[R] lapack routines cannot be loaded [Help request]

[Prof Brian Ripley]

On 22/11/2012 11:23, Manca Marco (PATH) wrote:
>
> Dear BioConductor and R fellow users
>
> I apologize in advance for double posting, but I am not sure which list would actually be best fit for this message.

The list relevant to the installation of R you used.  Was this a binary 
installation?: if so R-sig-debian.

See the NEWS for R 2.15.2, especially

     • chol(pivot = TRUE, LINPACK = FALSE) is now available using LAPACK
       3.2 subroutine DPSTRF.

     • If an external LAPACK is used, it must be version 3.2 or later.

Looks like yours is not (that is a >2.5 years old version of Ubuntu, but 
not as old as LAPACK 3.2: is it fully updated, as 'Ubuntu 10.04' does 
seem to have a package for LAPACK 3.2.1 available?).

A solution is to build R from the sources for yourself: R includes a 
tested LAPACK later than the one your Ubuntu provides, including lots of 
patches.

>
> I am experiencing a weird error with my R installation on Ubuntu 10.04.4 (LTS) 64bit:
>
> When I run R on the terminal everything goes smoothly:
>
> $R
> R version 2.15.2 (2012-10-26) -- "Trick or Treat"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>    Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.

That proves nothing much: try example(chol).

>
>
> However, as soon as I try to use limma (or WGCNA... I haven't tried other packages yet) the following mistake pops up ( lapack routines cannot be loaded )
>
>> library(limma)
>
>> fit <- lmFit(Data.rma, design)
> Error in chol2inv(fit$qr$qr, size = fit$qr$rank) :
>    lapack routines cannot be loaded
> In addition: Warning message:
> In chol2inv(fit$qr$qr, size = fit$qr$rank) :
>    unable to load shared object '/usr/lib64/R/modules//lapack.so':
>    /usr/lib64/R/modules//lapack.so: undefined symbol: dpstrf_
>>
>
> It is independent of the dataset I am using.
>
> I have already tried to recompile the whole BioConductor set of packages, and updated the general packages via CRAN, but nothing changed.
>
> Following I am attaching my sessionInfo(), and you will find enclosed to this email the (incriminated) lapack.so file, should you be willing/able to take a look at it.
>
> Any insights into what could be going on, and how to address the issue?
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=C                LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] limma_3.12.3          hgu133plus2cdf_2.10.0 AnnotationDbi_1.18.4
> [4] affy_1.34.0           Biobase_2.16.0        BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.24.0         BiocInstaller_1.4.9   DBI_0.2-5
> [4] IRanges_1.14.4        preprocessCore_1.18.0 RSQLite_0.11.2
> [7] stats4_2.15.2         tools_2.15.2          zlibbioc_1.2.0
>
>
>
> Thank you in advance,
> Marco
>
>
> --
> Dr Marco Manca
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
>
> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
> Visiting address: UNS40 West building - 5th floor Room5.544, Universiteit Singel 40, 6229  HX Maastricht
>
> E-mail: m.manca at maastrichtuniversity.nl
> Office telephone: +31(0)433884289
> Personal mobile: +31(0)626441205
> Twitter: @markomanka



-- 
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