Error in re-building vignettes:
  ...
Observations with missing time information found - removing 1 rows
Discrete time points created:  3
Warning:  measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
Extracting first non-missing value for time independent predictors
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Running ctsemCarefulFit with 16 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4176.87456133365

Solution found

Running ctsemCarefulFit with 15 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4196.73541494046

Solution found

NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command:  source('http://openmx.psyc.virginia.edu/getOpenMx.R') 
Running ctsem with 16 parameters
Running ctsemCarefulFit with 19 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4151.1313211327

Solution found

Plotting fit
Plotting fit
Running ctsemCarefulFit with 23 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4253.06395808303

 Not all eigenvalues of Hessian are greater than 0: 84545.121673376, 30424.2013809137, 20617.3018776738, 6299.4974140659, 2239.55798026428, 1587.45478504656, 943.926837364332, 742.902994395187, 581.73804012422, 399.987522564054, 303.793112400857, 239.917818341843, 217.759419492333, 197.19794021302, 149.382423751623, 80.5141327681844, 79.2770250056061, 39.9805818233241, 29.396009206909, 25.9350303873783, 7.65125750720584, 3.15562558212038, -0.0000000000000284217094310203

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4253.06395808303

Solution found

MANIFESTMEANS contained character labels - setting matrix to 0
MANIFESTVAR contained character labels - setting matrix to 0
T0TDPREDCOV contained character labels - setting matrix to 0
TRAITTDPREDCOV contained character labels - setting matrix to 0
Discrete time points created:  20
Warning:  measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
MANIFESTMEANS contained character labels - setting matrix to 0
MANIFESTVAR contained character labels - setting matrix to 0
T0TDPREDCOV contained character labels - setting matrix to 0
TRAITTDPREDCOV contained character labels - setting matrix to 0
Discrete time points created:  20
Warning:  measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
MANIFESTMEANS contained character labels - setting matrix to 0
MANIFESTVAR contained character labels - setting matrix to 0
T0TDPREDCOV contained character labels - setting matrix to 0
TRAITTDPREDCOV contained character labels - setting matrix to 0
Discrete time points created:  20
Warning:  measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
MANIFESTMEANS contained character labels - setting matrix to 0
MANIFESTVAR contained character labels - setting matrix to 0
T0TDPREDCOV contained character labels - setting matrix to 0
TRAITTDPREDCOV contained character labels - setting matrix to 0
Discrete time points created:  20
Warning:  measures of time dependent predictor 1 occurring at final measurement occasion removed, as they have no time to impact processes
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Time dependent predictors with 0 variance and free TDPREDVAR matrix detected - fixing TDPREDVAR matrix diagonal to 0.01 to allow estimation.
Running ctsemCarefulFit with 28 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  1593.04741819414

 OpenMx status code 6 not in list of acceptable status codes, 0
 OpenMx status code 6 not in list of acceptable status codes, 0

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  1593.04741819392

Solution found

Warning in (diag(TDPREDVAR)) + diag(ridging, n.TDpred) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in (diag(TDPREDVAR)) + diag(ridging, n.TDpred) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in (diag(TDPREDVAR)) + diag(ridging, n.TDpred) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in (diag(TDPREDVAR)) + diag(ridging, n.TDpred) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Time dependent predictors with 0 variance and free TDPREDVAR matrix detected - fixing TDPREDVAR matrix diagonal to 0.01 to allow estimation.
transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
Running ctsemCarefulFit with 30 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  1526.17588316697

 OpenMx status code 6 not in list of acceptable status codes, 0
 OpenMx status code 6 not in list of acceptable status codes, 0

 Not all eigenvalues of Hessian are greater than 0: 14595672.8151211, 232753.532364105, 213549.565061441, 45985.0639747247, 36398.7944004126, 20000.0545339033, 20000.0389192764, 20000.0369844407, 20000.0172719222, 20000.004046854, 20000.0021032666, 19999.9574645547, 10055.9222156796, 4767.28379810725, 1717.34050337615, 1384.0288424596, 1034.81892295357, 701.621094002874, 289.252496577965, 263.770983457475, 195.14405667135, 186.438034481651, 149.27107925182, 107.420256375453, 54.8083125688141, 18.0403056112492, 5.276509504604, 1.12199671575337, 0.000068817738769451, -0.00000000000165994411314809

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  1526.17588309358

Solution found

Warning in (diag(TDPREDVAR)) + diag(ridging, n.TDpred) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in (diag(TDPREDVAR)) + diag(ridging, n.TDpred) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Single subject dataset or Kalman objective specified - ignoring any specified between subject 
      variance matrices (TRAITVAR, T0TRAITEFFECT,MANIFESTTRAITVAR, TIPREDEFFECT, TIPREDVAR, TDTIPREDCOV, T0TIPREDEFFECT)
Running ctsemCarefulFit with 10 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  -119.382333796698

Solution found


Begin fit attempt 1 of at maximum 6 tries

 Lowest minimum so far:  2112.2450194744

Solution found

T0VAR contained character labels - setting matrix to 0
T0MEANS contained character labels - setting matrix to 0
MANIFESTMEANS contained character labels - setting matrix to 0
Discrete time points created:  200
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Plotting rows 1, 
Single subject dataset or Kalman objective specified - ignoring any specified between subject 
      variance matrices (TRAITVAR, T0TRAITEFFECT,MANIFESTTRAITVAR, TIPREDEFFECT, TIPREDVAR, TDTIPREDCOV, T0TIPREDEFFECT)
transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
Running ctsemCarefulFit with 8 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  701.710180916568

Solution found

transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  -3105.99405297895

 Not all eigenvalues of Hessian are greater than 0: 1485006.49902709, 10937.6541544582, 7405.4081964675, 1110.1113824616, 932.102857720826, 779.944383417724, 390.211472804247, 181.926546615814, -9.22618577885252e-28

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  -3105.99405297896

Solution found

Running ctsemCarefulFit with 16 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4176.87456133365

Solution found

Running ctsemCarefulFit with 19 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4151.13132113269

Solution found

Running ctsemCarefulFit with 19 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4206.54567796655

 Not all eigenvalues of Hessian are greater than 0: 16942.8954783873, 7130.05916737836, 1557.28227247794, 1534.91863990559, 762.077202269013, 355.015882737694, 281.149002132641, 240.16517562242, 214.073513238168, 168.094396808462, 166.596001203857, 57.8049339825673, 55.3634632893434, 18.373642804157, 6.6970500631111, 1.87364095918415, 1.12317680173291, 0.00119251267510231, -0.0000845412502174015

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4206.54567796654

Solution found

NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command:  source('http://openmx.psyc.virginia.edu/getOpenMx.R') 
Running ctsem with 19 parameters
NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command:  source('http://openmx.psyc.virginia.edu/getOpenMx.R') 
Running ctsem with 19 parameters
Minor inconsistencies in model found - removing param name, transform and indvarying from any parameters with a value specified
Unique discreteDRIFT calculations per step required = 6
Unique discreteCINT calculations per step required = 6
Unique discreteDIFFUSION calculations per step required = 6
2 / 2 latent variables required for covariance calculations
the number of chains is less than 1; sampling not done
The following numerical problems occured the indicated number of times on chain 2
                                                                                                     count
Exception thrown at line 361: multiply: A[1] is nan, but must not be nan!                                3
Exception thrown at line 361: multiply: B[1] is -nan, but must not be nan!                               2
Exception thrown at line 242: multiply: A[22] is -nan, but must not be nan!                              1
Exception thrown at line 430: cholesky_decompose: A is not symmetric. A[1,2] = -nan, but A[2,1] = -n     1
Exception thrown at line 430: cholesky_decompose: Matrix m is not positive definite                      1
Exception thrown at line 432: multiply: A[1] is -nan, but must not be nan!                               1
When a numerical problem occurs, the Hamiltonian proposal gets rejected.
See http://mc-stan.org/misc/warnings.html#exception-hamiltonian-proposal-rejected
If the number in the 'count' column is small, do not ask about this message on stan-users.
The following numerical problems occured the indicated number of times on chain 1
                                                                            count
Exception thrown at line 361: multiply: A[1] is nan, but must not be nan!       6
Exception thrown at line 432: multiply: A[1] is -nan, but must not be nan!      2
Exception thrown at line 242: multiply: A[22] is -nan, but must not be nan!     1
When a numerical problem occurs, the Hamiltonian proposal gets rejected.
See http://mc-stan.org/misc/warnings.html#exception-hamiltonian-proposal-rejected
If the number in the 'count' column is small, do not ask about this message on stan-users.
Getting discreteDRIFT, may take a moment...
Minor inconsistencies in model found - removing param name, transform and indvarying from any parameters with a value specified
removing T0VAR and T0MEANS from parameter matrices because stationary=TRUE
Unique discreteDRIFT calculations per step required = 2
Unique discreteCINT calculations per step required = 2
Unique discreteDIFFUSION calculations per step required = 2
2 / 2 latent variables required for covariance calculations
the number of chains is less than 1; sampling not done
The following numerical problems occured the indicated number of times on chain 1
                                                                          count
Exception thrown at line 281: multiply: A[1] is nan, but must not be nan!     9
When a numerical problem occurs, the Hamiltonian proposal gets rejected.
See http://mc-stan.org/misc/warnings.html#exception-hamiltonian-proposal-rejected
If the number in the 'count' column is small, do not ask about this message on stan-users.
The following numerical problems occured the indicated number of times on chain 2
                                                                                    count
Exception thrown at line 281: multiply: A[1] is nan, but must not be nan!               9
Exception thrown at line 350: cholesky_decompose: Matrix m is not positive definite     2
When a numerical problem occurs, the Hamiltonian proposal gets rejected.
See http://mc-stan.org/misc/warnings.html#exception-hamiltonian-proposal-rejected
If the number in the 'count' column is small, do not ask about this message on stan-users.
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 5077 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 5078 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 5091 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 5092 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 5105 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hierarchical.tex' failed.
LaTeX errors:
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8982 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8982 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8982 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.8982 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted