* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/corncob.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘corncob/DESCRIPTION’ ... OK
* this is package ‘corncob’ version ‘0.4.1’
* 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 ‘corncob’ can be installed ... [13s/17s] 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 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 ... [16s/18s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘corncob-Ex.R’ failed
The error most likely occurred in:

> ### Name: contrastsTest
> ### Title: Identify differentially-abundant and differentially-variable
> ###   taxa using contrasts
> ### Aliases: contrastsTest
> 
> ### ** Examples
> 
> 
> # data frame example
> data(soil_phylum_contrasts_sample)
> data(soil_phylum_contrasts_otu)
> da_analysis <- contrastsTest(formula = ~ DayAmdmt,
+                              phi.formula = ~ DayAmdmt,
+                              contrasts_DA = list("DayAmdmt21 - DayAmdmt11",
+                                                  "DayAmdmt22 - DayAmdmt21"),
+                              data = soil_phylum_contrasts_otu,
+                              sample_data = soil_phylum_contrasts_sample,
+                              fdr_cutoff = 0.05,
+                              try_only = 1:5)
Error in contrastsTest(formula = ~DayAmdmt, phi.formula = ~DayAmdmt, contrasts_DA = list("DayAmdmt21 - DayAmdmt11",  : 
  If you would like to test contrasts, please install the `limma` package, available through Bioconductor.
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [83s/109s]
 [83s/109s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [10s/14s] 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
* DONE

Status: 1 ERROR
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/corncob.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:46.13, 164.19 + 13.39