[Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor

[Martin Morgan]

Hi Kanika --

On 06/02/2010 05:48 AM, kanika arora wrote:
> Hi ALL,
> 
> * *
> 
> I am trying to install l.0.2 version Rsamtools from Bioconductor and facing
> problems. Please find the error message mentioned below:
> 
> 
> 
> 
> 
> ** help
> 
> *** installing help indices
> 
>   converting help for package âRsamtoolsâ
> 
>     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
> âGappedAlignmentsâ
> 
> Rd warning: ./man/readBamGappedAlignments.Rd:36: missing file link
> âGappedAlignmentsâ
> 
>     readPileup                              html
> 
> Rd warning: ./man/readPileup.Rd:34: missing file link âGRangesâ
> 
>     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/lib64/R/library/Rsamtools/libs/Rsamtools.so':
> 
>   /usr/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol:
> gzopen64


Rsamtools depends on having a system 'libz' installed. Does your system
have this (e.g., for me,

mtmorgan at mm:~> /sbin/ldconfig -p|grep libz
[...snip...]
	libz.so.1 (libc6,x86-64) => /lib64/libz.so.1
	libz.so.1 (libc6) => /lib/libz.so.1
	libz.so (libc6,x86-64) => /usr/lib64/libz.so

This should be checked during package configuration, so I'm a little
surprised that the error comes up at this point. Can you confirm that
you are installing this with

  biocLite('Rsamtools')

? I'm a little nervous that when you say you 'installed all the
dependencies' that you are doing something else -- biocLite('Rsamtools')
installs the correct version of the dependencies for your version of R.

Martin

> ERROR: loading failed
> 
> * removing â/usr/lib64/R/library/Rsamtoolsâ
> 
> 
> 
> 
> 
>> sessionInfo()
> 
> R version 2.11.0 (2010-04-22)
> 
> x86_64-redhat-linux-gnu
> 
> 
> 
> locale:
> 
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> 
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> 
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
> 
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> 
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> 
> 
> attached base packages:
> 
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> 
> other attached packages:
> 
> [1] goseq_1.0.1            geneLenDataBase_0.99.4 BiasedUrn_1.03
> 
> 
> 
> loaded via a namespace (and not attached):
> 
>  [1] AnnotationDbi_1.10.1 Biobase_2.8.0        Biostrings_2.16.2
> 
>  [4] BSgenome_1.16.1      DBI_0.2-5            GenomicRanges_1.0.1
> 
>  [7] grid_2.11.0          IRanges_1.6.4        lattice_0.18-5
> 
> [10] Matrix_0.999375-38   mgcv_1.6-1           nlme_3.1-96
> 
> [13] RCurl_1.4-2          RSQLite_0.9-1        rtracklayer_1.8.1
> 
> [16] tools_2.11.0         XML_3.1-0
> 
> 
> 
> 
> 
> I already installed all the dependencies of the package. Please guide me in
> this context.
> 
> Thanks in advance,
> 
> Kanika
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> 
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-- 
Martin Morgan
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