prcomp show "Error in La.svd(x, nu, nv) : LAPACK routines cannot be loaded"
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peirinl • 0
@peirinl-14078
Last seen 17 months ago

I am running a microarray data analysis, 

    raw_data = read.celfiles(....... )

    exp_raw <- log2(exprs(raw_data)) 

    PCA_raw <- prcomp(t(exp_raw), scale = FALSE)

but I got an error,

    Error in La.svd(x, nu, nv) : LAPACK routines cannot be loaded

    Besides: Warning message:

    In La.svd(x, nu, nv) :

       unable to load share-object'/Library/Frameworks/R.framework/Resources/modules//lapack.so' : `maximal number of DLLs reached...

 

this is the packages I loaded

library(Biobase, oligoClasses, knitr, BiocStyle, oligo, geneplotter, ggplot2, dplyr, LSD, gplots, RColorBrewer, ArrayExpress, arrayQualityMetrics, stringr, matrixStats, topGO, genefilter, pd.hugene.1.0.st.v1, hugene10sttranscriptcluster.db, pheatmap, mvtnorm, DAAG, multcomp, limma, ReactomePA, clusterProfiler, openxlsx, devtools, biomaRt, EnrichmentBrowser)

my session info

setting  value                       

 version  R version 3.4.1 (2017-06-30)

 system   x86_64, darwin15.6.0        

 ui       RStudio (1.0.153)           

 language (EN)                     

 date     2017-10-03   

Can someone tell me how to fix this?

prcomp affymetrix microarrays • 1.9k views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 2 hours ago
United States

While you may be trying to analyze data using Bioconductor packages, this isn't technically a Bioconductor issue, and would be better asked on R-help (r-help@r-project.org).

However, it just so happens that there was a rather lengthy discussion recently on Bioc-devel about this same subject, and the answer is to change the R environment variable R_MAX_NUM_DLLS. See for example the 'Note' section here.

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Entering edit mode

An alternative solution less technical solution might be to avoid loading so many packages at the same time, especially dplyr and friends, that might not be needed for the current calculation. That would avoid the DLL limit being exceeded.

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