Hi Martin,
I had the same issue only yesterday installing ShortRead on a R-2.11.0 fresh
source installation for redhat enterprise linux with
'--prefix=/opt/R/R-2.11.0.' The dependancy Rsamtools failed using
biocLite("ShortRead")

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library
'/opt/R/R-2.11.0/lib64/R/library/Rsamtools/libs/Rsamtools.so':
  /opt/R/R-2.11.0/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined
symbol: deflateSetHeader
ERROR: loading failed
* removing ‘/opt/R/R-2.11.0/lib64/R/library/Rsamtools’

I also traced this to libz.so.1, in this case it was incorrectly pointing to
an installation of staden on the machine, which I traced by also attempting
a manual install;

ldd /tmp/Rsamtools/src/Rsamtools.so
libz.so.1 =>
/opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries/libz.so.1
(0x00002acd7097d000)
...

locate libz.so.1
/opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries/libz.so.1
/opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries/libz.so.1.2.2
/usr/lib/libz.so.1
/usr/lib/libz.so.1.2.3
/usr/lib64/libz.so.1
/usr/lib64/libz.so.1.2.3

The environment variable LD_LIBRARY_PATH was being set to

/opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries

What seemed to be happening was the R ./configure was picking up the
LD_LIBRARY_PATH to staden (e.g. in ./configure log:  PATH:
/opt/staden-linux-x86_64-1-7-1b/linux-x86_64-bin), so I unset the
environment variable reinstalled R, then installed ShortRead using biocLite
without problems


Cheers,

Marcus

> version               _
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          11.0
year           2010
month          04
day            22
svn rev        51801
language       R
version.string R version 2.11.0 (2010-04-22)


On Thu, Jun 3, 2010 at 6:13 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> 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 āRsamtoolsā
> >
> >     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
> > āGappedAlignmentsā
> >
> > Rd warning: ./man/readBamGappedAlignments.Rd:36: missing file link
> > āGappedAlignmentsā
> >
> >     readPileup                              html
> >
> > Rd warning: ./man/readPileup.Rd:34: missing file link āGRangesā
> >
> >     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@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 ā/usr/lib64/R/library/Rsamtoolsā
> >
> >
> >
> >
> >
> >> 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]]
> >
> >
> >
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
>
> --
> 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
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

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