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:  4190.7977747028

 Not all eigenvalues of Hessian are greater than 0: 160837.767121905, 43192.3724335754, 21269.6223244685, 8473.8667618997, 1625.16819765816, 1449.82180932564, 343.282288682122, 312.919562291807, 249.071853150388, 159.628561533921, 107.965135691214, 100.181246428413, 62.0666353290783, 20.0037290335397, 0.336387394507556, -0.000366654101673944

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4190.79777470279

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:  4254.37894236724

 Not all eigenvalues of Hessian are greater than 0: 24915.8237702883, 4505.42565155991, 1516.3331176829, 1044.23862666819, 756.931896960835, 505.225492507852, 400.005744480216, 328.63155130723, 256.962826844048, 252.235944689021, 216.308930774934, 197.221138221622, 180.906579381315, 129.315221060647, 115.411997908541, 99.2108163456203, 77.969375283721, 45.8118003372634, 22.3575344001701, 5.7645013995108, 3.06166094038018, 1.07410816536032, -0.0000210208062994807

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4254.37894236723

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:  1756.29658138786

 Not all eigenvalues of Hessian are greater than 0: 20000.0189398798, 20000.0013807829, 19999.9960385372, 19999.9906818879, 19999.9859775401, 19999.9833280666, 19999.9795352122, 2948.07506211502, 2832.32495080226, 2079.17236741668, 1131.75315595098, 815.973371410617, 699.563376919324, 558.250806456062, 478.285763925858, 342.312663204618, 333.472087182907, 278.832468742709, 259.672245166353, 216.610618814193, 189.856899900458, 177.673178566427, 168.28228699588, 92.6295701938148, 8.03698909409026, 6.79617459361479, 0.0000850412439011692, -0.00029151963715289

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  1756.29658138781

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:  1588.79111393167

 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: 15365462788.5333, 1271025.50454834, 52917.9539608826, 21200.3159908756, 20000.0136429511, 20000.0083393653, 20000.0048737802, 19999.9965113285, 19999.9893619421, 19999.9884219623, 19999.9843003701, 4861.32877499888, 1931.65647387639, 1788.32939508105, 679.765149550443, 433.654950723573, 403.394020325376, 220.919777053678, 204.259392612902, 185.389438777787, 181.718168412706, 133.863471079381, 41.9712099360901, 13.2596422391113, 0.379148841028123, -0.00341787451790817, -0.00714771691105309, -525.624659810819, -7538.61254357975, -231091.598444261

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  1545.55492802136

 Not all eigenvalues of Hessian are greater than 0: 780639162.066895, 323451.800470213, 20275.4684805166, 20000.0100666855, 20000.0067427734, 20000.0063820697, 20000.001304548, 19999.9984014861, 19999.9899305867, 19999.9878002211, 18952.6642599163, 8588.11649060556, 3245.57231144031, 1657.30945204652, 1253.92919504117, 782.687844789922, 497.273278154726, 369.48807712715, 360.987862819972, 234.126211525996, 191.211288117516, 164.775610908102, 135.654084805169, 113.236552967158, 52.383881024113, 29.6325683940159, 0.864870649979489, 0.0000000163265062031659, -0.00000000000363797880709171, -0.0000000000983854719564439

Begin fit attempt 3 of at maximum 16 tries

 Lowest minimum so far:  1545.55492802136

 Not all eigenvalues of Hessian are greater than 0: 780639163.033909, 323451.856048683, 20275.5479106731, 20000.0122651158, 20000.0049509404, 20000.0002143638, 19999.9981436109, 19999.9965128021, 19999.9931246715, 19999.9884194134, 18952.6406964067, 8588.17969541156, 3245.57353927257, 1657.31137602636, 1253.98788600908, 782.718963161832, 497.276752337564, 369.512856936034, 360.984091033571, 234.124312073854, 191.201751119424, 164.779156650161, 135.665953805747, 113.254389242527, 52.3849775738163, 29.6279385304304, 0.865946046141193, 0.0000612082694715355, 0.00000000000268257832342675, -0.00000000000296679541773082

Begin fit attempt 4 of at maximum 16 tries

 Fit attempt worse than current best:  1785.11195860086 vs 1545.55492802136

Begin fit attempt 5 of at maximum 16 tries

 Fit attempt worse than current best:  1621.10187752003 vs 1545.55492802136

Begin fit attempt 6 of at maximum 16 tries

 Fit attempt worse than current best:  1545.55844358385 vs 1545.55492802136

Begin fit attempt 7 of at maximum 16 tries

 Fit attempt worse than current best:  1553.55779860924 vs 1545.55492802136

Begin fit attempt 8 of at maximum 16 tries

 Fit attempt worse than current best:  1545.55823565276 vs 1545.55492802136

Begin fit attempt 9 of at maximum 16 tries

 Fit attempt worse than current best:  1566.14484880176 vs 1545.55492802136

Begin fit attempt 10 of at maximum 16 tries

 Fit attempt worse than current best:  1545.87127855694 vs 1545.55492802136

Begin fit attempt 11 of at maximum 16 tries

 Fit attempt worse than current best:  1545.55844023852 vs 1545.55492802136

Begin fit attempt 12 of at maximum 16 tries

 Fit attempt worse than current best:  1545.64968655211 vs 1545.55492802136

Begin fit attempt 13 of at maximum 16 tries

 Fit attempt worse than current best:  1622.74121991728 vs 1545.55492802136

Begin fit attempt 14 of at maximum 16 tries

 Fit attempt worse than current best:  1545.64771754433 vs 1545.55492802136

Begin fit attempt 15 of at maximum 16 tries

 Fit attempt worse than current best:  1545.64667580897 vs 1545.55492802136

Begin fit attempt 16 of at maximum 16 tries

 Fit attempt worse than current best:  1545.55844448967 vs 1545.55492802136

Retry limit reached
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:  -119.382333796701

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:  726.224748189523

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:  -3462.15389493049

Solution found

Running ctsemCarefulFit with 16 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4190.79777467472

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:  4203.31303209702

 Not all eigenvalues of Hessian are greater than 0: 94317.1278113199, 6623.11297939351, 1636.11866167754, 1127.65562286712, 726.77220818326, 621.725823292021, 294.407418957277, 198.911923611934, 179.999734016754, 115.608709579371, 91.1845833222944, 71.0433077938259, 55.301191135789, 26.0238815529888, 9.24197481539484, 5.38098062315546, 4.01189030293512, 2.86687115536787, -0.0000397793652526642

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4203.31303209702

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
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
Compiling model - ignore below warning re number of chains
the number of chains is less than 1; sampling not done
Sampling...
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...
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
Compiling model - ignore below warning re number of chains
the number of chains is less than 1; sampling not done
Sampling...
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.
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.2208 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2208 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2208 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2208 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted