R help - Jun 2013 - Function nlme::lme in Ubuntu (but not Win or OS X): "Non-positive definite approximate variance-covariance"

Dear all,

I am estimating a mixed-model in Ubuntu Raring (13.04¸ amd64), with the
code:

fm0 <- lme(rt ~ run + group * stim * cond,
                 random=list(
                   subj=pdSymm(~ 1 + run),
                   subj=pdSymm(~ 0 + stim)),
                 data=mydat1)

When I check the approximate variance-covariance matrix, I get:
> fm0$apVar
[1] "Non-positive definite approximate variance-covariance"


*However*, if I do the same on a Windows or a Mac OS X machine, I get:
> fm0$apVar
               reStruct.subj1 reStruct.subj2 reStruct.subj3 reStruct.subj1
reStruct.subj1   1.952757e-01   3.130089e-01   5.766955e-01  -0.1034862377
reStruct.subj2   3.130089e-01   5.703211e-01   9.864047e-01  -0.1937902915
reStruct.subj3   5.766955e-01   9.864047e-01   1.861434e+00  -0.3303689957
reStruct.subj1  -1.034862e-01  -1.937903e-01  -3.303690e-01   0.0941652375
reStruct.subj2  -3.464557e-03  -5.933008e-03  -1.102904e-02   0.0163847582
reStruct.subj3  -6.826057e-01  -1.186231e+00  -2.122872e+00   0.3705613715
lSigma          -2.058254e-06  -4.764783e-06   1.653583e-05  -0.0000146693
               reStruct.subj2 reStruct.subj3        lSigma
reStruct.subj1  -3.464557e-03  -6.826057e-01 -2.058254e-06
reStruct.subj2  -5.933008e-03  -1.186231e+00 -4.764783e-06
reStruct.subj3  -1.102904e-02  -2.122872e+00  1.653583e-05
reStruct.subj1   1.638476e-02   3.705614e-01 -1.466930e-05
reStruct.subj2   1.931738e-02  -2.020354e-02 -1.925015e-05
reStruct.subj3  -2.020354e-02   2.825301e+00  2.967063e-05
lSigma          -1.925015e-05   2.967063e-05  6.299813e-05
attr(,"Pars")
reStruct.subj1 reStruct.subj2 reStruct.subj3 reStruct.subj1 reStruct.subj2
      4.570267       4.299735       1.282732       4.859346       3.206102
reStruct.subj3         lSigma
     -2.631377       5.308304
attr(,"natural")
[1] TRUE


I am unable to figure out the reason why I get such a difference in the
output: all the machines are running the latest version of R (3.0.1) and
nlme package (3.1-109) as of today (updated from the CRAN master site).

Many thanks in advance for any suggestions,

best

giuseppe



-- 
Giuseppe Pagnoni
Dip. Scienze Biomediche, Metaboliche e Neuroscienze
Sezione Fisiologia e Neuroscienze
Univ. di Modena e Reggio Emilia
Via Campi 287
I-41125 Modena, Italy
Tel: +39-059-205-5742
Fax: +39-059-205-5363

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