Thanks, I checked each of my libz installations for gzopen64 using the following command objdump -T /usr/local/lib/libz.zo.1 | grep gzopen64 I put the one that contained it in the LD_LIBRARY_PATH by creating a ~/.R/Makevars file. sourced the Makevars file and then was able to install it successfully. Hope these notes help others who may face the same problem. Cheers../Murli On Wed, Jul 11, 2012 at 4:30 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 07/11/2012 01:21 PM, Murli wrote: >> >> objdump -T /lib64/libz.so.1 |grep gzopen64 >> >> Did not return anything. Does that mean gzopen64 is not installed >> present on my system? > > > I think it means that your system has two (or more) versions of libz > installed, one with and one without gzopen64. The installation finds the > header file that says gzopen64 exists, but then finds the library file that > does not contain it. > > It might help to use your package manager to figure out what the system libz > is, and to update your installation to contain only that. Unfortunately, I'm > not a Redhat user and can't provide any further instructions. Perhaps > someone else on the list can. Martin > > > >> >> Thanks ../Murli >> >> >> On Wed, Jul 11, 2012 at 3:44 PM, Martin Morgan<mtmorgan at="" fhcrc.org=""> wrote: >>> >>> On 07/11/2012 12:42 PM, Murli wrote: >>>> >>>> >>>> Martin, >>>> I tried your suggested way again and I still get the same. >>>> >>>> ** testing if installed package can be loaded >>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>> unable to load shared object >>>> '/usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so': >>>> /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined >>>> symbol: gzopen64 >>>> Error: loading failed >>>> Execution halted >>>> ERROR: loading failed >>> >>> >>> >>> yes the installation still fails but you are left with the >>> trouble-shooting >>> artifacts >>> >>> >>> >>>> >>>> Here is other output >>>> R CMD ldd Rsamtools/src/Rsamtools.so >>>> linux-vdso.so.1 => (0x00007fff477d4000) >>>> libz.so.1 => /lib64/libz.so.1 (0x00002b190cb28000) >>>> libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00002b190cd3d000) >>>> libpthread.so.0 => /lib64/libpthread.so.0 >>>> (0x00002b190cf4a000) >>>> libc.so.6 => /lib64/libc.so.6 (0x00002b190d165000) >>>> librt.so.1 => /lib64/librt.so.1 (0x00002b190d4bd000) >>>> /lib64/ld-linux-x86-64.so.2 (0x00000035e2400000) >>>> >>>> objdump -T /lib/x86_64-linux-gnu/libz.so.1|grep gzopen64 >>> >>> >>> >>> use the path that R CMD ldd pointed to, for you >>> >>> objdump -T /lib64/libz.so.1 |grep gzopen64 >>> >>> >>> >>>> >>>> >>>> How do I define gzopen64? >>>> Thanks for you suggestions.../Murli >>>> >>>> On Wed, Jul 11, 2012 at 3:24 PM, Martin Morgan<mtmorgan at="" fhcrc.org=""> >>>> wrote: >>>>> >>>>> >>>>> On 07/11/2012 12:10 PM, Dan Tenenbaum wrote: >>>>>> >>>>>> >>>>>> >>>>>> On Wed, Jul 11, 2012 at 12:01 PM, Murli >>>>>> [guest]<guest at="" bioconductor.org=""> >>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> Hi, >>>>>>> I am trying to install Rsamtools (Redhat linux ) and I have been >>>>>>> getting >>>>>>> the following error >>>>>>> ####################################### >>>>>>> ** testing if installed package can be loaded >>>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>>>>>> unable to load shared object >>>>>>> '/usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so': >>>>>>> /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: >>>>>>> undefined >>>>>>> symbol: gzopen64 >>>>>>> Error: loading failed >>>>>>> Execution halted >>>>>>> ERROR: loading failed >>>>>>> * removing ???/usr/local/lib64/R/library/Rsamtools??? >>>>>>> ######################################### >>>>>>> >>>>>>> I have libz installed >>>>>>> /sbin/ldconfig -p|grep libz >>>>>>> libz.so.1 (libc6,x86-64) => /lib64/libz.so.1 >>>>>>> libz.so.1 (libc6,x86-64) => /usr/lib64/libz.so.1 >>>>>>> libz.so.1 (libc6) => /lib/libz.so.1 >>>>>>> libz.so.1 (libc6) => /usr/lib/libz.so.1 >>>>>>> libz.so (libc6,x86-64) => /lib64/libz.so >>>>>>> libz.so (libc6,x86-64) => /usr/lib64/libz.so >>>>>>> libz.so (libc6) => /lib/libz.so >>>>>>> libz.so (libc6) => /usr/lib/libz.so >>>>>>> >>>>>>> I checked the LD_LIBRARY_PATH using the following >>>>>>> R CMD env | grep LD_LIBRARY_PATH >>>>>>> >>>>>>> >>>>>>> >>>>>>> LD_LIBRARY_PATH=/usr/local/lib64/R/lib:/usr/local/lib64:/usr/l ib/jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jv m/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64 >>>>>>> >>>>>>> Please let me know if there is anything else that I need to check. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> What command are you using to try and install Rsamtools? >>>>>> Try this command: >>>>>> source("http://bioconductor.org/biocLite.R") >>>>>> biocLite("Rsamtools") >>>>>> >>>>>> It seems like the error you are getting is because zlibbioc is not >>>>>> being installed, but if you used the above command, it would be >>>>>> installed. >>>>> >>>>> >>>>> >>>>> >>>>> zlibbioc is primarily used for Windows compatibility; on Linux the >>>>> build >>>>> will use a system-supplied zlib. The possibilities are (a) that the >>>>> system >>>>> zlib does not contain gzopen64 or (b) R is not finding libz. >>>>> >>>>> I think to debug you'll want to download the source >>>>> >>>>> source("http://bioconductor.org/biocLite.R") >>>>> download.packages("Rsamtools", repos=biocinstallRepos(), dest=".") >>>>> >>>>> Then from the command line >>>>> >>>>> tar xzf Rsamtools_ >>>>> R CMD INSTALL Rsamtools >>>>> >>>>> and then check for the libz to which Rsamtools.so is linked >>>>> >>>>> R CMD ldd Rsamtools/src/Rsamtools.so >>>>> >>>>> which for me says >>>>> >>>>> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f83e6a2a000) >>>>> >>>>> and then verify gzopen64 is defined >>>>> >>>>> objdump -T /lib/x86_64-linux-gnu/libz.so.1|grep gzopen64 >>>>> 0000000000003580 g DF .text 000000000000000f Base gzopen64 >>>>> >>>>> Martin >>>>> >>>>> >>>>>> >>>>>> Dan >>>>>> >>>>>> >>>>>>> Thanks for your help. >>>>>>> Cheers../Murli >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- output of sessionInfo(): >>>>>>> >>>>>>> sessionInfo() >>>>>>> R version 2.15.0 (2012-03-30) >>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>>>>> >>>>>>> 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >>>>>>> [7] LC_PAPER=C 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 >>>>>>> >>>>>>> -- >>>>>>> Sent via the guest posting facility at bioconductor.org. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioconductor mailing list >>>>>>> Bioconductor at r-project.org >>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>> Search the archives: >>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: >>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>> >>> >>> >>> >>> -- >>> 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 > > > > -- > 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