Hi Martin and Marcus,
Thanks for your replies. libz library is installed in my machine.
[kanik...@localhost ~ ]# /sbin/ldconfig -p|grep libz
libz.so.1 (libc6,x86-64) => /usr/lib64/libz.so.1
libz.so.1 (libc6) => /usr/lib/libz.so.1
libz.so (libc6,x86-64) => /usr/lib64/libz.so
libz.so (libc6) => /usr/lib/libz.so
Since I was getting error while installing Rsamtools via biocLite, I also
tried building the package through its source. That is why I installed all
the dependencies of the package.
The value of the environment variable LD_LIBRARY_PATH is :
[kanik...@localhost ~ ]# R CMD env | grep LD_LIBRARY_PATH (*thanks
for sharing this nice Linux/R trick)
LD_LIBRARY_PATH=/usr/lib64/R/lib:/usr/local/lib64:/usr/lib64/gcj-4.1.2
I unset this environment variable and reinstalled R again but still
Rsamtools is showing the same error.
Regards,
Kanika
On Thu, Jun 3, 2010 at 6:42 AM, Marcus Davy <[email protected]> wrote:
> thanks, this is what I had when the environment variable was still set;
>
> $ R CMD env | grep LD_LIBRARY_PATH
>
> LD_LIBRARY_PATH=/opt/R/R-2.11.0/lib64/R/lib:/usr/local/lib64:/usr/lib64/gcj-4.1.2:/opt/staden-linux-x86_64-1-7-1b/lib/linux-x86_64-binaries
>
>
> Marcus
>
>
>
> On Thu, Jun 3, 2010 at 12:41 PM, Martin Morgan <[email protected]> wrote:
>
>> 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 <[email protected]>
>> 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,
>> >>
>> >> mtmor...@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
>> >>> [email protected]
>> >>> 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
>> >> [email protected]
>> >> 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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