[BioC] Rsamtools installation error

[Martin Morgan]

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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