Compiling graph on solaris
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Mark Cowley ▴ 400
@mark-cowley-2858
Last seen 8.5 years ago
Australia
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]]
graph graph • 1.4k views
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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States
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
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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
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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
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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
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Aric Gregson ▴ 50
@aric-gregson-3687
Last seen 9.6 years ago
The graph package appears to compile fine for me on SXCE build 121 using the Sun Studio 12.1 compilers. It even build BioC_graph.so. I just did a biocLite("graph") and it worked. If I could only figure out why flowClust refuses to link properly... Aric
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