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 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 > [[alternative HTML version deleted]]
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