svn version of rtracklayer error

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Michael Dondrup ▴ 550

@michael-dondrup-3849

Last seen 10.2 years ago

Hi, I am trying to install the the latest rtracklayer version from svn, it's revision 50298. But that doesn't install: ** testing if installed package can be loaded Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/Resou rces/library/rtracklayer/libs/x86_64/rtracklayer.so': dlopen(/Library/Frameworks/R.framework/Resources/library/rtracklayer /libs/x86_64/rtracklayer.so, 6): Symbol not found: _new_CHARACTER_from_CharAEAE Referenced from: /Library/Frameworks/R.framework/Resources/library/r tracklayer/libs/x86_64/rtracklayer.so Expected in: flat namespace in /Library/Frameworks/R.framework/Resources/library/rtracklayer/libs /x86_64/rtracklayer.so > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base >

rtracklayer rtracklayer • 1.3k views

ADD COMMENT • link 14.1 years ago Michael Dondrup ▴ 550

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Martin Morgan 25k

@martin-morgan-1513

Last seen 4 months ago

United States

On 10/18/2010 03:15 AM, Michael Dondrup wrote: > Hi, > > I am trying to install the the latest rtracklayer version from svn, it's revision 50298. > > But that doesn't install: > ** testing if installed package can be loaded > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library '/Library/Frameworks/R.framework/Res ources/library/rtracklayer/libs/x86_64/rtracklayer.so': > dlopen(/Library/Frameworks/R.framework/Resources/library/rtracklay er/libs/x86_64/rtracklayer.so, 6): Symbol not found: _new_CHARACTER_from_CharAEAE I would guess that your version of IRanges (and other dependencies / imports?) is out of date with respect to rtracklayer. Martin > Referenced from: /Library/Frameworks/R.framework/Resources/library /rtracklayer/libs/x86_64/rtracklayer.so > Expected in: flat namespace > in /Library/Frameworks/R.framework/Resources/library/rtracklayer/li bs/x86_64/rtracklayer.so > > > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > 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: M1-B861 Telephone: 206 667-2793

ADD COMMENT • link 14.1 years ago Martin Morgan 25k

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Michael Dondrup ▴ 550

@michael-dondrup-3849

Last seen 10.2 years ago

On Oct 18, 2010, at 3:32 PM, Martin Morgan wrote: > On 10/18/2010 03:15 AM, Michael Dondrup wrote: >> Hi, >> >> I am trying to install the the latest rtracklayer version from svn, it's revision 50298. >> >> But that doesn't install: >> ** testing if installed package can be loaded >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared library '/Library/Frameworks/R.framework/Res ources/library/rtracklayer/libs/x86_64/rtracklayer.so': >> dlopen(/Library/Frameworks/R.framework/Resources/library/rtracklay er/libs/x86_64/rtracklayer.so, 6): Symbol not found: _new_CHARACTER_from_CharAEAE > > I would guess that your version of IRanges (and other dependencies / > imports?) is out of date with respect to rtracklayer. > Yes, I think you are right. Do I have to update to R 2.12.0 in general, or to the svn version of R and Bioconductor even? > Martin > >> Referenced from: /Library/Frameworks/R.framework/Resources/library /rtracklayer/libs/x86_64/rtracklayer.so >> Expected in: flat namespace >> in /Library/Frameworks/R.framework/Resources/library/rtracklayer/li bs/x86_64/rtracklayer.so >> >> >> >>> sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> 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: M1-B861 > Telephone: 206 667-2793 Michael Dondrup Post-doctoral researcher Uni BCCS Thorm?hlensgate 55, N-5008 Bergen, Norway Phone: +47 55584157 Fax: +47 55584354 Please note my new phone number

ADD COMMENT • link 14.1 years ago Michael Dondrup ▴ 550

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Hi, On Mon, Oct 18, 2010 at 9:55 AM, Michael Dondrup <michael.dondrup at="" uni.no=""> wrote: > > On Oct 18, 2010, at 3:32 PM, Martin Morgan wrote: > >> On 10/18/2010 03:15 AM, Michael Dondrup wrote: >>> Hi, >>> >>> I am trying to install the the latest rtracklayer version from svn, it's revision 50298. >>> >>> But that doesn't install: >>> ** testing if installed package can be loaded >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> ?unable to load shared library '/Library/Frameworks/R.framework/Re sources/library/rtracklayer/libs/x86_64/rtracklayer.so': >>> ?dlopen(/Library/Frameworks/R.framework/Resources/library/rtrackla yer/libs/x86_64/rtracklayer.so, 6): Symbol not found: _new_CHARACTER_from_CharAEAE >> >> I would guess that your version of IRanges (and other dependencies / >> imports?) is out of date with respect to rtracklayer. >> > Yes, I think you are right. Do I have to update to R 2.12.0 in general, or to the svn version of R and Bioconductor even? If you want to be installing packages from SVN, then I believe the recommendation is to be using R-devel (so: svn version of R). It looks like you're on a Mac, so you can get R-devel builds that are built for you and easily installable from here: http://r.research.att.com/ Then use biocLite from the correct version of R to get the correct bioconductor ecosystem (then install your package from SVN if you can't wait for it's changing to auto-build + propagate to biocLite) Depending on how comfortable you are with that (or not), you might just consider installing R-2.12 which just came out, and installing rtracklayer with biocLite from there since I guess the one rolled for Bioconductor 2.7 (which goes with R-2.12) is very close to the version in SVN you what ... but I might be wrong. Also, I reckon it might take another day or two for bioconductor 2.7 to officially hit the shelves. -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

ADD REPLY • link 14.1 years ago Steve Lianoglou ★ 13k

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