[BioC] Rsamtools installation error

[Murli]

Martin,
I tried your suggested way again and I still get the same.

** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so':
  /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined
symbol: gzopen64
Error: loading failed
Execution halted
ERROR: loading failed

Here is other output
 R CMD ldd Rsamtools/src/Rsamtools.so
        linux-vdso.so.1 =>  (0x00007fff477d4000)
        libz.so.1 => /lib64/libz.so.1 (0x00002b190cb28000)
        libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00002b190cd3d000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b190cf4a000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b190d165000)
        librt.so.1 => /lib64/librt.so.1 (0x00002b190d4bd000)
        /lib64/ld-linux-x86-64.so.2 (0x00000035e2400000)

 objdump -T /lib/x86_64-linux-gnu/libz.so.1|grep gzopen64
objdump: '/lib/x86_64-linux-gnu/libz.so.1': No such file


How do I define gzopen64?
Thanks for you suggestions.../Murli

On Wed, Jul 11, 2012 at 3:24 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 07/11/2012 12:10 PM, Dan Tenenbaum wrote:
>>
>> On Wed, Jul 11, 2012 at 12:01 PM, Murli [guest]<guest at bioconductor.org>
>> wrote:
>>>
>>>
>>> Hi,
>>> I am trying to install Rsamtools (Redhat linux ) and I have been getting
>>> the following error
>>> #######################################
>>> ** testing if installed package can be loaded
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>    unable to load shared object
>>> '/usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so':
>>>    /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined
>>> symbol: gzopen64
>>> Error: loading failed
>>> Execution halted
>>> ERROR: loading failed
>>> * removing ‘/usr/local/lib64/R/library/Rsamtools’
>>> #########################################
>>>
>>> I have libz installed
>>> /sbin/ldconfig -p|grep libz
>>>          libz.so.1 (libc6,x86-64) =>  /lib64/libz.so.1
>>>          libz.so.1 (libc6,x86-64) =>  /usr/lib64/libz.so.1
>>>          libz.so.1 (libc6) =>  /lib/libz.so.1
>>>          libz.so.1 (libc6) =>  /usr/lib/libz.so.1
>>>          libz.so (libc6,x86-64) =>  /lib64/libz.so
>>>          libz.so (libc6,x86-64) =>  /usr/lib64/libz.so
>>>          libz.so (libc6) =>  /lib/libz.so
>>>          libz.so (libc6) =>  /usr/lib/libz.so
>>>
>>> I checked the LD_LIBRARY_PATH using the following
>>> R CMD env | grep LD_LIBRARY_PATH
>>>
>>> LD_LIBRARY_PATH=/usr/local/lib64/R/lib:/usr/local/lib64:/usr/lib/jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64
>>>
>>> Please let me know if there is anything else that I need to check.
>>
>>
>>
>> What command are you using to try and install Rsamtools?
>> Try this command:
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("Rsamtools")
>>
>> It seems like the error you are getting is because zlibbioc is not
>> being installed, but if you used the above command, it would be
>> installed.
>
>
> zlibbioc is primarily used for Windows compatibility; on Linux the build
> will use a system-supplied zlib. The possibilities are (a) that the system
> zlib does not contain gzopen64 or (b) R is not finding libz.
>
> I think to debug you'll want to download the source
>
>   source("http://bioconductor.org/biocLite.R")
>   download.packages("Rsamtools", repos=biocinstallRepos(), dest=".")
>
> Then from the command line
>
>   tar xzf Rsamtools_
>   R CMD INSTALL Rsamtools
>
> and then check for the libz to which Rsamtools.so is linked
>
>   R CMD ldd Rsamtools/src/Rsamtools.so
>
> which for me says
>
> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f83e6a2a000)
>
> and then verify gzopen64 is defined
>
>  objdump -T /lib/x86_64-linux-gnu/libz.so.1|grep gzopen64
> 0000000000003580 g    DF .text  000000000000000f  Base        gzopen64
>
> Martin
>
>
>>
>> Dan
>>
>>
>>> Thanks for your help.
>>> Cheers../Murli
>>>
>>>
>>>
>>>
>>>   -- output of sessionInfo():
>>>
>>> sessionInfo()
>>> R version 2.15.0 (2012-03-30)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> 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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=C                 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
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
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>>
>>
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>
>
>
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