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

[Martin Morgan]

On 11/22/2012 03:23 AM, 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.

It helps to narrow the problem down. It looks like the problem occurs when 
chol2inv is invoked, and in a plain R session

   R --vanilla

the following would fail

   example(chol2inv)

hence a problem with your installed R (since chol2inv is in the 'base' package), 
rather than Bioconductor. How did you install your R, especially how was it 
configured to use LAPACK? Have you modified your system's LAPACK after installing R?

Martin

>
>
> 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:
>
> $R
> R version 2.15.2 (2012-10-26) -- "Trick or Treat"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
>    Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>
> However, as soon as I try to use limma (or WGCNA... I haven't tried other packages yet) the following mistake pops up ( lapack routines cannot be loaded )
>
>> library(limma)
>
>> fit <- lmFit(Data.rma, design)
> Error in chol2inv(fit$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
>
>
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