Error(s) in re-building vignettes:
  ...
--- re-building ‘stockR.Rnw’ using knitr
Removing any SNP with no variation amongst *any* fish (there are 87 of them)
Finding starting values using K-means on rotated data (using specified number of PCAs)
Maximising the log-likelihood to obtain parameter estimates
Iter: 0 | Marg. Logl: -304832.654 | pis: 0.3 0.258 0.442 | Max change: Inf
Iter: 1 | Marg. Logl: -304813.806 | pis: 0.25 0.144 0.606 | Max change: 0.16375
Iter: 2 | Marg. Logl: -297901.731 | pis: 0.22 0.076 0.704 | Max change: 0.21
Iter: 3 | Marg. Logl: -294081.482 | pis: 0.206 0.044 0.75 | Max change: 0.1845091
Iter: 4 | Marg. Logl: -292034.948 | pis: 0.201 0.033 0.766 | Max change: 0.283562
Iter: 5 | Marg. Logl: -291230.411 | pis: 0.2 0.03 0.77 | Max change: 0.2242654
Iter: 6 | Marg. Logl: -291066.455 | pis: 0.2 0.03 0.77 | Max change: 0.0727568
Iter: 7 | Marg. Logl: -291057.875 | pis: 0.2 0.03 0.77 | Max change: 0.0088197
Converged | Marg. Logl: -291057.875 | pis: 0.2 0.03 0.77 | Max change: 0
Done!
Removing any SNP with no variation amongst *any* fish (there are 64 of them)
Finding starting values using K-means on rotated data (using specified number of PCAs)
Maximising the log-likelihood to obtain parameter estimates
Iter: 0 | Marg. Logl: -306336.884 | pis: 0.3 0.333 0.367 | Max change: Inf
Iter: 1 | Marg. Logl: -306336.536 | pis: 0.25 0.333 0.417 | Max change: 0.05
Iter: 2 | Marg. Logl: -293977.255 | pis: 0.22 0.333 0.447 | Max change: 0.195
Iter: 3 | Marg. Logl: -289505.139 | pis: 0.206 0.333 0.461 | Max change: 0.1595455
Iter: 4 | Marg. Logl: -288359.221 | pis: 0.201 0.333 0.465 | Max change: 0.0903575
Iter: 5 | Marg. Logl: -288186.585 | pis: 0.2 0.333 0.467 | Max change: 0.0338744
Iter: 6 | Marg. Logl: -288177.04 | pis: 0.2 0.333 0.467 | Max change: 0.0078457
Iter: 7 | Marg. Logl: -288176.99 | pis: 0.2 0.333 0.467 | Max change: 0.000877
Converged | Marg. Logl: -288176.99 | pis: 0.2 0.333 0.467 | Max change: 0
Done!
Removing any SNP with no variation amongst *any* fish (there are 0 of them)
Finding starting values using K-means on rotated data (using specified number of PCAs)
Maximising the log-likelihood to obtain parameter estimates
Iter: 0 | Marg. Logl: -214046.816 | pis: 0.315 0.318 0.368 | Max change: Inf
Iter: 1 | Marg. Logl: -214045.154 | pis: 0.288 0.294 0.419 | Max change: 0.05125
Iter: 2 | Marg. Logl: -204480.391 | pis: 0.271 0.279 0.45 | Max change: 0.1884454
Iter: 3 | Marg. Logl: -200961.073 | pis: 0.263 0.273 0.464 | Max change: 0.1507497
Iter: 4 | Marg. Logl: -200044.62 | pis: 0.261 0.271 0.469 | Max change: 0.0864159
Iter: 5 | Marg. Logl: -199899.674 | pis: 0.26 0.27 0.47 | Max change: 0.0325932
Iter: 6 | Marg. Logl: -199892.211 | pis: 0.26 0.27 0.47 | Max change: 0.0075643
Iter: 7 | Marg. Logl: -199892.177 | pis: 0.26 0.27 0.47 | Max change: 0.0008459
Converged | Marg. Logl: -199892.177 | pis: 0.26 0.27 0.47 | Max change: 0
Done!
Error: processing vignette ‘stockR.Rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘stockR.tex’ failed.
LaTeX errors:
! You can't use `macro parameter character #' in horizontal mode.
l.105 set.seed( 747)  #
                       a 747 is a big plane
? 
! Emergency stop.
! Emergency stop.
l.105 set.seed( 747)  #
                       a 747 is a big plane
End of file on the terminal!

!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘stockR.Rnw’

SUMMARY: processing the following file failed:
  ‘stockR.Rnw’

Error: Vignette re-building failed.
Execution halted