On 06/03/2010 05:46 AM, kanika arora wrote: > 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.
My guess is that Rsamtools is compiled against headers for your 64-bit library, but linking against the 32 bit. So I'm guessing that objdump -T /usr/lib64/libz.so.1 | grep gzopen (or the file pointed to by /usr/lib64/libz.so if it's a symbolic link) finds gzopen64 but objdump -T /usr/lib/libz.so.1 | grep gzopen finds gzopen. And that if you obtain the source of Rsamtools and unpack it tar xzf Rsamtools_1.0.2.tar.gz then try to install it R CMD INSTALL Rsamtools there should be a file Rsamtools/src/Rsamtools.so. I'm guessing that R CMD ldd Rsamtools/src/Rsamtools.so points to /usr/lib/libz.so.1, whereas we want it to point to /usr/lib64/libz.so. If that's the case then it might be the Rsamtools configure script and as a work-around you could try replacing in Rsamtools/configure.ac AC_CHECK_LIB([z], [gzeof],,[AC_MSG_ERROR([need libz with gzeof])]) with AC_CHECK_LIB([z], [gzeof64],,[AC_MSG_ERROR([need libz with gzeof])]) and then cd Rsamtools && autoconf && cd .. R CMD INSTALL --preclean Rsamtools It would help to have the full output of this last command; feel free to mail it to me off-list. Martin > > > > 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 >>> >> >> > -- 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
