Error in re-building vignettes:
  ...
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
Running ctsemCarefulFit with 16 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  Requested improper value (1, 1) from (2, 0) matrix
Error in lapply(model@matrices, getParametersHelper, model@name, free,  : 
  trying to get slot "matrices" from an object (class "try-error") that is not an S4 object 

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4225.23103212387

 Not all eigenvalues of Hessian are greater than 0: 72502.2310512849, 13946.1586622957, 3972.29301050854, 2624.94875667333, 1313.26614257177, 400.004276017077, 335.823036400968, 314.811391248112, 292.40542865552, 116.125012604807, 97.7883801536205, 85.1764625835707, 52.2518373844169, 30.5341873201463, 3.44828237933014, -0.000125471246279875

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4176.87456133366

Solution found

Running ctsemCarefulFit with 15 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4196.73541494047

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:  4245.25700750461

Solution found

MANIFESTMEANS contained character labels - setting matrix to 0
MANIFESTVAR contained character labels - setting matrix to diagonal 0.00001
TDPREDVAR contained character labels - setting matrix to diagonal 0.00001
Discrete time points created:  19
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 diagonal 0.00001
TDPREDVAR contained character labels - setting matrix to diagonal 0.00001
Discrete time points created:  19
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 diagonal 0.00001
TDPREDVAR contained character labels - setting matrix to diagonal 0.00001
Discrete time points created:  19
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 diagonal 0.00001
TDPREDVAR contained character labels - setting matrix to diagonal 0.00001
Discrete time points created:  19
imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
No missing time dependent predictors - TDPREDVAR and TDPREDMEANS fixed to observed moments for speed
Running ctsemCarefulFit with 18 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  -692.131169742273

Solution found

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

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  -662.527264389058

 Not all eigenvalues of Hessian are greater than 0: 3722.23589395342, 111.459449791537, 55.7351414088586, 27.4637673396346, 26.4024041117694, 22.8531911010586, 11.5175643440967, 9.92068336801988, 4.24408863984103, 1.43966589589984, 0.470542351196095, 0.15720521320145, 0.00185529072383173, 0.000080559292887205, 0.00000789745973691329, 0.000000295582759662336, -4.48631000520226e-18, -0.0000572398593728463

Begin fit attempt 2 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 3722.23589395342, 111.459449791537, 55.7351414088586, 27.4637673396346, 26.4024041117694, 22.8531911010586, 11.5175643440967, 9.92068336801988, 4.24408863984103, 1.43966589589984, 0.470542351196095, 0.15720521320145, 0.00185529072383173, 0.000080559292887205, 0.00000789745973691329, 0.000000295582759662336, -4.48631000520226e-18, -0.0000572398593728463

Begin fit attempt 3 of at maximum 16 tries

 Fit attempt worse than current best:  -662.527242183783 vs -662.527264389058

Begin fit attempt 4 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 3721.96158418289, 111.463637443661, 55.7268007467129, 27.4653328067697, 26.4034672750747, 22.8564905138362, 11.5185839856453, 9.92675398814079, 4.24332374525836, 1.4405393945194, 0.466947366136572, 0.155872925244966, 0.00180246619075414, 0.0000804689898953074, 0.0000511533884684894, 0.000000019423820868359, -2.73761048572006e-18, -0.00000951574303138687

Begin fit attempt 5 of at maximum 16 tries

 Lowest minimum so far:  -698.543948752437

Solution found

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:  -119.382333796695

Solution found

Begin carefulFit start value estimation for group g1
Begin carefulFit start value estimation for group g2

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  -70.8548131955317

Solution found

T0VAR contained character labels - setting matrix to diagonal 0.00001
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 7 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  753.383330356621

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:  -3462.15389493048

Solution found

Running ctsemCarefulFit with 16 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4345.68643275754

 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: 3429955072.42846, 933363.303610273, 203157.797368939, 108308.454645388, 2395.46912262037, 2138.21873332943, 704.962009688378, 444.984169885683, 338.108655189383, 91.6733337525271, 80.6175106184213, 0.215694964839715, 0.0000000000000018080298796678, -0.0000000000000496352942462092, -0.00550317416914767, -1008.06048470055

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4344.90505015353

 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: 688064751224.974, 24302638.2278844, 2897669.89926644, 2345588.52224139, 2398.33850075052, 1201.04917033671, 984.94841531479, 400.547577832025, 339.318381374716, 180.325789127394, 80.8126767660019, 0.338049067648708, 0.000163542486432221, 0.0000000000000307079665698101, -0.000000000000000124180231554294, -173.263606941974

Begin fit attempt 3 of at maximum 16 tries

 Lowest minimum so far:  4344.70708926969

 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: 364997340162.698, 18640792.6074462, 2229736.7454453, 1702897.21279045, 2398.18240923631, 1995.88486175033, 664.236979695588, 448.538469978179, 340.453023676374, 107.081048912609, 80.9676714485559, 0.355277441703922, 0.0000264523763255977, 0.0000000000000735358339018106, -5.90398248458391e-18, -539.108324110454

Begin fit attempt 4 of at maximum 16 tries

 Lowest minimum so far:  4299.35513498496

 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: 2242353845.04676, 157787571.923895, 25612.8320925274, 3100.54919476841, 1569.19980554708, 1364.85704093494, 564.245086261509, 436.273511030998, 229.559465290163, 182.638582368837, 103.245272541387, 66.5186661621375, 0.000342739288232414, 0.0000000000000353486038602113, 0.000000000000000178532791105848, -0.40958881861567

Begin fit attempt 5 of at maximum 16 tries

 Lowest minimum so far:  4285.35061995129

 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: 1049904288537.51, 72758299938.3935, 29629.9721221427, 3492.42789196989, 1527.10436405539, 1467.97049342863, 583.831114666689, 462.784971909218, 269.160474076876, 218.821796824763, 92.3287246330339, 83.3532725102997, 0.000012469192143725, 0.0000000780628567700803, -0.000000000000000337451405341625, -0.00000000000000490455742109161

Begin fit attempt 6 of at maximum 16 tries

 Fit attempt worse than current best:  6279.53369766509 vs 4285.35061995129

Begin fit attempt 7 of at maximum 16 tries

 Fit attempt worse than current best:  4743.09766156794 vs 4285.35061995129

Begin fit attempt 8 of at maximum 16 tries

 Fit attempt worse than current best:  13948.3370161962 vs 4285.35061995129

Begin fit attempt 9 of at maximum 16 tries

 Lowest minimum so far:  4176.87456133366

Solution found

Running ctsemCarefulFit with 19 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  4151.1313211327

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
Running ctsemCarefulFit with 19 parameters

Begin fit attempt 1 of at maximum 16 tries

 Lowest minimum so far:  22988.1392415328

 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: 3648524930658.39, 3193884520213.22, 2831875191572.06, 2668397545470.05, 2226361954948.65, 1882457070728.23, 1514661534841.66, 1332506371355.01, 1093100435407.93, 833593693771.54, 543978726677.618, 286467068869.164, 151095810943.653, 4635275763.49475, 362252637.286322, -520202112.173234, -1322109432.44023, -265812948851.466, -6254511144601.09

Begin fit attempt 2 of at maximum 16 tries

 Lowest minimum so far:  4216.2492746151

 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: 198579.369951124, 15616.6863960458, 15198.4424453625, 1984.49691872487, 1318.24965645089, 967.070902678712, 323.113142301397, 262.202928463355, 202.732020975488, 147.349608487421, 106.458635998351, 91.5662185425194, 61.9588960693732, 51.7782697685277, 16.4480700064709, 3.09161086516443, 0.204254512272087, 0.0169765296067585, -0.011621762392164

Begin fit attempt 3 of at maximum 16 tries

 Lowest minimum so far:  4206.15742306297

 Not all eigenvalues of Hessian are greater than 0: 33424.8195956998, 4273.64710086899, 2915.18816361355, 1574.34838064477, 1220.2407031505, 399.85290397257, 330.835726506523, 228.359608385762, 202.734842676118, 167.060509386733, 132.4506167284, 123.378280390459, 105.537092035284, 55.6237259796182, 17.1774319046534, 8.95873734425236, 1.14939813833253, 0.000103589973588033, -1.09927985257781e-30

Begin fit attempt 4 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 33424.8689255756, 4273.63304303848, 2915.17122141628, 1574.33946772599, 1220.23865005364, 399.842010957533, 330.834518531425, 228.360617202733, 202.735065508242, 167.046384028547, 132.450457677623, 123.37053984549, 105.535629949218, 55.6221917370255, 17.1756441754983, 8.95776400064524, 1.14789788636548, -1.02858187603302e-31, -0.000000373111114458684

Begin fit attempt 5 of at maximum 16 tries

 Fit attempt worse than current best:  27694.3273727165 vs 4206.15742306297

Begin fit attempt 6 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 33424.8894918548, 4273.63302518123, 2915.15990807838, 1574.31936416918, 1220.21599709718, 399.815918867368, 330.81481783776, 228.355638511406, 202.736424971495, 167.034082294633, 132.440038652941, 123.345852414908, 105.523282339831, 55.614489224545, 17.1587499661392, 8.95795552634863, 1.12080886277328, -2.55898739617563e-30, -0.000121732660596407

Begin fit attempt 7 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 33424.8846208237, 4273.65151789747, 2915.18620292892, 1574.35024578677, 1220.25578386642, 399.85282794583, 330.857418562348, 228.361051387313, 202.735290635231, 167.070240990172, 132.459735025967, 123.385126844026, 105.541729165103, 55.6277477930686, 17.186065767054, 8.96090015246979, 1.15201054143619, 0.000124503024150416, -1.80217678924793e-30

Begin fit attempt 8 of at maximum 16 tries

 Lowest minimum so far:  4206.1574228182

 Not all eigenvalues of Hessian are greater than 0: 33424.8918339675, 4273.6315394522, 2915.18499580064, 1574.34213857475, 1220.24327598684, 399.847733974025, 330.855472205988, 228.356720002881, 202.73719779763, 167.057224235934, 132.452114852306, 123.364938385735, 105.53606859664, 55.6223144041572, 17.1751372922046, 8.96183572005805, 1.13432516149807, 0.0000997805994225626, -1.46146609541896e-31

Begin fit attempt 9 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 33424.8918339675, 4273.6315394522, 2915.18499580064, 1574.34213857475, 1220.24327598684, 399.847733974025, 330.855472205988, 228.356720002881, 202.73719779763, 167.057224235934, 132.452114852306, 123.364938385735, 105.53606859664, 55.6223144041572, 17.1751372922046, 8.96183572005805, 1.13432516149807, 0.0000997805994225626, -1.46146609541896e-31

Begin fit attempt 10 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 33424.8795025774, 4273.6436773264, 2915.17748200629, 1574.34895511606, 1220.25045056825, 399.844572393557, 330.846893964696, 228.358019700591, 202.735528674567, 167.062661192958, 132.45670816458, 123.371115849551, 105.537895946243, 55.6223052602159, 17.1774632543943, 8.95642144176294, 1.14373522966207, -2.45671563855915e-30, -0.0000102211151819787

Begin fit attempt 11 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 33424.9094628587, 4273.64129760218, 2915.18143349358, 1574.3352473595, 1220.23441026324, 399.849435399638, 330.856983681187, 228.357523837538, 202.731042300837, 167.05557450556, 132.436114225413, 123.373707046825, 105.53040457725, 55.6222493699684, 17.169727356434, 8.95742883479793, 1.15001243869438, -6.24360435210644e-31, -0.0000108070769638958

Begin fit attempt 12 of at maximum 16 tries

 Not all eigenvalues of Hessian are greater than 0: 33424.8888752482, 4273.63719325283, 2915.16900750244, 1574.33577264896, 1220.22515811454, 399.827689155768, 330.828509276047, 228.356956584604, 202.735370404734, 167.037143279463, 132.439243509195, 123.347823124454, 105.529585525651, 55.619763062519, 17.1685296681633, 8.95769495577798, 1.12572612572787, -4.84423002067204e-31, -0.000230420924515831

Begin fit attempt 13 of at maximum 16 tries

 Lowest minimum so far:  -124836.549792134

 OpenMx status code 6 not in list of acceptable status codes, 0
 OpenMx status code 6 not in list of acceptable status codes, 0
Error in eigen(fit$output$calculatedHessian, symmetric = T, only.values = T) : 
  infinite or missing values in 'x'

 Eigenvalues of Hessian could not be calculated

Begin fit attempt 14 of at maximum 16 tries

 OpenMx status code 6 not in list of acceptable status codes, 0
 OpenMx status code 6 not in list of acceptable status codes, 0
Error in eigen(fit$output$calculatedHessian, symmetric = T, only.values = T) : 
  infinite or missing values in 'x'

 Eigenvalues of Hessian could not be calculated

Begin fit attempt 15 of at maximum 16 tries

 Fit attempt generated errors

Begin fit attempt 16 of at maximum 16 tries

 Fit attempt generated errors

Retry limit reached
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
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)
Unique discreteDRIFT calculations per step required = 5
Unique discreteCINT calculations per step required = 5
Unique discreteDIFFUSION calculations per step required = 5
2 / 2 latent variables required for covariance calculations
Compiling model, ignore forthcoming warning re number of chains...
Warning: running command '/home/ripley/R/cc/bin/R CMD SHLIB file2a255c7e62c2.cpp 2> file2a255c7e62c2.cpp.err.txt' had status 1 and error message 'Illegal seek'
Quitting from lines 296-298 (hierarchical.rnw) 
Error: processing vignette 'hierarchical.rnw' failed with diagnostics:
Compilation ERROR, function(s)/method(s) not created! "/home/ripley/R/Lib32/StanHeaders/include/stan/math/memory/stack_alloc.hpp", line 39: Error: The function "malloc" must have a prototype.
"/home/ripley/R/Lib32/StanHeaders/include/stan/math/memory/stack_alloc.hpp", line 39: Error: Using static_cast to convert from int to char* not allowed.
"/home/ripley/R/Lib32/StanHeaders/include/stan/math/memory/stack_alloc.hpp", line 147: Error: The function "free" must have a prototype.
"/home/ripley/R/Lib32/StanHeaders/include/stan/math/memory/stack_alloc.hpp", line 234: Error: The function "free" must have a prototype.
"/home/ripley/R/Lib32/BH/include/boost/config/compiler/sunpro_cc.hpp", line 117: Warning (Anachronism): Attempt to redefine BOOST_NO_CXX11_RVALUE_REFERENCES without using #undef.
"/home/ripley/R/Lib32/RcppEigen/include/Eigen/src/Core/arch/CUDA/Half.h", line 391: Error: expf is not a member of file level.
"/h
Execution halted