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.ma...@maastrichtuniversity.nl
Office telephone: +31(0)433884289
Personal mobile: +31(0)626441205
Twitter: @markomanka
--
Brian D. Ripley, rip...@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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