Last updated on 2019-01-24 08:48:46 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-linux-x86_64-fedora-clang | 2.7.6 | 2093.17 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 2.7.6 | 1432.33 | 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-patched-solaris-x86 | 2.7.6 | 983.20 | ERROR | |||
| 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 |
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, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-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-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, 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
Check: installed package size
Result: NOTE
installed size is 102.2Mb
sub-directories of 1Mb or more:
data 1.8Mb
doc 4.0Mb
libs 95.2Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, 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: 4345.85704965914
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 3025276234.97094, 1027772.76105094, 202840.599383073, 131009.6254217, 2390.92434411858, 1733.56240229181, 737.656728251163, 450.902317199587, 337.660105339132, 87.8485072027062, 81.2306042750578, 0.274195450755541, 0.00017189018157032, 0.0000136037835630938, -0.0000441226533961325, -345.273094458416
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: 4345.63675427699
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 3068696327.53377, 919462.730881126, 185223.313668631, 105745.46955202, 2404.8045096936, 1190.0942035333, 808.100329582061, 336.06664672927, 293.095293200804, 80.1378657460264, 72.0358778973945, 7.27862838057943, 0.00100715838876966, 0.00000607824952665219, -0.000064375028675515, -0.929713935657619
Beginning fit attempt 2 of at maximum 15 extra tries
Lowest minimum so far: 4344.98630498651
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 12485178762.1022, 3641443.73187642, 447212.52427646, 321172.373100449, 2396.78133131925, 1527.62049656738, 681.79888840539, 387.605643064321, 336.160175182028, 81.2762914370872, 42.4050275704264, 5.5580970809399, 0.0386965696235385, 0.000850510096282118, 0.0000100946129401466, -0.000070438124169421
Beginning fit attempt 3 of at maximum 15 extra tries
Fit attempt worse than current best: 4345.6273853634 vs 4344.98630498651
Beginning fit attempt 4 of at maximum 15 extra tries
Fit attempt worse than current best: 4367.90998851759 vs 4344.98630498651
Beginning fit attempt 5 of at maximum 15 extra tries
Fit attempt worse than current best: 4359.2054702813 vs 4344.98630498651
Beginning fit attempt 6 of at maximum 15 extra tries
Fit attempt worse than current best: 4865.94856616849 vs 4344.98630498651
Beginning fit attempt 7 of at maximum 15 extra tries
Fit attempt worse than current best: 4395.28740566715 vs 4344.98630498651
Beginning fit attempt 8 of at maximum 15 extra tries
Lowest minimum so far: 4176.87456133428
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: 4196.73541494079
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: 4245.2570075146
Solution found
Solution found! Final fit=4245.257 (started at 4370.0898) (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: -477.756816091883
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: -464.451719088975
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 36452.4118620206, 1200.87792120504, 116.887836713988, 34.5266167527439, 26.9938885372416, 25.5700148130414, 11.8067955083843, 7.51410487781495, 4.44076980108636, 2.82537182433211, 2.00286256682685, 0.869083302890023, 0.0106912500444183, 0.00349844550717514, 0.000438369331371314, 0.0000516171206534574, 0.000000592485883531389, -0.00000000000000341697827027302
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: -464.451898390146
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: -138.198676577416
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
OMP: Warning #96: Cannot form a team with 10 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
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: -3462.15389492833
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: 4190.79777582722
Not all eigenvalues of Hessian are greater than 0: 160837.972562465, 43192.3679428252, 21269.5456382794, 8473.80461715315, 1625.18026712444, 1449.83707937379, 343.324990028389, 312.923849955446, 249.102797009127, 159.656098966452, 107.991153335545, 100.180007447747, 62.1041096503756, 20.0160961706942, 0.332647756784511, -0.0000000000000426325641456207
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: 4190.79777582664
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: 4203.31303234544
Not all eigenvalues of Hessian are greater than 0: 94314.8310197235, 6623.116504527, 1636.1523526676, 1127.62164097167, 726.786237543391, 621.78221264138, 294.42778456506, 198.914001640179, 180.022855915759, 115.63616333384, 91.1959348555048, 71.0451303907574, 55.3242656998623, 26.0365990654221, 9.28021017659102, 5.38063228503748, 4.02505536624336, 2.87742690114492, -0.000000281022701969819
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: 4203.31303234444
Solution found
Solution found! Final fit=4203.313 (started at 4349.5532) (2 attempt(s): 2 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-fedora-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: 4345.85704965914
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 3025276234.97094, 1027772.76105094, 202840.599383073, 131009.6254217, 2390.92434411858, 1733.56240229181, 737.656728251163, 450.902317199587, 337.660105339132, 87.8485072027062, 81.2306042750578, 0.274195450755541, 0.00017189018157032, 0.0000136037835630938, -0.0000441226533961325, -345.273094458416
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: 4345.63675427699
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 3068696327.53377, 919462.730881126, 185223.313668631, 105745.46955202, 2404.8045096936, 1190.0942035333, 808.100329582061, 336.06664672927, 293.095293200804, 80.1378657460264, 72.0358778973945, 7.27862838057943, 0.00100715838876966, 0.00000607824952665219, -0.000064375028675515, -0.929713935657619
Beginning fit attempt 2 of at maximum 15 extra tries
Lowest minimum so far: 4344.98630498651
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 12485178762.1022, 3641443.73187642, 447212.52427646, 321172.373100449, 2396.78133131925, 1527.62049656738, 681.79888840539, 387.605643064321, 336.160175182028, 81.2762914370872, 42.4050275704264, 5.5580970809399, 0.0386965696235385, 0.000850510096282118, 0.0000100946129401466, -0.000070438124169421
Beginning fit attempt 3 of at maximum 15 extra tries
Fit attempt worse than current best: 4345.6273853634 vs 4344.98630498651
Beginning fit attempt 4 of at maximum 15 extra tries
Fit attempt worse than current best: 4367.90998851759 vs 4344.98630498651
Beginning fit attempt 5 of at maximum 15 extra tries
Fit attempt worse than current best: 4359.2054702813 vs 4344.98630498651
Beginning fit attempt 6 of at maximum 15 extra tries
Fit attempt worse than current best: 4865.94856616849 vs 4344.98630498651
Beginning fit attempt 7 of at maximum 15 extra tries
Fit attempt worse than current best: 4395.28740566715 vs 4344.98630498651
Beginning fit attempt 8 of at maximum 15 extra tries
Lowest minimum so far: 4176.87456133428
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: 4196.73541494079
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: 4245.2570075146
Solution found
Solution found! Final fit=4245.257 (started at 4370.0898) (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: -477.756816091883
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: -464.451719088975
OpenMx status code 6 not in list of acceptable status codes, (0,0)
Not all eigenvalues of Hessian are greater than 0: 36452.4118620206, 1200.87792120504, 116.887836713988, 34.5266167527439, 26.9938885372416, 25.5700148130414, 11.8067955083843, 7.51410487781495, 4.44076980108636, 2.82537182433211, 2.00286256682685, 0.869083302890023, 0.0106912500444183, 0.00349844550717514, 0.000438369331371314, 0.0000516171206534574, 0.000000592485883531389, -0.00000000000000341697827027302
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: -464.451898390146
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: -138.198676577416
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: 4190.79777582722
Not all eigenvalues of Hessian are greater than 0: 160837.972562465, 43192.3679428252, 21269.5456382794, 8473.80461715315, 1625.18026712444, 1449.83707937379, 343.324990028389, 312.923849955446, 249.102797009127, 159.656098966452, 107.991153335545, 100.180007447747, 62.1041096503756, 20.0160961706942, 0.332647756784511, -0.0000000000000426325641456207
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: 4190.79777582664
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: 4203.31303234544
Not all eigenvalues of Hessian are greater than 0: 94314.8310197235, 6623.116504527, 1636.1523526676, 1127.62164097167, 726.786237543391, 621.78221264138, 294.42778456506, 198.914001640179, 180.022855915759, 115.63616333384, 91.1959348555048, 71.0451303907574, 55.3242656998623, 26.0365990654221, 9.28021017659102, 5.38063228503748, 4.02505536624336, 2.87742690114492, -0.000000281022701969819
Beginning fit attempt 1 of at maximum 15 extra tries
Lowest minimum so far: 4203.31303234444
Solution found
Solution found! Final fit=4203.313 (started at 4349.5532) (2 attempt(s): 2 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-fedora-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: examples
Result: ERROR
Running examples in ‘ctsem-Ex.R’ failed
The error most likely occurred in:
> ### Name: ctGenerateFromFit
> ### Title: Generates data according to the model estimated in a ctsemFit
> ### object.#'
> ### Aliases: ctGenerateFromFit
>
> ### ** Examples
>
>
> data(AnomAuth)
> AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2),
+ Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2))
> AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
Running ctsemCarefulFit with 14 parameters
*** caught segfault ***
address 56d429b7, cause 'memory not mapped'
Flavor: r-patched-solaris-x86
Version: 2.7.6
Check: tests
Result: ERROR
Running ‘testthat.R’ [14s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ctsem)
Loading required package: Rcpp
Loading required package: OpenMx
To take full advantage of multiple cores, use:
mxOption(NULL, 'Number of Threads', parallel::detectCores()) #now
Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
>
> test_check("ctsem")
*** caught segfault ***
address 0, cause 'memory not mapped'
Traceback:
1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
2: mxRun(model, suppressWarnings = T, unsafe = T, silent = T, intervals = FALSE)
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
7: try(mxRun(model, suppressWarnings = T, unsafe = T, silent = T, intervals = FALSE))
8: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
9: suppressWarnings(try(mxRun(model, suppressWarnings = T, unsafe = T, silent = T, intervals = FALSE)))
10: mxTryHard(model, initialTolerance = 1e-14, initialGradientIterations = 1, showInits = showInits, checkHess = TRUE, greenOK = FALSE, iterationSummary = iterationSummary, bestInitsOutput = FALSE, verbose = verbose, extraTries = retryattempts, loc = 0.5, scale = 0.2, paste = FALSE)
11: ctFit(AnomAuth, AnomAuthmodel)
12: eval(code, test_env)
13: eval(code, test_env)
14: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
15: doTryCatch(return(expr), name, parentenv, handler)
16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
17: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
22: test_code(desc, code, env = parent.frame())
23: test_that("anomauth", { data(AnomAuth) AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2), n.latent = 2, n.manifest = 2, MANIFESTVAR = diag(0, 2), Tpoints = 5) AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel) expect_equal(23415.929, AnomAuthfit$mxobj$output$Minus2LogLikelihood)})
24: eval(code, test_env)
25: eval(code, test_env)
26: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
34: test_code(NULL, exprs, env)
35: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
36: force(code)
37: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) end_context() })
38: FUN(X[[i]], ...)
39: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
40: force(code)
41: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
43: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
44: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
45: test_check("ctsem")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86
Version: 2.7.6
Check: re-building of vignette outputs
Result: WARN
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 index (1) from vector of Rf_length (0).
Error in lapply(names(model@matrices), getParametersHelper, model, free, :
trying to get slot "matrices" from an object (class "try-error") that is not an S4 object
Beginning initial fit attempt
Lowest minimum so far: 4176.87456133426
Solution found
Solution found! Final fit=4176.8746 (started at 8240.9725) (1 attempt(s): 1 valid, 0 errors)
Running ctsemCarefulFit with 15 parameters
Beginning initial fit attempt
Lowest minimum so far: 4196.73541494076
Solution found
Solution found! Final fit=4196.7354 (started at 4882.1498) (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
*** caught segfault ***
address fa367b50, cause 'memory not mapped'
Traceback:
1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
2: mxRun(ctfitobj$mxobj, intervals = TRUE)
3: ctCI(example1fit, confidenceintervals = "DRIFT")
4: eval(expr, envir, enclos)
5: eval(expr, envir, enclos)
6: withVisible(eval(expr, envir, enclos))
7: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
8: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
9: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
10: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
11: evaluate::evaluate(...)
12: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
13: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
14: block_exec(params)
15: call_block(x)
16: process_group.block(group)
17: process_group(group)
18: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
19: process_file(text, output)
20: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
21: engine$weave(file, quiet = quiet, encoding = enc)
22: doTryCatch(return(expr), name, parentenv, handler)
23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
24: tryCatchList(expr, classes, parentenv, handlers)
25: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
26: buildVignettes(dir = "/home/ripley/R/packages/tests32/ctsem.Rcheck/vign_test/ctsem")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86