• using R version 4.0.0 alpha (2020-04-01 r78130)
• using platform: x86_64-apple-darwin17.0 (64-bit)
• using session charset: UTF-8
• checking for file ‘BacArena/DESCRIPTION’ ... OK
• this is package ‘BacArena’ version ‘1.8.1’
• 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 whether package ‘BacArena’ can be installed ... [56s/86s] OK
• checking installed package size ... NOTE
    installed size is 8.1Mb
    sub-directories of 1Mb or more:
      R 1.2Mb
      data 3.3Mb
      libs 2.9Mb
• 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 R 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 ... NOTE
  Namespace in Imports field not imported from: ‘glpkAPI’
    All declared Imports should be used.
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [13s/18s] OK
• checking Rd files ... OK
• checking Rd metadata ... 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 data for ASCII and uncompressed saves ... OK
• checking line endings in C/C++/Fortran sources/headers ... OK
• checking compiled code ... OK
• checking sizes of PDF files under ‘inst/doc’ ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... ERROR
  Running examples in ‘BacArena-Ex.R’ failed
  The error most likely occurred in:
  
  > ### Name: HeatMapFeeding
  > ### Title: Function for plotting heatmap of feeding between two selected
  > ### cell models
  > ### Aliases: HeatMapFeeding HeatMapFeeding,Eval-method
  >
  > ### ** Examples
  >
  > sim <- sihumi_test
  > HeatMapFeeding(object = sim, speciesA = 1, speciesB = 2, var_nr = 78)
  Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
    sim_step 1 : No crossfeeding found. Try other metaboites or time points.
  Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
    sim_step 2 : No crossfeeding found. Try other metaboites or time points.
  Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
    sim_step 3 : No crossfeeding found. Try other metaboites or time points.
  Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
    sim_step 4 : No crossfeeding found. Try other metaboites or time points.
  Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
    sim_step 5 : No crossfeeding found. Try other metaboites or time points.
  Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
    sim_step 6 : No crossfeeding found. Try other metaboites or time points.
  Warning in BacArena::findFeeding3(object, time = t, mets = A$sub[1:var_nr], :
    sim_step 7 : No crossfeeding found. Try other metaboites or time points.
  Error in if (z[h, 1] == names(object@specs)[speciesA]) d[h, 1] <- 1 else if (z[h, :
    argument is of length zero
  Calls: HeatMapFeeding -> HeatMapFeeding
  Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [1s/1s] NONE
    ‘BacArena-Introduction.Rmd’... [1s/1s] OK
• checking re-building of vignette outputs ... [55s/78s] WARNING
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘BacArena-Introduction.Rmd’ using rmarkdown
  Loading required package: sybil
  Loading required package: Matrix
  Loading required package: lattice
  Loading required package: ReacTran
  Loading required package: rootSolve
  Loading required package: deSolve
  Loading required package: shape
  BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
   Tutorials: https://bacarena.github.io
   Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
   Development and help: https://github.com/euba/bacarena
  Warning in simEnv(arena, time = 10) :
    If growth is limited by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
  Quitting from lines 231-232 (BacArena-Introduction.Rmd)
  Error: processing vignette 'BacArena-Introduction.Rmd' failed with diagnostics:
  Faceting variables must have at least one value
  --- failed re-building ‘BacArena-Introduction.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘BacArena-Introduction.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted
  
• checking PDF version of manual ... OK
• DONE
  Status: 1 ERROR, 1 WARNING, 2 NOTEs