Manca Marco (PATH)
2012-Nov-22 11:23 UTC
[R] lapack routines cannot be loaded [Help request]
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. 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 ********************************************************************************************************************* This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or doctor-patient/consultant-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA *********************************************************************************************************************
Martin Morgan
2012-Nov-22 18:43 UTC
[R] [BioC] lapack routines cannot be loaded [Help request]
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 > > > ********************************************************************************************************************* > > This email and any files transmitted with it are confidential and solely for the use of the intended recipient. > > It may contain material protected by privacy or doctor-patient/consultant-client privilege. If you are not the intended recipient or the person responsible for > > delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. > > If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA > > ********************************************************************************************************************* > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
Prof Brian Ripley
2012-Nov-23 08:08 UTC
[R] lapack routines cannot be loaded [Help request]
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