Error(s) in re-building vignettes:
  ...
--- re-building ‘hierarchicalmanual.rnw’ using knitr
System dimensions inferred from LAMBDA
n.TDpred inferred  inferred from TDpredNames
n.TIpred inferred  inferred from TIpredNames
Custom par cint2 set as: param = cint2; transform = 10 * param; indvarying = TRUE; sdscale = 1; cint2 tipred effects from: TI1
System dimensions inferred from manifestNames and latentNames
n.TDpred inferred  inferred from TDpredNames
n.TIpred inferred  inferred from TIpredNames
LAMBDA vector spec input rowwise into 2 * 2 matrix:
MANIFESTMEANS specified via single value -- filling 2 * 1 matrix:
CINT vector spec input rowwise into 2 * 1 matrix:
Custom par cint2 set as: param = cint2; transform = 10 * param; indvarying = TRUE; sdscale = 1; cint2 tipred effects from: TI1
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Maximum a posteriori estimation requested
NA's in TIpreds - imputing 1  NA's to allow optimization -- TIpred effect estimates may be overly confident.
NA's in TDpreds! Replaced by zeroes, consider appropriateness...
Using 1/16 logical CPU cores
Doing 1st pass optimize...
Converged -- lp and par change within tolerances
Including TI predictors...
Converged -- lp and par change within tolerances
Optimizing...
Converged -- lp change within itertol
Estimating Hessian
Computing posterior with 1000 samples
Computing temporal regression coefficients for 100 samples, may take a moment...
Fitting model to empty dataset...
Maximum a posteriori estimation requested
Using 2/16 logical CPU cores
starting worker pid=6598 on localhost:11358 at 11:39:22.235
starting worker pid=6599 on localhost:11358 at 11:39:22.238
Optimizing...
Estimating Hessian
Computing posterior with 10000 samples
Loading required package: data.table
Loading required package: data.table
Computing state estimates..
Computing quantities for 1 samples...
Getting 100 samples by 20 subjects for 2000 total samples
Calculating time independent predictor effects...
Computing quantities for 2000 samples...
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Free T0VAR parameters as well as indvarying T0MEANS -- fixing T0VAR pars to diag matrix of 1e-3
Custom par ma1 set as: param = ma1; transform = log(1+(exp(param))); indvarying = FALSE; sdscale = 1; 
Custom par a21 set as: param = a21; transform = -log(1+exp(param)); indvarying = FALSE; sdscale = 1; 
Custom par m1 set as: param = m1; transform = param*10+44; indvarying = TRUE; sdscale = 1; 
Bayesian estimation via Stan's NUTS sampler requested
Individual variation not possible as only 1 subject! indvarying set to FALSE on all parameters
Free T0VAR parameters fixed to diagonal matrix of 1 as only 1 subject - consider appropriateness!
Setting DRIFT diagonals of 0 to approximate 0 of -0.000001
Sampling...
Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#tail-ess
Error: processing vignette 'hierarchicalmanual.rnw' failed with diagnostics:
Running 'texi2dvi' on 'hierarchicalmanual.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 365:  5656 Killed                  "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
--- failed re-building ‘hierarchicalmanual.rnw’

SUMMARY: processing the following file failed:
  ‘hierarchicalmanual.rnw’

Error: Vignette re-building failed.
Execution halted