Thanks Herv? and Martin, that fix worked a treat Mark On 22/09/2009, at 11:25 AM, Mark Cowley wrote: > Dear Herv?, > Thanks for looking into this for me, i really appreciate it. > > www.bioconductor.org seems to be down at the moment, but i'll report > back if i have success > > I'm using GNU ld and gcc > $ which ld > /opt/csw/bin/ld > $ ld -v > GNU ld version 2.17 > $ gcc -v > Reading specs from /usr/local/lib/gcc/i386-pc- solaris2.10/3.4.6/specs > Configured with: ../configure --with-as=/usr/ccs/bin/as --with-ld=/ > usr/ccs/bin/ld --enable-shared --enable-languages=c,c++,f77 > Thread model: posix > gcc version 3.4.6 > > Mark > ----------------------------------------------------- > Mark Cowley, PhD > > Peter Wills Bioinformatics Centre > Garvan Institute of Medical Research, Sydney, Australia > ----------------------------------------------------- > > On 19/09/2009, at 4:05 AM, Hervé Pagès wrote: > >> Hi Mark, >> >> I've applied a fix (sent to me off-list by Martin Morgan, thanks >> Martin) that should make the mechanism used for the renaming of >> graph.(so/dll) to BioC_graph.(so/dll) much more portable. >> >> This fix should take about 24 hours to propagate to the public >> package repositories. Then you will be able to reinstall graph >> using biocLite(). The fixed versions are 1.22.3 (release) and >> 1.23.5 (devel). >> >> Please let us know how it works for you. >> >> Cheers, >> H. >> >> >> Hervé Pagès wrote: >>> Hi Mark, >>> The graph package is doing something quite non-standard by adding >>> explicitly -o BioC_graph.so to the gcc arguments in order to take >>> control over the name given to the shared object (otherwise, by >>> default, this object would be called graph.so). >>> This was achieved by adding a Makevars file to the package with >>> the following line in it: >>> PKG_LIBS=-o BioC_graph.so >>> At compilation time the value of PKG_LIBS is inserted in the >>> gcc command *after* -o graph.so, and, so far, the trick worked >>> fine on many platforms, because ld on these platforms was using >>> the last -o setting. >>> Your ld command seems to behave differently though. What's its >>> version? Is it GNU ld? We have GNU ld v2.19 on our Linux build >>> machine. >>> I don't know what the solution is but any additional information >>> you can provide about your ld/gcc could help. Also you could check >>> your ld man page for any hint. >>> Cheers, >>> H. >>> Mark Cowley wrote: >>>> Dear list, >>>> I just upgraded to R 2.9.2, on solaris 10, and stumbled across a >>>> problem with graph. >>>> The package installed with 1 warning, but no errors. When I load >>>> it, I get the following error: >>>> > library(graph) >>>> Error in library.dynam(lib, package, package.lib) : >>>> shared library 'BioC_graph' not found >>>> Error: package/namespace load failed for 'graph' >>>> >>>> This is using the version of graph that biocLite downloaded for me >>>> Using R version 2.9.2, biocinstall version 2.4.12. >>>> Installing Bioconductor version 2.4 packages: >>>> >>>> I looked more closely at the install output, and spotted the >>>> problem, but don't know how to fix it: >>>> $ R CMD INSTALL -l /usr/local/R/library graph >>>> * Installing *source* package 'graph' ... >>>> ** libs >>>> gcc -std=gnu99 -I/usr/local/R-2.9.2/lib/R/include -I/usr/local/ >>>> include -fpic -I/usr/local/include -c graph.c -o graph.o >>>> gcc -std=gnu99 -G -L/usr/local/lib -o graph.so graph.o -o >>>> BioC_graph.so -L/usr/local/R-2.9.2/lib/R/lib -lR >>>> ld: warning: option -o appears more than once, first setting taken >>>> ** R >>>> ** data >>>> ** inst >>>> ** preparing package for lazy loading >>>> ** help >>>> *** installing help indices >>>> >>> Building/Updating help pages for package 'graph' >>>> Formats: text html latex example >>>> Note: ignoring empty \keyword entries in file 'graphRendering.Rd' >>>> Note: removing empty section \details in file 'graphRendering.Rd' >>>> Note: removing empty section \examples in file 'graphRendering.Rd' >>>> Note: removing empty section \seealso in file 'graphRendering.Rd' >>>> ** building package indices ... >>>> * DONE (graph) >>>> >>>> The ld warning indicates that there are two -o statements, it >>>> chooses the first, therefore ignore the '-o BioC_graph.so'. >>>> >>>> some googling found this message in the Bioconductor change logs (http://fgc.lsi.umich.edu/cgi-bin/blosxom3.cgi/2009/04/25 >>>> ): >>>> graph >>>> Renamed graph.(so/dll) BioC_graph.(so/dll) to avoid conflicts >>>> with graphviz. >>>> googling also showed that the build logs on OSX seem to tolerate >>>> two - o arguments (-o graph.so and -o BioC_graph.so) >>>> >>>> i'd appreciate any help >>>> >>>> cheers, >>>> Mark >>>> >>>> sessionInfo() >>>> R version 2.9.2 (2009-08-24) >>>> i386-pc-solaris2.10 >>>> >>>> locale: >>>> C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods >>>> base >>>> >>>> loaded via a namespace (and not attached): >>>> [1] tcltk_2.9.2 tools_2.9.2 >>>> >>>> >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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