[Bioc-sig-seq] Problem compiling Rsamtools 1.0.7

[Martin Morgan]

On 08/10/2010 02:25 PM, Lapointe, David wrote:
> Hi I using R-2.11 (with shared libs) and trying to installl Rsamtools  ( 2.6.26.8-57.fc8  x86_64).
> 
> I am using the R CMD method to get this to work.
> R CMD INSTALL Rsamtools_1.0.7.tar.gz
> ...
> ** installing help indices
>   converting help for package ‘Rsamtools’
>     finding HTML links ... done
>     BamViews-class                          html
>     finding level-2 HTML links ... done
> 
>     Rsamtools-package                       html
>     ScanBamParam-class                      html
>     readBamGappedAlignments                 html
> Rd warning: ./man/readBamGappedAlignments.Rd:10: missing file link ‘GappedAlignments’
> Rd warning: ./man/readBamGappedAlignments.Rd:36: missing file link ‘GappedAlignments’
>     readPileup                              html
> Rd warning: ./man/readPileup.Rd:34: missing file link ‘GRanges’
>     scanBam                                 html
> ** building package indices ...
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library '/usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so':
>   /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol: ecrc32
> ERROR: loading failed
> * removing ‘/usr/local/lib64/R/library/Rsamtools’
> 
> libz.so.1 is present in /usr/lib64
> 
> I am not sure what library contains ecrc32 

My guess is in a version of zlib (which has crc32) distributed by EMBOSS
(which prepends 'e' to zlib symbols, so ecrc32), as in

http://article.gmane.org/gmane.science.biology.informatics.conductor/28862

When you built Rsamtools I guess it found the zlib.h from EMBOSS, but
when trying to run it finds the system library. I don't know why zlib.h
from EMBOSS gets found by other applications; it is a configuration
nuance on EMBOSS' side.

Martin

> 
> Davdi
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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