[BioC] Rsamtools installation error
Murli
murlinair at gmail.com
Wed Jul 11 22:59:33 CEST 2012
Thanks, I checked each of my libz installations for gzopen64 using
the following command
objdump -T /usr/local/lib/libz.zo.1 | grep gzopen64
I put the one that contained it in the LD_LIBRARY_PATH by creating a
~/.R/Makevars file.
sourced the Makevars file and then was able to install it
successfully. Hope these notes help others who may face the same
problem.
Cheers../Murli
On Wed, Jul 11, 2012 at 4:30 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 07/11/2012 01:21 PM, Murli wrote:
>>
>> objdump -T /lib64/libz.so.1 |grep gzopen64
>>
>> Did not return anything. Does that mean gzopen64 is not installed
>> present on my system?
>
>
> I think it means that your system has two (or more) versions of libz
> installed, one with and one without gzopen64. The installation finds the
> header file that says gzopen64 exists, but then finds the library file that
> does not contain it.
>
> It might help to use your package manager to figure out what the system libz
> is, and to update your installation to contain only that. Unfortunately, I'm
> not a Redhat user and can't provide any further instructions. Perhaps
> someone else on the list can. Martin
>
>
>
>>
>> Thanks ../Murli
>>
>>
>> On Wed, Jul 11, 2012 at 3:44 PM, Martin Morgan<mtmorgan at fhcrc.org> wrote:
>>>
>>> On 07/11/2012 12:42 PM, Murli wrote:
>>>>
>>>>
>>>> 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
>>>
>>>
>>>
>>> yes the installation still fails but you are left with the
>>> trouble-shooting
>>> artifacts
>>>
>>>
>>>
>>>>
>>>> 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
>>>
>>>
>>>
>>> use the path that R CMD ldd pointed to, for you
>>>
>>> objdump -T /lib64/libz.so.1 |grep gzopen64
>>>
>>>
>>>
>>>>
>>>>
>>>> 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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>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>
>>>
>>>
>>>
>>> --
>>> 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
>
>
>
> --
> 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
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