Error in re-building vignettes:
  ...
Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in mu + as.numeric(ctx) %*% as.numeric(alpha.c) + as.numeric(x %*%  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.


Error: processing vignette 'ecoreg-guide.Rnw' failed with diagnostics:
 chunk 17 
Error in beta %*% x : requires numeric/complex matrix/vector arguments
Execution halted