* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/rbiom.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 ‘rbiom/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rbiom’ version ‘1.0.3’
* 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 ‘rbiom’ can be installed ... [108s/113s] OK
* used C++ compiler: ‘g++-13 (GCC) 13.2.0’
* 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 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 ... [15s/17s] 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 line endings in C/C++/Fortran sources/headers ... 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 examples ... ERROR
Running examples in ‘rbiom-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.biom
> ### Title: Extracts counts, metadata, taxonomy, and phylogeny from a biom
> ###   file.
> ### Aliases: read.biom
> 
> ### ** Examples
> 
>     library(rbiom)
> 
>     infile <- system.file("extdata", "hmp50.bz2", package = "rbiom")
>     biom <- read.biom(infile)
> 
>     summary(biom)
          Length Class                 Mode     
counts       6   simple_triplet_matrix list     
metadata     6   data.frame            list     
taxonomy  2940   -none-                character
phylogeny    4   phylo                 list     
sequences  490   -none-                character
info        10   -none-                list     
> 
>     # Taxa Abundances
>     as.matrix(biom$counts[1:4,1:4])
         HMP01 HMP02 HMP03 HMP04
UncO2713     0     0     0     0
UncO4101     1     5     6    18
AnmMass2     0     0     0     0
PreBivi6     0     0     0     0
> 
>     top5 <- names(head(rev(sort(slam::row_sums(biom$counts))), 5))
>     biom$taxonomy[top5,c('Family', 'Genus')]
         Family                 Genus                
Unc01yki "__Lactobacillaceae"   "__Lactobacillus"    
Unc53100 "__Streptococcaceae"   "__Streptococcus"    
LtbAci52 "__Lactobacillaceae"   "__Lactobacillus"    
CnbTube3 "__Corynebacteriaceae" "__Corynebacterium_1"
Unc02qsf "__Staphylococcaceae"  "__Staphylococcus"   
>     as.matrix(biom$counts[top5, 1:6])
         HMP01 HMP02 HMP03 HMP04 HMP05 HMP06
Unc01yki     0     0     0     0     0     0
Unc53100  1083   543   301   223  2672   748
LtbAci52     0     0     0     0     0     0
CnbTube3     0     0     0     0     0     0
Unc02qsf     0     0     0     0     0     0
> 
>     # Metadata
>     table(biom$metadata$Sex, biom$metadata$`Body Site`)
        
         Anterior nares Buccal mucosa Mid vagina Saliva Stool
  Female              5             5         10      5     5
  Male                5             5          0      5     5
>     sprintf("Mean age: %.1f", mean(biom$metadata$Age))
[1] "Mean age: 27.8"
> 
>     # Phylogenetic tree
>     tree <- biom$phylogeny
>     top5.tree <- rbiom::subtree(tree, top5)
>     ape::plot.phylo(top5.tree)
Error in loadNamespace(x) : there is no package called ‘ape’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("rbiom")
  Loading required package: rbiom
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_subsetting.r:21:3'): Rarefaction ───────────────────────────────
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(x)`: there is no package called 'reshape2'
  Backtrace:
      ▆
   1. ├─base::merge(...) at test_subsetting.r:21:3
   2. └─base::loadNamespace(x)
   3.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   4.     └─base (local) withOneRestart(expr, restarts[[1L]])
   5.       └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 51 ]
  Error: Test failures
  Execution halted
* checking PDF version of manual ... [9s/12s] 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: 2 ERRORs
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/rbiom.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:15.97, 158.65 + 15.72