Running examples in ‘orthGS-Ex.R’ failed
The error most likely occurred in:

> ### 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
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: /data/gannet/ripley/R/packages/tests-clang/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 = 19334 bytes
Input file size = 19436 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 15210
  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 = 15210

Output IDAT size = 15210 bytes (4124 bytes decrease)
Output file size = 15288 bytes (4148 bytes = 21.34% 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
Running examples in ‘orthGS-Ex.R’ failed
The error most likely occurred in:

> ### 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
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: /data/gannet/ripley/R/packages/tests-devel/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 = 18628 bytes
Input file size = 18730 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14489
  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 = 14489

Output IDAT size = 14489 bytes (4139 bytes decrease)
Output file size = 14567 bytes (4163 bytes = 22.23% 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