Package: orthGS
Check: examples
New result: ERROR
  Running examples in ‘orthGS-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: gapless_msa
  > ### Title: Remove Gaps in a MSA
  > ### Aliases: gapless_msa
  > 
  > ### ** Examples
  > 
  > gapless_msa(msa(sequences = c("APGW", "AGWC", "CWGA"),ids = c("a", "b", "c"))$ali)
  Error in msa(sequences = c("APGW", "AGWC", "CWGA"), ids = c("a", "b",  : 
    You must install the package muscle in order to use this function
  Calls: gapless_msa -> as.matrix -> msa
  Execution halted

Package: orthGS
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘Searching_for_Orthologous.Rmd’ using rmarkdown
  
  Quitting from lines 56-61 [unnamed-chunk-5] (Searching_for_Orthologous.Rmd)
  Error: processing vignette 'Searching_for_Orthologous.Rmd' failed with diagnostics:
  You must install the package muscle in order to use this function
  --- failed re-building ‘Searching_for_Orthologous.Rmd’
  
  --- re-building ‘Unraveling_the_hiden_paralogous.Rmd’ using rmarkdown
  ** Processing: /home/hornik/tmp/CRAN_recheck/orthGS.Rcheck/vign_test/orthGS/vignettes/Unraveling_the_hiden_paralogous_files/figure-html/unnamed-chunk-6-1.png
  288x288 pixels, 3x8 bits/pixel, RGB
  Input IDAT size = 18661 bytes
  Input file size = 18763 bytes
  
  Trying:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14808
    zc = 9  zm = 8  zs = 1  f = 0
    zc = 1  zm = 8  zs = 2  f = 0
    zc = 9  zm = 8  zs = 3  f = 0
    zc = 9  zm = 8  zs = 0  f = 5
    zc = 9  zm = 8  zs = 1  f = 5
    zc = 1  zm = 8  zs = 2  f = 5
    zc = 9  zm = 8  zs = 3  f = 5
                                 
  Selecting parameters:
    zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14808
  
  Output IDAT size = 14808 bytes (3853 bytes decrease)
  Output file size = 14886 bytes (3877 bytes = 20.66% decrease)
  
  --- finished re-building ‘Unraveling_the_hiden_paralogous.Rmd’
  
  SUMMARY: processing the following file failed:
    ‘Searching_for_Orthologous.Rmd’
  
  Error: Vignette re-building failed.
  Execution halted