[BioC] Rsamtools installation error
Martin Morgan
mtmorgan at fhcrc.org
Wed Jul 11 21:44:54 CEST 2012
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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>>
>>
>>
>> --
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>> 1100 Fairview Ave. N.
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>>
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--
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PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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