Rsamtools installation error
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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/lib/jvm/j ava-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/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. 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.
Rsamtools Rsamtools • 2.8k views
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Dan Tenenbaum ★ 8.2k
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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/lib/jvm /java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/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. 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
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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/lib/jv m/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/jav a-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
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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 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 objdump: '/lib/x86_64-linux-gnu/libz.so.1': No such file 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/lib/j vm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/ja va-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
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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/lib/ jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/j ava-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
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objdump -T /lib64/libz.so.1 |grep gzopen64 Did not return anything. Does that mean gzopen64 is not installed present on my system? 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/lib /jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm/ 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
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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/li b/jvm/java-1.6.0-sun-1.6.0.31.x86_64/jre/lib/amd64/server:/usr/lib/jvm /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
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Entering edit mode
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
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Entering edit mode

Hi,I came across the same problem and I followed the steps that you discussed .

$/lustre1/cxu_pkuhpc/program/R-3.5.1/bin/R CMD ldd Rsamtools/src/Rsamtools.so

    linux-vdso.so.1 (0x00007fffec7ff000)

    libz.so.1 => /lib64/libz.so.1 (0x00002b4ce4d61000)

    libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b4ce4f77000)

    libm.so.6 => /lib64/libm.so.6 (0x00002b4ce5306000)

    libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00002b4ce5608000)

    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b4ce5829000)

    libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b4ce5a40000)

    libc.so.6 => /lib64/libc.so.6 (0x00002b4ce5c5c000)

    /lib64/ld-linux-x86-64.so.2 (0x0000003711e00000)

    libdl.so.2 => /lib64/libdl.so.2 (0x00002b4ce5ffa000)

$objdump -T   /lib64/libz.so.1 | grep gzopen

0000003713204340 g    DF .text 000000000000000a  Base        gzopen

 

[cxu_pkuhpc@hs@homeserver01@20:34:55]/lustre1/cxu_pkuhpc/hs/software/BaGFoot

$lsb_release -a

LSB Version: :base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch

Distributor ID: CentOS

Description: CentOS release 6.5 (Final)

Release: 6.5

Codename: Final

files under /lib64/

lrwxrwxrwx 1 root root    13 Jul 25 01:01 libz.so.1 -> libz.so.1.2.3
-rwxr-xr-x 1 root root  117K Jul 24 23:27 libz.so.1.2.11
-rwxr-xr-x 1 root root   89K Feb 22  2013 libz.so.1.2.3

$objdump -T libz.so.1.2.11 | grep gzopen64 

0000000000011190 g    DF .text 000000000000000d  ZLIB_1.2.3.3 gzopen64

$objdump -T libz.so.1.2.3 | grep gzopen64  

without anything return .

because I can't change the system file(link libz.so.1.2.11 to libz.so.1),then can I  change the Rsamtools/src/Rsamtools.so file ?

 let  "libz.so.1 => /lib64/libz.so.1 (0x00002b4ce4d61000) " become "libz.so.1.2.11 =>  /lib64/libz.so.1.2.11/

 

 

 

What else can I do ?

Thank you very much !!

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