I should clarify, similar issue... Marcus
On Thu, Jun 3, 2010 at 12:05 PM, Marcus Davy <[email protected]> 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 > > > 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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