Wonderful! Installing "libopenblas-base" and "libopenblas-dev" worked like a charm.
Thank you so much for your help, I would have never figured this out myself⦠very best giuseppe -- Giuseppe Pagnoni, PhD 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 On Jun 7, 2013, at 1:52 PM, Dirk Eddelbuettel <[email protected]> wrote: > > On 7 June 2013 at 11:01, Giuseppe Pagnoni wrote: > | 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$apVar > | [1] "Non-positive definite approximate variance-covariance" > > This comes from the BLAS / LAPACK libraries which you can switch in Debian / > Ubuntu. Eg I (currently) have both defaults and openblas installed: > > edd@max:~$ COLUMNS=72 dpkg -l | grep -i "blas\|lapack" > ii libblas-dev 1.2.20110419 amd64 Basic Linear Algebra Subroutines > ii libblas-test 1.2.20110419 amd64 Basic Linear Algebra Subroutines > ii libblas3 1.2.20110419 amd64 Basic Linear Algebra Reference im > ii libblas3gf 1.2.20110419 all Transitional package for libblas > ii liblapack-dev 3.4.2-1~exp3 amd64 Library of linear algebra routine > ii liblapack-pic 3.4.2-1~exp3 amd64 Library of linear algebra routine > ii liblapack3 3.4.2-1~exp3 amd64 Library of linear algebra routine > ii liblapack3gf 3.4.2-1~exp3 all Transitional package for liblapac > ii libopenblas-ba 0.2.6-1~exp1 amd64 Optimized BLAS (linear algebra) l > ii libopenblas-de 0.2.6-1~exp1 amd64 Optimized BLAS (linear algebra) l > edd@max:~$ > > The virtual package libblas is provided by the reference blas, atlas > ("tuned") and openblas (multicore); similar for lapack. > > edd@max:~$ apt-cache search libblas > libblas-dev - Basic Linear Algebra Subroutines 3, static library > libblas-doc - Basic Linear Algebra Subroutines 3, documentation > libblas3 - Basic Linear Algebra Reference implementations, shared library > libatlas-base-dev - Automatically Tuned Linear Algebra Software, generic > static > libatlas3-base - Automatically Tuned Linear Algebra Software, generic shared > libblas-test - Basic Linear Algebra Subroutines 3, testing programs > libblas3gf - Transitional package for libblas > libopenblas-base - Optimized BLAS (linear algebra) library based on GotoBLAS2 > libopenblas-dev - Optimized BLAS (linear algebra) library based on GotoBLAS2 > edd@max:~$ > > Try installing another package and see if that matters. > > The Windows and OS X versions of R will have used its internally packaged > (not tuned, not multicore) BLAS/LAPACK. This can be changed there too; see > the R Admin+Inst manual. > > Dirk > > | *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 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 > | > | [[alternative HTML version deleted]] > | > | > | ---------------------------------------------------------------------- > | _______________________________________________ > | R-SIG-Debian mailing list > | [email protected] > | https://stat.ethz.ch/mailman/listinfo/r-sig-debian > > -- > Dirk Eddelbuettel | [email protected] | http://dirk.eddelbuettel.com [[alternative HTML version deleted]]
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