CRAN Package Check Results for Package ctsem

Last updated on 2019-01-24 09:49:30 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.7.6 649.41 657.01 1306.42 WARN
r-devel-linux-x86_64-debian-gcc 2.7.6 569.44 662.18 1231.62 WARN
r-devel-windows-ix86+x86_64 2.7.6 866.00 644.00 1510.00 NOTE --no-vignettes
r-patched-linux-x86_64 2.7.6 619.92 1576.39 2196.31 WARN
r-release-linux-x86_64 2.7.6 505.80 1580.43 2086.23 NOTE
r-release-windows-ix86+x86_64 2.7.6 609.00 710.00 1319.00 NOTE --no-vignettes
r-release-osx-x86_64 2.7.6 NOTE
r-oldrel-windows-ix86+x86_64 2.7.6 879.00 681.00 1560.00 NOTE --no-vignettes
r-oldrel-osx-x86_64 2.7.6 NOTE

Additional issues

rchk

Check Details

Version: 2.7.6
Check: line endings in C/C++/Fortran sources/headers
Result: NOTE
    Found the following sources/headers with CR or CRLF line endings:
     inst/include/meta_header.hpp
    Some Unix compilers require LF line endings.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.7.6
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.7.6
Check: re-building of vignette outputs
Result: WARN
    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
    Running ctsemCarefulFit with 16 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4345.86257632205
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 3311049125.22432, 1041696.60387923, 214305.512725886, 131985.095712239, 2405.65662920448, 1769.95653444597, 739.286500747171, 453.144793021724, 333.890562802462, 90.9674218772033, 80.8042405395784, 0.266912386115123, 0.00000551006615406393, -0.00000186479885700195, -0.000308845832050684, -370.423096548114
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Lowest minimum so far: 4345.67885673806
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 2618047817.04154, 837167.043413461, 188690.838160515, 100154.892263763, 2406.6463572125, 1271.13777562244, 818.840020541056, 352.309610575625, 336.910679894538, 80.9945982532131, 49.3241960769404, 16.8978275087531, 0.00117383504586971, 0.0000481691551617197, 0.00000630535623986245, -0.155409814592485
    
    Beginning fit attempt 2 of at maximum 15 extra tries
    
     Lowest minimum so far: 4344.85653907275
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 17038701402.6611, 5368656.73133398, 656536.388994895, 380554.155793236, 2396.50661057766, 1573.61116152958, 638.677128704107, 389.542887985698, 335.316002192624, 81.1566816953806, 44.4534173009722, 7.39914100031829, 0.0542374315205481, 0.00298124445836008, -0.000122247252460285, -0.000191552664981736
    
    Beginning fit attempt 3 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4601.73308025476 vs 4344.85653907275
    
    Beginning fit attempt 4 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4574.8590324841 vs 4344.85653907275
    
    Beginning fit attempt 5 of at maximum 15 extra tries
    
     Lowest minimum so far: 4192.2947983328
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
    Beginning fit attempt 6 of at maximum 15 extra tries
    
     Lowest minimum so far: 4192.29441116291
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
    Beginning fit attempt 7 of at maximum 15 extra tries
    
     Lowest minimum so far: 4192.26366461216
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 625836055.269236, 81018763.6742807, 46361.9030738562, 9548.00488014118, 1619.55293403945, 1495.68075978127, 364.977031507008, 286.366796625077, 259.530016024719, 168.598144062121, 114.488460882015, 88.8898986783138, 49.3742744856584, 0.00498095669552536, 0.0000580459773729196, -0.000000971916921386466
    
    Beginning fit attempt 8 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4727.62667671092 vs 4192.26366461216
    
    Beginning fit attempt 9 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4865.47097947429 vs 4192.26366461216
    
    Beginning fit attempt 10 of at maximum 15 extra tries
    
     Lowest minimum so far: 4182.94163747832
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
    Beginning fit attempt 11 of at maximum 15 extra tries
    
     Lowest minimum so far: 4182.94163723687
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
    Beginning fit attempt 12 of at maximum 15 extra tries
    
     Lowest minimum so far: 4182.84944360135
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 3338752461.75017, 583315497.234517, 37579.88424366, 9281.98672738018, 1371.21871600081, 1183.62891484916, 377.652888797401, 349.66852296476, 255.688659425226, 204.777373781073, 113.877555901117, 106.829980176956, 88.4263946462315, 41.6004413374527, 0.000421711289572595, -0.000000319884601454731
    
    Beginning fit attempt 13 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4182.90477138925 vs 4182.84944360135
    
    Beginning fit attempt 14 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4182.90032210653 vs 4182.84944360135
    
    Beginning fit attempt 15 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 33422.4841631746 vs 4182.84944360135
    
    Retry limit reached
    
    Retry limit reached; solution not found. Best fit=4182.8494 (started at 4727.4693) (16 attempt(s): 16 valid, 0 errors)
    
    
    Uncertain solution found - consider parameter validity, try again, increase extraTries, change inits, change model, or check data!
    
    Running ctsemCarefulFit with 15 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4196.73541494078
    
    Solution found
    
    
    Solution found! Final fit=4196.7354 (started at 4882.1501) (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)
    Running ctsemCarefulFit with 19 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4151.13132113271
    
    Solution found
    
    
    Solution found! Final fit=4151.1313 (started at 4301.6568) (1 attempt(s): 1 valid, 0 errors)
    
    Plotting fit
    Plotting fit
    Running ctsemCarefulFit with 23 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4245.2570075149
    
    Solution found
    
    
    Solution found! Final fit=4245.257 (started at 4370.0908) (1 attempt(s): 1 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -477.756816533166
    
    Solution found
    
    
    Solution found! Final fit=-477.75682 (started at -378.62728) (1 attempt(s): 1 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -464.45189720933
    
     Not all eigenvalues of Hessian are greater than 0: 1555.73732751274, 696.888081707533, 119.47580511205, 34.6853297420144, 28.2661786119732, 26.4946545536491, 25.1637283204315, 11.7919401255018, 10.3800089229896, 7.51503312004016, 4.42599554958514, 2.1330961146387, 0.90219804168257, 0.481790830955707, 0.0572689503543451, 0.00345646043246331, 0.0000239211371344081, -0.0000115075539180561
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Lowest minimum so far: -464.451897214569
    
    Solution found
    
    
    Solution found! Final fit=-464.4519 (started at 91.032871) (2 attempt(s): 2 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -138.198676577264
    
    Solution found
    
    
    Solution found! Final fit=-138.19868 (started at 670.38458) (1 attempt(s): 1 valid, 0 errors)
    
    Begin carefulFit start value estimation for group g1
    Begin carefulFit start value estimation for group g2
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -129.417753910738
    
    Solution found
    
    
    Solution found! Final fit=-129.41775 (started at 6385.5734) (1 attempt(s): 1 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 734.559496680369
    
    Solution found
    
    
    Solution found! Final fit=734.5595 (started at 1245.5141) (1 attempt(s): 1 valid, 0 errors)
    
    transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -3462.15389492832
    
    Solution found
    
    
    Solution found! Final fit=-3462.1539 (started at -3145.5663) (1 attempt(s): 1 valid, 0 errors)
    
    Running ctsemCarefulFit with 16 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4345.80042566897
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 2797530735.86189, 942168.013390252, 190430.203819022, 116323.354091487, 2406.20513401938, 1567.5965795799, 747.620835819653, 416.04160858936, 338.363857960901, 81.9984646998796, 74.508210581129, 0.17516923894178, -0.0000474507860910557, -0.0000877285190659991, -0.000755799841649613, -172.845419651062
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Lowest minimum so far: 4345.67742534029
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 2664970280.80583, 895943.200211433, 187195.369838031, 108914.229206819, 2402.44862340016, 1240.75179871985, 843.214364122878, 362.923769193723, 336.950751934997, 87.8961873777338, 81.3918661595573, 4.22678168713948, 0.000954417849069098, -0.0000412479644479814, -0.0000704475248668029, -2.33077467222463
    
    Beginning fit attempt 2 of at maximum 15 extra tries
    
     Lowest minimum so far: 4344.97082338614
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 14173793019.0965, 3832194.11861145, 474889.446286017, 344441.595430301, 2396.95674427955, 1463.36542928768, 699.063940197222, 387.347750176315, 334.153460843244, 81.4703777324769, 65.0018408667777, 27.1051312427594, 0.0034577372998172, 0.0000667235321845871, -0.000753392873491946, -0.0102282339361983
    
    Beginning fit attempt 3 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4347.34621942492 vs 4344.97082338614
    
    Beginning fit attempt 4 of at maximum 15 extra tries
    
     Lowest minimum so far: 4176.87456133429
    
    Solution found
    
    
    Solution found! Final fit=4176.8746 (started at 4727.4693) (5 attempt(s): 5 valid, 0 errors)
    
    Running ctsemCarefulFit with 19 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4151.13132113271
    
    Solution found
    
    
    Solution found! Final fit=4151.1313 (started at 4301.6567) (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
    Running ctsemCarefulFit with 19 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4203.31303297246
    
     Not all eigenvalues of Hessian are greater than 0: 94313.725561503, 6623.16262442306, 1636.16701250111, 1127.62394964895, 726.811801294046, 621.795193372155, 294.431802773454, 198.915708199826, 180.032489067593, 115.665197148067, 91.1999304105221, 71.046969774319, 55.3337552002444, 26.045356735675, 9.29601829362489, 5.38036936558734, 4.03419723493502, 2.88403046784757, -0.0000118636982341065
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Not all eigenvalues of Hessian are greater than 0: 94313.725561503, 6623.16262442306, 1636.16701250111, 1127.62394964895, 726.811801294046, 621.795193372155, 294.431802773454, 198.915708199826, 180.032489067593, 115.665197148067, 91.1999304105221, 71.046969774319, 55.3337552002444, 26.045356735675, 9.29601829362489, 5.38036936558734, 4.03419723493502, 2.88403046784757, -0.0000118636982341065
    
    Beginning fit attempt 2 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4206.15742272025 vs 4203.31303297246
    
    Beginning fit attempt 3 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4263.99127328494 vs 4203.31303297246
    
    Beginning fit attempt 4 of at maximum 15 extra tries
    
     Lowest minimum so far: 4203.31303262956
    
     Not all eigenvalues of Hessian are greater than 0: 94314.1020577418, 6623.17870329296, 1636.16610705694, 1127.62254788299, 726.795332008526, 621.80160567408, 294.441577993583, 198.916916814052, 180.029285373746, 115.642812692212, 91.1942266013496, 71.0465396075011, 55.3306947419066, 26.0396349631213, 9.28618863994962, 5.37758436207964, 4.02879343875189, 2.88584119220764, -0.0000109346727969575
    
    Beginning fit attempt 5 of at maximum 15 extra tries
    
     Not all eigenvalues of Hessian are greater than 0: 94314.1020577418, 6623.17870329296, 1636.16610705694, 1127.62254788299, 726.795332008526, 621.80160567408, 294.441577993583, 198.916916814052, 180.029285373746, 115.642812692212, 91.1942266013496, 71.0465396075011, 55.3306947419066, 26.0396349631213, 9.28618863994962, 5.37758436207964, 4.02879343875189, 2.88584119220764, -0.0000109346727969575
    
    Beginning fit attempt 6 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4206.25957640419 vs 4203.31303262956
    
    Beginning fit attempt 7 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4747.14993463876 vs 4203.31303262956
    
    Beginning fit attempt 8 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4206.287335726 vs 4203.31303262956
    
    Beginning fit attempt 9 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4217.65712989184 vs 4203.31303262956
    
    Beginning fit attempt 10 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4215.98769418956 vs 4203.31303262956
    
    Beginning fit attempt 11 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4263.99127328506 vs 4203.31303262956
    
    Beginning fit attempt 12 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4226.76054650124 vs 4203.31303262956
    
    Beginning fit attempt 13 of at maximum 15 extra tries
    
     Lowest minimum so far: 4203.31303215508
    
     Not all eigenvalues of Hessian are greater than 0: 94314.3094840541, 6623.17067996646, 1636.15534354814, 1127.63178515869, 726.79608589914, 621.790560986501, 294.422753420846, 198.913828482721, 180.024828699278, 115.649765775199, 91.1910661754233, 71.0407352934033, 55.3269445655557, 26.0397563458786, 9.27332604169298, 5.37478356985331, 4.01382882189171, 2.87699600502012, -0.000103455185866493
    
    Beginning fit attempt 14 of at maximum 15 extra tries
    
     Lowest minimum so far: 4203.31303215508
    
    Solution found
    
    
    Solution found! Final fit=4203.313 (started at 4349.5533) (15 attempt(s): 15 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
    --- finished re-building ‘ctsem.rnw’
    
    --- re-building ‘hierarchical.rnw’ using knitr
    Quitting from lines 114-151 (hierarchical.rnw)
    Error: processing vignette 'hierarchical.rnw' failed with diagnostics:
    object ‘knit_hooks’ not found
    --- failed re-building ‘hierarchical.rnw’
    
    SUMMARY: processing the following file failed:
     ‘hierarchical.rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.7.6
Check: re-building of vignette outputs
Result: WARN
    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
    Running ctsemCarefulFit with 16 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4345.84618843183
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 2781400099.67246, 959016.615002559, 193939.710398236, 120807.324495143, 2397.68735870303, 1602.71915371364, 746.925475307084, 435.77501472556, 335.677009526487, 82.280047821868, 77.646695707429, 0.243584871575008, 0.000456237696309928, 0.000110755322367954, 0.0000467295777426189, -202.002239599035
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Lowest minimum so far: 4345.51974342798
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 3341117686.06814, 1145456.70482891, 175748.883000962, 131942.258815767, 2395.1404270832, 1346.27250577225, 718.90248639319, 338.214165689257, 320.156284107233, 80.614001652682, 51.1616999035079, 0.146549236340977, 0.00223031772994454, 0.0000352964958808608, -0.0000164918111350852, -60.9376958509356
    
    Beginning fit attempt 2 of at maximum 15 extra tries
    
     Lowest minimum so far: 4344.85392303168
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 14223187313.6717, 4730841.22123706, 576830.036807925, 346034.037455157, 2397.05599968874, 1579.53589251496, 639.300607771846, 389.664400956465, 336.774787325735, 81.2416035991056, 45.2294786001518, 0.0341354483649126, 0.00244846559986561, 0.000361518823064477, -0.000127547377773881, -23.216104171156
    
    Beginning fit attempt 3 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4358.17599312153 vs 4344.85392303168
    
    Beginning fit attempt 4 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4369.34600232578 vs 4344.85392303168
    
    Beginning fit attempt 5 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4345.38374236282 vs 4344.85392303168
    
    Beginning fit attempt 6 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 4377.16636138604 vs 4344.85392303168
    
    Beginning fit attempt 7 of at maximum 15 extra tries
    
     Fit attempt worse than current best: 17603.5123029422 vs 4344.85392303168
    
    Beginning fit attempt 8 of at maximum 15 extra tries
    
     Lowest minimum so far: 4176.87456133431
    
    Solution found
    
    
    Solution found! Final fit=4176.8746 (started at 4727.4693) (9 attempt(s): 9 valid, 0 errors)
    
    Running ctsemCarefulFit with 15 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4196.73541494077
    
    Solution found
    
    
    Solution found! Final fit=4196.7354 (started at 4882.15) (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
    Running ctsemCarefulFit with 19 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4151.13132113271
    
    Solution found
    
    
    Solution found! Final fit=4151.1313 (started at 4301.6569) (1 attempt(s): 1 valid, 0 errors)
    
    Plotting fit
    Plotting fit
    Running ctsemCarefulFit with 23 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4245.25700751458
    
    Solution found
    
    
    Solution found! Final fit=4245.257 (started at 4370.0907) (1 attempt(s): 1 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -477.756816321184
    
     Not all eigenvalues of Hessian are greater than 0: 6709.35185151051, 3468.20345875516, 522.980743392382, 304.061103549625, 140.637626311234, 98.3645719975857, 69.6230305704327, 48.3857957377269, 22.8517164916416, 20.1310465475527, 15.963321433692, 12.546682745029, 8.32094809238165, 7.10794579454276, 4.18742875319023, 2.89672588147804, 0.153421552757007, -0.00000830117301158251
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Lowest minimum so far: -477.756816349576
    
    Solution found
    
    
    Solution found! Final fit=-477.75682 (started at -378.62728) (2 attempt(s): 2 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -464.44985946927
    
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
    
     Not all eigenvalues of Hessian are greater than 0: 24287.1090892912, 1192.59672906677, 114.06847888136, 34.4925728181617, 27.0929265488296, 25.6660515125482, 11.8237296419703, 7.52438639830523, 4.46222832823169, 2.95941638652114, 2.00614848483394, 1.0456339437581, 0.0435902482533143, 0.00524592027148591, 0.000624439378546061, 0.0000506326693473514, 0.000000965420936551977, -0.00000000000000930812359842289
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Lowest minimum so far: -464.451895572321
    
    Solution found
    
    
    Solution found! Final fit=-464.4519 (started at 88.974358) (2 attempt(s): 2 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -138.198676577048
    
    Solution found
    
    
    Solution found! Final fit=-138.19868 (started at 670.38461) (1 attempt(s): 1 valid, 0 errors)
    
    Begin carefulFit start value estimation for group g1
    Begin carefulFit start value estimation for group g2
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -129.417753909793
    
    Solution found
    
    
    Solution found! Final fit=-129.41775 (started at 6179.8858) (1 attempt(s): 1 valid, 0 errors)
    
    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
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 738.419875077806
    
    Solution found
    
    
    Solution found! Final fit=738.41988 (started at 1245.3665) (1 attempt(s): 1 valid, 0 errors)
    
    transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
    
    Beginning initial fit attempt
    
     Lowest minimum so far: -3462.15389492831
    
    Solution found
    
    
    Solution found! Final fit=-3462.1539 (started at -3145.5663) (1 attempt(s): 1 valid, 0 errors)
    
    Running ctsemCarefulFit with 16 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4190.7977758273
    
     Not all eigenvalues of Hessian are greater than 0: 160837.974983202, 43192.3333612445, 21269.5229739658, 8473.80295673972, 1625.15463603447, 1449.82352612066, 343.302784252528, 312.90828858995, 249.0705888761, 159.62804866534, 107.972977837089, 100.171266688371, 62.0746667759964, 20.0050449816844, 0.329815385402892, -0.0000000000000426325641456129
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    
     Lowest minimum so far: 4190.79777582628
    
    Solution found
    
    
    Solution found! Final fit=4190.7978 (started at 4997.0475) (2 attempt(s): 2 valid, 0 errors)
    
    Running ctsemCarefulFit with 19 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4151.13132113272
    
    Solution found
    
    
    Solution found! Final fit=4151.1313 (started at 4301.6569) (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
    Running ctsemCarefulFit with 19 parameters
    
    Beginning initial fit attempt
    
     Lowest minimum so far: 4203.31303213657
    
    Solution found
    
    
    Solution found! Final fit=4203.313 (started at 4349.5532) (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
    --- finished re-building ‘ctsem.rnw’
    
    --- re-building ‘hierarchical.rnw’ using knitr
    Quitting from lines 114-151 (hierarchical.rnw)
    Error: processing vignette 'hierarchical.rnw' failed with diagnostics:
    object ‘knit_hooks’ not found
    --- failed re-building ‘hierarchical.rnw’
    
    SUMMARY: processing the following file failed:
     ‘hierarchical.rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 2.7.6
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 14.8Mb
     sub-directories of 1Mb or more:
     data 1.8Mb
     doc 4.0Mb
     libs 7.8Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.7.6
Flags: --no-vignettes
Check: line endings in C/C++/Fortran sources/headers
Result: NOTE
    Found the following sources/headers with CR or CRLF line endings:
     inst/include/meta_header.hpp
    Some Unix compilers require LF line endings.
Flavor: r-devel-windows-ix86+x86_64

Version: 2.7.6
Flags: --no-vignettes
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.7.6
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: S3 methods ‘[.fun_list’, ‘[.grouped_df’, ‘all.equal.tbl_df’, ‘anti_join.data.frame’, ‘anti_join.tbl_df’, ‘arrange.data.frame’, ‘arrange.default’, ‘arrange.grouped_df’, ‘arrange.tbl_df’, ‘arrange_.data.frame’, ‘arrange_.tbl_df’, ‘as.data.frame.grouped_df’, ‘as.data.frame.rowwise_df’, ‘as.data.frame.tbl_cube’, ‘as.table.tbl_cube’, ‘as.tbl.data.frame’, ‘as.tbl.tbl’, ‘as.tbl_cube.array’, ‘as.tbl_cube.data.frame’, ‘as.tbl_cube.matrix’, ‘as.tbl_cube.table’, ‘as_tibble.grouped_df’, ‘as_tibble.tbl_cube’, ‘auto_copy.tbl_cube’, ‘auto_copy.tbl_df’, ‘cbind.grouped_df’, ‘collapse.data.frame’, ‘collect.data.frame’, ‘common_by.NULL’, ‘common_by.character’, ‘common_by.default’, ‘common_by.list’, ‘compute.data.frame’, ‘copy_to.DBIConnection’, ‘copy_to.src_local’, ‘default_missing.data.frame’, ‘default_missing.default’, ‘dim.tbl_cube’, ‘distinct.data.frame’, ‘distinct.default’, ‘distinct.grouped_df’, ‘distinct.tbl_df’, ‘distinct_.data.frame’, ‘distinct_.grouped_df’, ‘distinct_.tbl_df’, ‘do.NULL’, ‘do.data.frame’, ‘do.default’, ‘do.grouped_df’, ‘do.rowwise_df’, ‘do_.NULL’, ‘do_.data.frame’, ‘do_.grouped_df’, ‘do_.rowwise_df’, ‘filter.data.frame’, ‘filter.default’, ‘filter.tbl_cube’, ‘filter.tbl_df’, ‘filter.ts’, ‘filter_.data.frame’, ‘filter_.tbl_cube’, ‘filter_.tbl_df’, ‘format.src_local’, ‘full_join.data.frame’, ‘full_join.tbl_df’, ‘group_by.data.frame’, ‘group_by.default’, ‘group_by.rowwise_df’, ‘group_by.tbl_cube’, ‘group_by_.data.frame’, ‘group_by_.rowwise_df’, ‘group_by_.tbl_cube’, ‘group_indices.data.frame’, ‘group_indices.default’, ‘group_indices.grouped_df’, ‘group_indices_.data.frame’, ‘group_indices_.grouped_df’, ‘group_size.data.frame’, ‘group_size.grouped_df’, ‘group_size.rowwise_df’, ‘group_vars.default’, ‘group_vars.grouped_df’, ‘group_vars.tbl_cube’, ‘groups.data.frame’, ‘groups.grouped_df’, ‘groups.tbl_cube’, ‘inner_join.data.frame’, ‘inner_join.tbl_df’, ‘intersect.data.frame’, ‘intersect.default’, ‘left_join.data.frame’, ‘left_join.tbl_df’, ‘mutate.data.frame’, ‘mutate.default’, ‘mutate.tbl_df’, ‘mutate_.data.frame’, ‘mutate_.tbl_df’, ‘n_groups.data.frame’, ‘n_groups.grouped_df’, ‘n_groups.rowwise_df’, ‘print.BoolResult’, ‘print.all_vars’, ‘print.any_vars’, ‘print.fun_list’, ‘print.location’, ‘print.rowwise_df’, ‘print.src’, ‘print.tbl_cube’, ‘pull.data.frame’, ‘rbind.grouped_df’, ‘recode.character’, ‘recode.factor’, ‘recode.numeric’, ‘rename.data.frame’, ‘rename.default’, ‘rename.grouped_df’, ‘rename.tbl_cube’, ‘rename_.data.frame’, ‘rename_.grouped_df’, ‘rename_.tbl_cube’, ‘right_join.data.frame’, ‘right_join.tbl_df’, ‘same_src.data.frame’, ‘same_src.tbl_cube’, ‘sample_frac.data.frame’, ‘sample_frac.default’, ‘sample_frac.grouped_df’, ‘sample_n.data.frame’, ‘sample_n.default’, ‘sample_n.grouped_df’, ‘select.data.frame’, ‘select.default’, ‘select.grouped_df’, ‘select.tbl_cube’, ‘select_.data.frame’, ‘select_.grouped_df’, ‘select_.tbl_cube’, ‘semi_join.data.frame’, ‘semi_join.tbl_df’, ‘setdiff.data.frame’, ‘setdiff.default’, ‘setequal.data.frame’, ‘setequal.default’, ‘slice.data.frame’, ‘slice.default’, ‘slice.tbl_df’, ‘slice_.data.frame’, ‘slice_.tbl_df’, ‘src_tbls.src_local’, ‘summarise.data.frame’, ‘summarise.default’, ‘summarise.tbl_cube’, ‘summarise.tbl_df’, ‘summarise_.data.frame’, ‘summarise_.tbl_cube’, ‘summarise_.tbl_df’, ‘tbl.DBIConnection’, ‘tbl.src_local’, ‘tbl_sum.grouped_df’, ‘tbl_vars.data.frame’, ‘tbl_vars.tbl_cube’, ‘transmute.default’, ‘transmute.grouped_df’, ‘transmute_.default’, ‘transmute_.grouped_df’, ‘ungroup.data.frame’, ‘ungroup.grouped_df’, ‘ungroup.rowwise_df’, ‘union.data.frame’, ‘union.default’, ‘union_all.data.frame’, ‘union_all.default’ were declared in NAMESPACE but not found
Flavor: r-patched-linux-x86_64

Version: 2.7.6
Check: installed package size
Result: NOTE
     installed size is 87.2Mb
     sub-directories of 1Mb or more:
     data 1.8Mb
     doc 4.0Mb
     libs 80.2Mb
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64