[BioC] Rsamtools installation error
Martin Morgan
mtmorgan at fhcrc.org
Wed Jul 11 22:30:28 CEST 2012
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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