘/data/localhost/ripley/R/packages/tests-donttest/PhytoIn.Rcheck’
* using R Under development (unstable) (2026-08-24 r90445)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
    GNU Fortran (GCC) 16.1.1 20260515 (Red Hat 16.1.1-2)
* running under: Fedora Linux 44 (Server Edition)
* using session charset: UTF-8
* current time: 2026-08-24 18:25:44 UTC
* checking for file ‘PhytoIn/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhytoIn’ version ‘0.2.0’
* 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 ‘PhytoIn’ can be installed ... [23s/62s] 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 ... [7s/17s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/17s] OK
* checking whether the package can be unloaded cleanly ... [7s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/16s] OK
* checking loading without being on the library search path ... [7s/15s] 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 ... [32s/84s] 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 ... [14s/39s] OK
* checking examples with --run-donttest ... [8s/41s] ERROR
Running examples in ‘PhytoIn-Ex.R’ failed
The error most likely occurred in:

> ### Name: AGB
> ### Title: Estimate the above-ground biomass
> ### Aliases: AGB
> 
> ### ** Examples
> 
> data <- quadrat.df
> head(data)
  Plot      Family                Species  CBH  h
1 X2Y3 Leguminosae       Albizia hassleri  170 12
2 X4Y4 Leguminosae       Albizia hassleri 26,7 10
3 X4Y1 Leguminosae   Caesalpinia pluviosa 13,7  4
4 X4Y2 Leguminosae   Caesalpinia pluviosa 11,5  4
5 X4Y1  Araliaceae Didymopanax morototoni 10,4  3
6 X1Y1 Sapindaceae      Dimocarpus longan   10  5
> ## No test: 
> resul1 <- AGB(
+   data, measure.label = "CBH", h = "h", taxon = "Species", dead = "Morta",
+   circumference = TRUE, su = "Plot", area = 0.0625, rm.dead = TRUE,
+   check.spelling = FALSE, correct.taxon = TRUE, sort = TRUE,
+   decreasing = TRUE, long = TRUE
+ )
7 dead individuals removed from the dataset.
Using useCache=TRUE is recommended to reduce online search time for the next query

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Warning: There seem to be a problem reaching the TNRS API!
Failed to perform HTTP request.
Error in BIOMASS::getWoodDensity(genus = taxon.names$genus, species = taxon.names$species,  : 
  Your stand vector and your genus/species vectors do not have the same length
Calls: AGB -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
 OK
* checking PDF version of manual ... OK
* checking HTML 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/localhost/ripley/R/packages/tests-donttest/PhytoIn.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 10:27.80, 211.52 + 26.05