CRAN Package Check Results for Package ctsem

Last updated on 2019-05-26 16:48:19 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.9.0 576.39 768.30 1344.69 NOTE
r-devel-linux-x86_64-debian-gcc 2.9.0 554.34 880.17 1434.51 NOTE
r-devel-linux-x86_64-fedora-clang 2.9.0 2.41 ERROR
r-devel-linux-x86_64-fedora-gcc 2.9.0 1218.65 NOTE
r-devel-windows-ix86+x86_64 2.9.0 350.00 801.00 1151.00 NOTE --no-vignettes
r-patched-linux-x86_64 2.9.0 NOTE
r-patched-solaris-x86 2.9.0 9.30 ERROR
r-release-linux-x86_64 2.9.0 598.14 1116.31 1714.45 WARN
r-release-windows-ix86+x86_64 2.9.0 489.00 617.00 1106.00 NOTE --no-vignettes
r-release-osx-x86_64 2.9.0 FAIL
r-oldrel-windows-ix86+x86_64 2.9.0 464.00 592.00 1056.00 NOTE --no-vignettes
r-oldrel-osx-x86_64 2.9.0 NOTE

Additional issues

rchk

Check Details

Version: 2.9.0
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-gcc, r-patched-linux-x86_64, r-release-linux-x86_64, r-oldrel-osx-x86_64

Version: 2.9.0
Check: package dependencies
Result: ERROR
    Package required but not available: ‘OpenMx’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.9.0
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 7.1Mb
     sub-directories of 1Mb or more:
     data 1.4Mb
     libs 3.8Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.9.0
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: 2.9.0
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-patched-solaris-x86

Version: 2.9.0
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
    Running ctsem with 16 parameters
    
    Beginning initial fit attempt
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4345.86257632205
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 3311049125.22432, 1041696.60387924, 214305.512725799, 131985.095712234, 2405.65662920449, 1769.95653433505, 739.286500700386, 453.144793018098, 333.890562802412, 90.9674218693461, 80.8042405395096, 0.266912385998877, 0.0000055100226464512, -0.00000186480020024136, -0.000308846890295564, -370.423096784689
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4345.67885673806
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 2618047817.04154, 837167.043413461, 188690.838160603, 100154.892263768, 2406.6463572125, 1271.13777569503, 818.840020645678, 352.309610580106, 336.910679893635, 80.9945982540137, 49.3241961232139, 16.897827652578, 0.00117383616346471, 0.0000481691555906827, 0.00000630535682628709, -0.15540981206422
    
    Beginning fit attempt 2 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4344.85653907275
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 17038701402.6611, 5368656.73133397, 656536.388994896, 380554.155793188, 2396.50661057778, 1573.61116145428, 638.677128730737, 389.542887973285, 335.316002191182, 81.1566816949651, 44.4534173100504, 7.39914113800361, 0.0542374305128759, 0.00298124445951044, -0.000122247270197416, -0.000191552916788729
    
    Beginning fit attempt 3 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4601.73308025476 vs 4344.85653907275
    
    Beginning fit attempt 4 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4574.8590324841 vs 4344.85653907275
    
    Beginning fit attempt 5 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     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
    Running ctsem with 16 parameters
    
     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
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4192.26366461216
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 625836055.269236, 81018763.6742807, 46361.903073859, 9548.00488013767, 1619.55293403991, 1495.68075978095, 364.977031507107, 286.366796625717, 259.530016033797, 168.598144062836, 114.488460881861, 88.8898986786303, 49.3742744857105, 0.00498096562110518, 0.0000580459854706916, -0.000000970959143398613
    
    Beginning fit attempt 8 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4727.62667671092 vs 4192.26366461216
    
    Beginning fit attempt 9 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4865.47097947429 vs 4192.26366461216
    
    Beginning fit attempt 10 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     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
    Running ctsem with 16 parameters
    
     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
    Running ctsem with 16 parameters
    
     Lowest minimum so far: 4182.84944360135
     OpenMx status code 6 not in list of acceptable status codes, (0,0)
     Not all eigenvalues of the Hessian are positive: 3338752461.75017, 583315497.234517, 37579.8842436549, 9281.98672739842, 1371.21871599967, 1183.62891484842, 377.652888797112, 349.6685229624, 255.688659664077, 204.777373780502, 113.877555901521, 106.829980177414, 88.4263946545114, 41.6004413386318, 0.000421925567755154, -0.000000286465952562453
    
    Beginning fit attempt 13 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4182.90477138925 vs 4182.84944360135
    
    Beginning fit attempt 14 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 4182.90032210653 vs 4182.84944360135
    
    Beginning fit attempt 15 of at maximum 15 extra tries
    Running ctsem with 16 parameters
    
     Fit attempt worse than current best: 33422.4841631746 vs 4182.84944360135
    
    Retry limit reached
    
     Retry limit reached; 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
    Running ctsem with 15 parameters
    
    Beginning initial fit attempt
    Running ctsem with 15 parameters
    
     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
    Running ctsem with 19 parameters
    
    Beginning initial fit attempt
    Running ctsem with 19 parameters
    
     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
    Running ctsem with 23 parameters
    
    Beginning initial fit attempt
    Running ctsem with 23 parameters
    
     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 0
    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 0
    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 0
    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 0
    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
    Running ctsem with 18 parameters
    
    Beginning initial fit attempt
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -486.477231264032
     Not all eigenvalues of the Hessian are positive: 3277.9592085502, 1424.19126296187, 455.880772892058, 288.390643087629, 236.815726350881, 103.681758725295, 70.8796372792756, 38.5593710518425, 24.9222452327192, 18.0205023407241, 15.1226515563004, 13.3411803531168, 9.01069959630285, 4.89762271802782, 2.16337324442878, 0.0000199233030990023, 0.00000667980480678951, -4.65882068686477e-20
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -486.477231264032
    
    Solution found
    
    
     Solution found! Final fit=-486.47723 (started at -393.83023) (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
    Running ctsem with 18 parameters
    
    Beginning initial fit attempt
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -467.644388488913
     Not all eigenvalues of the Hessian are positive: 11278.719840117, 2923.94751410656, 1487.81676234198, 616.963187653252, 431.437589781431, 238.364094905609, 203.210699806806, 105.937982634067, 36.4376023478689, 28.5806328522575, 18.3351627785344, 9.31686627704905, 8.30381140537423, 2.62339714738621, 0.75309017407005, 0.000106255919688584, 0.0000452858980633776, -0.00000311986054826905
    
    Beginning fit attempt 1 of at maximum 15 extra tries
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -467.673111363843
     Not all eigenvalues of the Hessian are positive: 11074.1368302195, 2935.80924201668, 1539.97622261394, 641.189695170188, 437.131429560212, 230.335194780463, 196.641206707523, 104.774016988609, 37.3389990456653, 28.8423478875588, 18.6542294075633, 9.32480650952623, 8.31475235480669, 2.58385696206127, 0.770323391102798, 0.232340585532681, 0.00000987861554734859, -0.000000714958012305043
    
    Beginning fit attempt 2 of at maximum 15 extra tries
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -467.673111363864
     Not all eigenvalues of the Hessian are positive: 11074.1229425048, 2935.8060781009, 1539.97129568288, 641.183557100991, 437.123414748954, 230.329179430085, 196.633034166261, 104.770356587222, 37.335312585661, 28.842311018792, 18.6536554192359, 9.3238150987864, 8.31417409332615, 2.58454970923145, 0.770119761212594, 0.232640963840872, 0.00000170350404718277, -0.00000922737065733501
    
    Beginning fit attempt 3 of at maximum 15 extra tries
    Running ctsem with 18 parameters
    
     Lowest minimum so far: -471.600336675471
    
    Solution found
    
    
     Solution found! Final fit=-471.60034 (started at 92.435111) (4 attempt(s): 4 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
    Running ctsem with 11 parameters
    
    Beginning initial fit attempt
    Running ctsem with 11 parameters
    
     Lowest minimum so far: -138.198676576818
    
    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
    Running ctsem multigroup with 13 parameters
    
    Beginning initial fit attempt
    Running ctsem multigroup with 13 parameters
    
     Lowest minimum so far: -192.388341205028
    
    Solution found
    
    
     Solution found! Final fit=-192.38834 (started at 6331.5841) (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
    Running ctsem with 7 parameters
    
    Beginning initial fit attempt
    Running ctsem with 7 parameters
    
     Lowest minimum so far: 741.671385049888
    
    Solution found
    
    
     Solution found! Final fit=741.67139 (started at 1245.9723) (1 attempt(s): 1 valid, 0 errors)
    
    transformedParams=TRUE and non positive DIFFUSION diagonal specified, setting to .00001.
    Running ctsem with 9 parameters
    
    Beginning initial fit attempt
    Killed
Flavor: r-release-linux-x86_64

Version: 2.9.0
Check: installed package size
Result: NOTE
     installed size is 86.7Mb
     sub-directories of 1Mb or more:
     data 1.4Mb
     libs 83.3Mb
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.9.0
Check: S3 generic/method consistency
Result: FAIL
    
Flavor: r-release-osx-x86_64