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 > [[alternative HTML version deleted]]
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