[Bioc-sig-seq] Problem installing latest version (1.0.2) RSamtools from Bioconductor

Martin Morgan mtmorgan at fhcrc.org
Thu Jun 3 02:41:03 CEST 2010


On 06/02/2010 05:05 PM, Marcus Davy wrote:
> Hi Martin,
> I had the same issue only yesterday installing ShortRead on a R-2.11.0 fresh
> source installation for redhat enterprise linux with
> '--prefix=/opt/R/R-2.11.0.' The dependancy Rsamtools failed using
> biocLite("ShortRead")
> 
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library
> '/opt/R/R-2.11.0/lib64/R/library/Rsamtools/libs/Rsamtools.so':
>   /opt/R/R-2.11.0/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined
> symbol: deflateSetHeader
> ERROR: loading failed
> * removing ‘/opt/R/R-2.11.0/lib64/R/library/Rsamtools’
> 
> I also traced this to libz.so.1, in this case it was incorrectly pointing to
> an installation of staden on the machine, which I traced by also attempting
> a manual install;
> 
> ldd /tmp/Rsamtools/src/Rsamtools.so
> libz.so.1 =>
> /opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries/libz.so.1
> (0x00002acd7097d000)
> ...
> 
> locate libz.so.1
> /opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries/libz.so.1
> /opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries/libz.so.1.2.2
> /usr/lib/libz.so.1
> /usr/lib/libz.so.1.2.3
> /usr/lib64/libz.so.1
> /usr/lib64/libz.so.1.2.3
> 
> The environment variable LD_LIBRARY_PATH was being set to
> 
> /opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries
> 
> What seemed to be happening was the R ./configure was picking up the
> LD_LIBRARY_PATH to staden (e.g. in ./configure log:  PATH:
> /opt/staden-linux-x86_64-1-7-1b/linux-x86_64-bin), so I unset the
> environment variable reinstalled R, then installed ShortRead using biocLite
> without problems

Thanks Marcus -- this helps to clarify -- an incomplete rather than
non-existent libz; the configure script in Rsamtools looks for a
particular function that I thought was relatively diagnostic of a modern
libz, so definitely this allows Rsamtools to get past configure before
breaking.

A couple of linux / R tricks. Preceding commands with 'R CMD' sets up
the environment to be the way R sees it, so

  R CMD env | grep LD_LIBRARY_PATH

might differ from env |grep LD_LIBRARY_PATH, and likewise for ldd; this
can be helpful to distinguish between 'my system is kind of funky' from
'my R is kind of funky'. It's also helpful in general, e.g., R CMD
Sweave someFile.Rnw sets the R environment so that Sweave.sty (in the R
distribution) is found.

Also, R reads variables from R_HOME/etc/Makevars, and you can override
settings there with values in ~/.R/Makevars. This makes it cheaper to
experiment, e.g., with CFLAGS or LD_LIBRARY_PATH, and also to see what
value LD_LIBRARY_PATH took when R was configured (in R_HOME/etc/Makevars).

Martin

> 
> 
> Cheers,
> 
> Marcus
> 
>> version               _
> platform       x86_64-unknown-linux-gnu
> arch           x86_64
> os             linux-gnu
> system         x86_64, linux-gnu
> status
> major          2
> minor          11.0
> year           2010
> month          04
> day            22
> svn rev        51801
> language       R
> version.string R version 2.11.0 (2010-04-22)
> 
> 
> On Thu, Jun 3, 2010 at 6:13 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 
>> Hi Kanika --
>>
>> On 06/02/2010 05:48 AM, kanika arora wrote:
>>> Hi ALL,
>>>
>>> * *
>>>
>>> I am trying to install l.0.2 version Rsamtools from Bioconductor and
>> facing
>>> problems. Please find the error message mentioned below:
>>>
>>>
>>>
>>>
>>>
>>> ** help
>>>
>>> *** installing help indices
>>>
>>>   converting help for package âRsamtoolsâ
>>>
>>>     finding HTML links ... done
>>>
>>>     BamViews-class                          html
>>>
>>>     finding level-2 HTML links ... done
>>>
>>>
>>>
>>>     Rsamtools-package                       html
>>>
>>>     ScanBamParam-class                      html
>>>
>>>     readBamGappedAlignments                 html
>>>
>>> Rd warning: ./man/readBamGappedAlignments.Rd:10: missing file link
>>> âGappedAlignmentsâ
>>>
>>> Rd warning: ./man/readBamGappedAlignments.Rd:36: missing file link
>>> âGappedAlignmentsâ
>>>
>>>     readPileup                              html
>>>
>>> Rd warning: ./man/readPileup.Rd:34: missing file link âGRangesâ
>>>
>>>     scanBam                                 html
>>>
>>> ** building package indices ...
>>>
>>> ** testing if installed package can be loaded
>>>
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>
>>>   unable to load shared library
>>> '/usr/lib64/R/library/Rsamtools/libs/Rsamtools.so':
>>>
>>>   /usr/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol:
>>> gzopen64
>>
>>
>> Rsamtools depends on having a system 'libz' installed. Does your system
>> have this (e.g., for me,
>>
>> mtmorgan at mm:~> /sbin/ldconfig -p|grep libz
>> [...snip...]
>>        libz.so.1 (libc6,x86-64) => /lib64/libz.so.1
>>        libz.so.1 (libc6) => /lib/libz.so.1
>>        libz.so (libc6,x86-64) => /usr/lib64/libz.so
>>
>> This should be checked during package configuration, so I'm a little
>> surprised that the error comes up at this point. Can you confirm that
>> you are installing this with
>>
>>  biocLite('Rsamtools')
>>
>> ? I'm a little nervous that when you say you 'installed all the
>> dependencies' that you are doing something else -- biocLite('Rsamtools')
>> installs the correct version of the dependencies for your version of R.
>>
>> Martin
>>
>>> ERROR: loading failed
>>>
>>> * removing â/usr/lib64/R/library/Rsamtoolsâ
>>>
>>>
>>>
>>>
>>>
>>>> sessionInfo()
>>>
>>> R version 2.11.0 (2010-04-22)
>>>
>>> x86_64-redhat-linux-gnu
>>>
>>>
>>>
>>> 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=C              LC_MESSAGES=en_US.UTF-8
>>>
>>>  [7] LC_PAPER=en_US.UTF-8       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
>>>
>>>
>>>
>>> other attached packages:
>>>
>>> [1] goseq_1.0.1            geneLenDataBase_0.99.4 BiasedUrn_1.03
>>>
>>>
>>>
>>> loaded via a namespace (and not attached):
>>>
>>>  [1] AnnotationDbi_1.10.1 Biobase_2.8.0        Biostrings_2.16.2
>>>
>>>  [4] BSgenome_1.16.1      DBI_0.2-5            GenomicRanges_1.0.1
>>>
>>>  [7] grid_2.11.0          IRanges_1.6.4        lattice_0.18-5
>>>
>>> [10] Matrix_0.999375-38   mgcv_1.6-1           nlme_3.1-96
>>>
>>> [13] RCurl_1.4-2          RSQLite_0.9-1        rtracklayer_1.8.1
>>>
>>> [16] tools_2.11.0         XML_3.1-0
>>>
>>>
>>>
>>>
>>>
>>> I already installed all the dependencies of the package. Please guide me
>> in
>>> this context.
>>>
>>> Thanks in advance,
>>>
>>> Kanika
>>>
>>>       [[alternative HTML version deleted]]
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>> --
>> Martin Morgan
>> 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
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
> 


-- 
Martin Morgan
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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