[R] make check for R-1.6.2 on IBM AIX

[Laurent Gautier]

On Mon, Jan 20, 2003 at 08:05:53AM +0000, ripley at stats.ox.ac.uk wrote:
> Is this a vanilla installation, not using any BLAS routines?  If so, that
> error code means that the svd was called with a negative number of columns
> (&p in the call).  I don't see how that can happen without some memory
> corruption.

Thanks for fast answer.

This is a vanilla (trial of) install. The funny thing is that it


I tried a 
source("tests/Examples/mva.R")

and get:

Error in optim(start, FAfn, FAgr, method = "L-BFGS-B", lower = lower,  : 
        non-finite value supplied by optim
In addition: Warning messages: 
1: dist(.,"binary"): treating non-finite values as NA 
2: dist(.,"binary"): treating non-finite values as NA 
>
> traceback()
6: optim(start, FAfn, FAgr, method = "L-BFGS-B", lower = lower, 
       upper = 1, control = c(list(fnscale = 1, parscale = rep(0.01, 
           length(start))), control), q = factors, S = cmat)
5: factanal.fit.mle(cv, factors, start[, i], max(cn$lower, 0), cn$opt)
4: factanal(~v1 + v2 + v3 + v4 + v5 + v6, factors = 3, scores = "Bartlett")
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1: source("tests/Examples/mva-Ex.R")


I tried make check on the 1.6.1 I installed 2 weeks ago (I can't remember
for sure if I did 'make check', but usually I do).. and make check dies
on base (see below)

> ## Keywords: 'math'.
> 
> 
> cleanEx(); ..nameEx <- "kronecker"
> ###--- >>> `kronecker' <<<----- Kronecker products on arrays
> 
>       ## alias         help(kronecker)
>       ## alias         help(\%x\%)
> 
> ##___ Examples ___:
> 
> # simple scalar multiplication
> ( M <- matrix(1:6, ncol=2) )
     [,1] [,2]
[1,]    1    4
[2,]    2    5
[3,]    3    6
> stopifnot(kronecker(4, M)==4 * M)
Error in if (!(is.logical(r <- eval(ll[[i]])) && all(r))) stop(paste(deparse(mc[[i +  : 
        missing value where logical needed
Execution halted


Your hypothesis of 'physical' reasons for the fail seems really worth a look at.
Would anyone know how to check hardware integrity on an IBM AIX ?


Thanks in advance,



L.

> 
> The usual ideas apply: run that example on its own, then look at
> traceback(), add debugging code etc ....
> 
> We have seen similar (but not the same) issues where a BLAS was used that 
> contained (broken) parts of LAPACK.
> 
> On Mon, 20 Jan 2003, Laurent Gautier wrote:
> 
> > Dear all,
> > 
> > The 'make check' step fails for the pacakge mva on IBM AIX.
> > The tail of the Rout log file looks like:
> > 
> > > for(factors in 2:4) print(update(Harman23.FA, factors = factors))
> > 
> > Call:
> > factanal(factors = factors, covmat = Harman23.cor)
> > 
> > Uniquenesses:
> >         height       arm.span        forearm      lower.leg         weight 
> >          0.170          0.107          0.166          0.199          0.089 
> > bitro.diameter    chest.girth    chest.width 
> >          0.364          0.416          0.537 
> > 
> > Loadings:
> >                Factor1 Factor2
> > height         0.865   0.287  
> > arm.span       0.927   0.181  
> > forearm        0.895   0.179  
> > lower.leg      0.859   0.252  
> > weight         0.233   0.925  
> > bitro.diameter 0.194   0.774  
> > chest.girth    0.134   0.752  
> > chest.width    0.278   0.621  
> > 
> >                Factor1 Factor2
> > SS loadings      3.335   2.617
> > Proportion Var   0.417   0.327
> > Cumulative Var   0.417   0.744
> > 
> > Test of the hypothesis that 2 factors are sufficient.
> > The chi square statistic is 75.74 on 13 degrees of freedom.
> > The p-value is 6.94e-11 
> > 
> > Call:
> > factanal(factors = factors, covmat = Harman23.cor)
> > 
> > Uniquenesses:
> >         height       arm.span        forearm      lower.leg         weight 
> >          0.127          0.005          0.193          0.157          0.090 
> > bitro.diameter    chest.girth    chest.width 
> >          0.359          0.411          0.490 
> > 
> > Loadings:
> >                Factor1 Factor2 Factor3
> > height          0.886   0.267  -0.130 
> > arm.span        0.937   0.195   0.280 
> > forearm         0.874   0.188         
> > lower.leg       0.877   0.230  -0.145 
> > weight          0.242   0.916  -0.106 
> > bitro.diameter  0.193   0.777         
> > chest.girth     0.137   0.755         
> > chest.width     0.261   0.646   0.159 
> > 
> >                Factor1 Factor2 Factor3
> > SS loadings      3.379   2.628   0.162
> > Proportion Var   0.422   0.329   0.020
> > Cumulative Var   0.422   0.751   0.771
> > 
> > Test of the hypothesis that 3 factors are sufficient.
> > The chi square statistic is 22.81 on 7 degrees of freedom.
> > The p-value is 0.00184 
> > Error in La.svd(B) : error code 3 from Lapack routine dgesdd
> > Execution halted
> > 
> > 
> > Any hint ?
> > 
> > 
> > 
> > Laurent
> > 
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list
> > http://www.stat.math.ethz.ch/mailman/listinfo/r-help
> > 
> 
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595
> 

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