On 08/10/2010 02:25 PM, Lapointe, David wrote: > Hi I using R-2.11 (with shared libs) and trying to installl Rsamtools ( > 2.6.26.8-57.fc8 x86_64). > > I am using the R CMD method to get this to work. > R CMD INSTALL Rsamtools_1.0.7.tar.gz > ... > ** installing help indices > converting help for package ‘Rsamtools’ > 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 > ‘GappedAlignments’ > Rd warning: ./man/readBamGappedAlignments.Rd:36: missing file link > ‘GappedAlignments’ > readPileup html > Rd warning: ./man/readPileup.Rd:34: missing file link ‘GRanges’ > 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/local/lib64/R/library/Rsamtools/libs/Rsamtools.so': > /usr/local/lib64/R/library/Rsamtools/libs/Rsamtools.so: undefined symbol: > ecrc32 > ERROR: loading failed > * removing ‘/usr/local/lib64/R/library/Rsamtools’ > > libz.so.1 is present in /usr/lib64 > > I am not sure what library contains ecrc32
My guess is in a version of zlib (which has crc32) distributed by EMBOSS (which prepends 'e' to zlib symbols, so ecrc32), as in http://article.gmane.org/gmane.science.biology.informatics.conductor/28862 When you built Rsamtools I guess it found the zlib.h from EMBOSS, but when trying to run it finds the system library. I don't know why zlib.h from EMBOSS gets found by other applications; it is a configuration nuance on EMBOSS' side. Martin > > Davdi > _______________________________________________ > 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
