Error(s) in re-building vignettes:
  ...
--- re-building ‘ctsem.rnw’ using knitr
Observations with missing time information found - removing 1 rows
Discrete time points created:  4
Extracting first non-missing value for time independent predictors
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
Running ctsemCarefulFit with 16 parameters
Running ctsem with 16 parameters

Beginning initial fit attempt
Running ctsem with 16 parameters

 Lowest minimum so far:  4345.82935547639
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 2697965092.90253, 948410.765100112, 189247.012640173, 118391.161867668, 2399.36382344214, 1641.82432925366, 741.236105601636, 433.897748372479, 338.133907152148, 82.6061066667198, 79.4838901205983, 0.271470130027958, 0.000208784986872642, 0.0000979690372726275, -0.00005811920113924, -242.797449278468

Beginning fit attempt 1 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Lowest minimum so far:  4345.42204778261
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 6943933073.38318, 1914178.65187166, 265179.218313578, 237602.195099868, 2382.48715649097, 1167.32567073695, 889.479617144363, 402.135309221194, 317.099700283054, 160.578469049286, 81.1711825392785, 0.262598982596864, 0.00182746139876344, 0.000310852664484221, -0.0000331601978317798, -50.1026393489383

Beginning fit attempt 2 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Lowest minimum so far:  4345.24285990567
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 6498389061.22832, 1829443.52031728, 251528.281547602, 219955.819257456, 2388.48142900942, 1580.49303526594, 708.34362529176, 395.807445868798, 337.578759790468, 81.1529430647473, 63.3363980721132, 0.113383745209947, 0.000104424470806031, -0.000287898050341371, -0.000500183442074389, -181.744151471244

Beginning fit attempt 3 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Fit attempt worse than current best:  4351.68013750398 vs 4345.24285990567

Beginning fit attempt 4 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Fit attempt worse than current best:  4571.87944555015 vs 4345.24285990567

Beginning fit attempt 5 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Fit attempt worse than current best:  4359.51459391979 vs 4345.24285990567

Retry limit reached

 Retry limit reached; Best fit=4345.2429 (started at 4727.4692)  (6 attempt(s): 6 valid, 0 errors)


 Uncertain solution found - consider parameter validity, try again, increase extraTries, change inits, change model, or check data!

Warning in mxSE(paste0(ifelse(is.na(group[1]), "", paste0(group, ".")),  :
  Some diagonal elements of the repeated-sampling covariance matrix of the point estimates are less than zero or NA.
I know, right? Set details=TRUE and check the 'Cov' element of this object.
Warning in mxSE(paste0(ifelse(is.na(group[1]), "", paste0(group, ".")),  :
  Some diagonal elements of the repeated-sampling covariance matrix of the point estimates are less than zero or NA.
I know, right? Set details=TRUE and check the 'Cov' element of this object.
wide format data detected
Running ctsemCarefulFit with 15 parameters
Running ctsem with 15 parameters

Beginning initial fit attempt
Running ctsem with 15 parameters

 Lowest minimum so far:  4196.73541494081

Solution found


 Solution found!  Final fit=4196.7354 (started at 4882.1499)  (1 attempt(s): 1 valid, 0 errors)

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
Warning: In model 'ctsem' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)
Warning in mxSE(paste0(ifelse(is.na(group[1]), "", paste0(group, ".")),  :
  Some diagonal elements of the repeated-sampling covariance matrix of the point estimates are less than zero or NA.
I know, right? Set details=TRUE and check the 'Cov' element of this object.
Warning in mxSE(paste0(ifelse(is.na(group[1]), "", paste0(group, ".")),  :
  Some diagonal elements of the repeated-sampling covariance matrix of the point estimates are less than zero or NA.
I know, right? Set details=TRUE and check the 'Cov' element of this object.
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
Running ctsemCarefulFit with 19 parameters
Running ctsem with 19 parameters

Beginning initial fit attempt
Running ctsem with 19 parameters

 Lowest minimum so far:  4151.13132113276

Solution found


 Solution found!  Final fit=4151.1313 (started at 4301.6568)  (1 attempt(s): 1 valid, 0 errors)

Plotting fit
Warning in mxSE(paste0(ifelse(is.na(group[1]), "", paste0(group, ".")),  :
  Some diagonal elements of the repeated-sampling covariance matrix of the point estimates are less than zero or NA.
I know, right? Set details=TRUE and check the 'Cov' element of this object.
Warning in mxSE(paste0(ifelse(is.na(group[1]), "", paste0(group, ".")),  :
  Some diagonal elements of the repeated-sampling covariance matrix of the point estimates are less than zero or NA.
I know, right? Set details=TRUE and check the 'Cov' element of this object.
Plotting fit
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
Running ctsemCarefulFit with 23 parameters
Running ctsem with 23 parameters

Beginning initial fit attempt
Running ctsem with 23 parameters

 Lowest minimum so far:  4245.25700751561

Solution found


 Solution found!  Final fit=4245.257 (started at 4370.0906)  (1 attempt(s): 1 valid, 0 errors)

Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Some free parameters in matrices set to zero!
Discrete time points created:  19
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Some free parameters in matrices set to zero!
Discrete time points created:  19
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Some free parameters in matrices set to zero!
Discrete time points created:  19
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Some free parameters in matrices set to zero!
Discrete time points created:  19
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
No missing time dependent predictors - TDPREDVAR and TDPREDMEANS fixed to observed moments for speed
Running ctsemCarefulFit with 18 parameters
Running ctsem with 18 parameters

Beginning initial fit attempt
Running ctsem with 18 parameters

 Lowest minimum so far:  -461.76333099737
 Not all eigenvalues of the Hessian are positive: 2132.26662898137, 1085.07993804621, 425.964108852407, 202.775833061135, 147.78323205114, 66.5305793135038, 56.8011892884947, 31.3445595501926, 26.776217929913, 23.8728287405234, 15.4904308870807, 12.688305023076, 10.5473716056175, 3.32514222815209, 2.26167036129472, 1.3566150153681, 0.0000352217696646264, -0.000000426099413346125

Beginning fit attempt 1 of at maximum 5 extra tries
Running ctsem with 18 parameters

 Lowest minimum so far:  -461.763330997373
 Not all eigenvalues of the Hessian are positive: 2132.26566381443, 1085.08119603461, 425.961143898751, 202.7752303909, 147.780493154988, 66.5285010154418, 56.8031182256159, 31.3428604190016, 26.776419631781, 23.8749184295035, 15.4904956146105, 12.6880986087935, 10.5473282089059, 3.32450240030295, 2.26803161571333, 1.35632398466834, 0.0000121447204748906, -0.00000377360084729949

Beginning fit attempt 2 of at maximum 5 extra tries
Running ctsem with 18 parameters
 Not all eigenvalues of the Hessian are positive: 2132.26566381443, 1085.08119603461, 425.961143898751, 202.7752303909, 147.780493154988, 66.5285010154418, 56.8031182256159, 31.3428604190016, 26.776419631781, 23.8749184295035, 15.4904956146105, 12.6880986087935, 10.5473282089059, 3.32450240030295, 2.26803161571333, 1.35632398466834, 0.0000121447204748906, -0.00000377360084729949

Beginning fit attempt 3 of at maximum 5 extra tries
Running ctsem with 18 parameters

 Fit attempt generated errors

Beginning fit attempt 4 of at maximum 5 extra tries
Running ctsem with 18 parameters

 Lowest minimum so far:  -461.763330999426
 Not all eigenvalues of the Hessian are positive: 2132.26391631192, 1085.08333721875, 425.964547210994, 202.776616067873, 147.783794843478, 66.5303569187029, 56.8031991370716, 31.3449778853827, 26.7773364590524, 23.8738370573092, 15.4927410980068, 12.688684018282, 10.5482507705678, 3.3271665171816, 2.2664583395895, 1.35798932149127, -0.00000000000000214257322635567, -0.00000209439032007954

Beginning fit attempt 5 of at maximum 5 extra tries
Running ctsem with 18 parameters

 Lowest minimum so far:  -461.763330999439
 Not all eigenvalues of the Hessian are positive: 2132.26549225378, 1085.08350437539, 425.962868304868, 202.77638883887, 147.784452607602, 66.5334408325953, 56.8024432543847, 31.3456932259265, 26.7768783599771, 23.8754902916703, 15.4934564260934, 12.6887131899842, 10.5478609012247, 3.32516043220887, 2.26553052242738, 1.35793118981208, 0.00000536727338747418, -0.0000000000000148332841716943

Retry limit reached

 Retry limit reached; Best fit=-461.76333 (started at -404.21165)  (6 attempt(s): 5 valid, 1 errors)

Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
No missing time dependent predictors - TDPREDVAR and TDPREDMEANS fixed to observed moments for speed
transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
Running ctsemCarefulFit with 18 parameters
Running ctsem with 18 parameters

Beginning initial fit attempt
Running ctsem with 18 parameters

 Lowest minimum so far:  -456.192136791877

Solution found


 Solution found!  Final fit=-456.19214 (started at 88.428444)  (1 attempt(s): 1 valid, 0 errors)

Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
Single subject dataset or Kalman objective specified - ignoring any specified between subject 
      variance matrices (TRAITVAR, T0TRAITEFFECT,MANIFESTTRAITVAR, TIPREDEFFECT, TIPREDVAR, TDTIPREDCOV, T0TIPREDEFFECT)
Running ctsemCarefulFit with 11 parameters
Running ctsem with 11 parameters

Beginning initial fit attempt
Running ctsem with 11 parameters

 Lowest minimum so far:  519.319660585414
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 36471683061.1367, 1199.30881874774, 479.874253981682, 402.016069497876, 400.054466220869, 399.985725112796, 382.872217862466, 0.00000653026004385172, 0.0000000000000551433729590785, -0.0000000447475783341517, -0.0000512735931229734

Beginning fit attempt 1 of at maximum 5 extra tries
Running ctsem with 11 parameters

 Lowest minimum so far:  519.300115144658
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 36415609486.6519, 1198.0780979265, 479.852466277121, 401.46140319868, 400.03837438574, 399.989029856541, 382.721881056043, 0.00000276403445393966, 0.00000000000000469533511650484, -0.0000000452807752307817, -0.0000351572640398448

Beginning fit attempt 2 of at maximum 5 extra tries
Running ctsem with 11 parameters

 Lowest minimum so far:  519.295652434665
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 36290483053.8153, 1195.12504087845, 479.813403344886, 400.091929956534, 400.006139093611, 400.002542853313, 382.367470378491, 0.0000060492092852424, 0.000000000000164366143341272, -0.0000000450440521483275, -0.00000137223956699897

Beginning fit attempt 3 of at maximum 5 extra tries
Running ctsem with 11 parameters

 Fit attempt worse than current best:  889.888555652682 vs 519.295652434665

Beginning fit attempt 4 of at maximum 5 extra tries
Running ctsem with 11 parameters

 Lowest minimum so far:  -138.198673270201

Solution found


 Solution found!  Final fit=-138.19867 (started at 10233.068)  (5 attempt(s): 5 valid, 0 errors)

Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Begin carefulFit start value estimation for group g1
Begin carefulFit start value estimation for group g2
Running ctsem multigroup with 13 parameters

Beginning initial fit attempt
Running ctsem multigroup with 13 parameters

 Lowest minimum so far:  -109.136426537257

Solution found


 Solution found!  Final fit=-109.13643 (started at 6142.2348)  (1 attempt(s): 1 valid, 0 errors)

Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
Some free parameters in matrices set to zero!
Discrete time points created:  200
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
Plotting rows 1, 
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
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 7 parameters
Running ctsem with 7 parameters

Beginning initial fit attempt
Running ctsem with 7 parameters

 Lowest minimum so far:  757.823869858032

Solution found


 Solution found!  Final fit=757.82387 (started at 1246.0293)  (1 attempt(s): 1 valid, 0 errors)

Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
Running ctsem with 9 parameters

Beginning initial fit attempt
Running ctsem with 9 parameters

 Lowest minimum so far:  -3462.15389492796

Solution found


 Solution found!  Final fit=-3462.1539 (started at -3145.5663)  (1 attempt(s): 1 valid, 0 errors)

wide format data detected
Running ctsem with 16 parameters

Beginning initial fit attempt
Running ctsem with 16 parameters

 Lowest minimum so far:  4345.23643673044
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 6567719315.55458, 1848121.55655954, 252764.335898372, 222843.639113631, 2391.43212951336, 1349.98411731578, 775.598474458293, 363.016776925275, 337.301329019402, 81.0909604129017, 77.9160594834779, 15.3326579641773, 0.000579622104120837, -0.0000276006625268209, -0.000533648632599573, -0.205075300100618

Beginning fit attempt 1 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Lowest minimum so far:  4345.22691792892
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 6393165218.36308, 1794978.85011111, 248785.258488944, 216001.707740848, 2397.84005933199, 1323.49951173489, 781.301280527032, 356.011619485994, 335.950002854594, 85.5057499881262, 81.0078514343316, 13.4169333313584, 0.00131849647195561, -0.0000604316766508663, -0.000475535755815645, -0.259745141117879

Beginning fit attempt 2 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Lowest minimum so far:  4345.22641657694
 OpenMx status code 6 not in list of acceptable status codes, (0,0)
 Not all eigenvalues of the Hessian are positive: 6387843418.03404, 1793132.68729707, 248728.103948958, 215827.414352178, 2397.82411035932, 1387.59440767365, 749.893048364888, 364.132971801977, 336.319185634429, 81.03391443603, 41.0445915482293, 14.4920950518752, 0.0193818530808201, -0.0000377638604548699, -0.000060852480542463, -0.0011978401577337

Beginning fit attempt 3 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Fit attempt worse than current best:  4757.16037937652 vs 4345.22641657694

Beginning fit attempt 4 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Fit attempt worse than current best:  4372.92828465342 vs 4345.22641657694

Beginning fit attempt 5 of at maximum 5 extra tries
Running ctsem with 16 parameters

 Fit attempt worse than current best:  4690.28629441617 vs 4345.22641657694

Retry limit reached

 Retry limit reached; Best fit=4345.2264 (started at 4345.2429)  (6 attempt(s): 6 valid, 0 errors)


 Uncertain solution found - consider parameter validity, try again, increase extraTries, change inits, change model, or check data!

Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
wide format data detected
Running ctsemCarefulFit with 19 parameters
Running ctsem with 19 parameters

Beginning initial fit attempt
Running ctsem with 19 parameters

 Lowest minimum so far:  4151.13132113277

Solution found


 Solution found!  Final fit=4151.1313 (started at 4301.6568)  (1 attempt(s): 1 valid, 0 errors)

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
wide format data detected
Running ctsemCarefulFit with 19 parameters
Running ctsem with 19 parameters

Beginning initial fit attempt
Running ctsem with 19 parameters

 Lowest minimum so far:  4203.31303218986

Solution found


 Solution found!  Final fit=4203.313 (started at 4349.5533)  (1 attempt(s): 1 valid, 0 errors)

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
Error: processing vignette ‘ctsem.rnw’ failed with diagnostics:
Running ‘texi2dvi’ on ‘ctsem.tex’ failed.
LaTeX errors:
! Missing $ inserted.
<inserted text> 
                $
l.278   Y1_
           T0 Y2_T0 Y3_T0 Y1_T1 Y2_T1 Y3_T1 Y1_T2 Y2_T2 Y3_T2 TD1_T0 TD1_T1 ...
! Emergency stop.
<inserted text> 
                $
l.278   Y1_
           T0 Y2_T0 Y3_T0 Y1_T1 Y2_T1 Y3_T1 Y1_T2 Y2_T2 Y3_T2 TD1_T0 TD1_T1 ...
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘ctsem.rnw’

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

Error: Vignette re-building failed.
Execution halted