[BioC] Rsamtools installation error
Murli
murlinair at gmail.com
Wed Jul 11 22:21:49 CEST 2012
objdump -T /lib64/libz.so.1 |grep gzopen64
Did not return anything. Does that mean gzopen64 is not installed
present on my system?
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
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