GOStats/RBGL installation error
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@nicolas-servant-1466
Last seen 7 months ago
France
Hi, I try to install the GoStats (BioC 2.0, GoStat.2.2.6) package on R 2.5.1, but I have some C++ compilation errors due to RBGL package. The errors are link to the boost library and namespace definition. Does anybody have an idea ? > sessionInfo() R version 2.5.1 (2007-06-27) sparc-sun-solaris2.9 Error : * checking for file 'RBGL/DESCRIPTION' ... OK * preparing 'RBGL': * checking DESCRIPTION meta-information ... OK * cleaning src * running cleanup removing exploded boost header source... * installing the package to re-build vignettes * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs /opt/SUNWspro/bin/CC -xO5 -xdepend -xlic_lib=sunperf -xmemalign=8s -xprefetch=auto,explicit -xtarget=native -lCstd -I/bioinfo/local/SunR/lib/R/include -I/bioinfo/local/SunR/lib/R/include -I/usr/local/include -IboostIncl -KPIC -O -c bbc.cpp -o bbc.o CC: Warning: -O overwrites previously set optimization level of -O5 CC: Warning: -xarch=native has been explicitly specified, or implicitly specified by a macro option, -xarch=native on this architecture implies -xarch=v8plusb which generates code that does not run on pre UltraSPARC III processors "boostIncl/boost/graph/betweenness_centrality.hpp", line 439: Error: Could not find a match for boost::make_iterator_property_map<boost::raiter, boost::value,="" boost::id="">(std::vector<boost::detail::edge_desc_impl<boost::undirected _tag,="" unsigned=""> >*, ........ boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_index_ t,="" int,="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property="">>, unsigned>). "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: While instantiating "boost::detail::graph::brandes_betweenness_centrality_dispatch2<boost: :adjacency_list<boost::vecs,="" ........="" boost::property<boost::vertex_centrality_t,="" double,="" boost::no_property="">>, unsigned>)". "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: Instantiated from boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vec s,="" boost::vecs,="" .........="" boost::vertex_centrality_t="">, boost::vertex_centrality_t, boost::no_property>>>&). "bbc.cpp", line 43: Where: Instantiated from non-template code. "boostIncl/boost/graph/betweenness_centrality.hpp", line 440: Error: Could not find a match for boost::make_iterator_property_map<boost::raiter, boost::value,="" boost::id="">(double*, .......... boost::property<boost::vertex_centrality_t, double,="" boost::no_property="">>, unsigned>)". "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: Instantiated from boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vec s,="" boost::vecs,="" ............="" boost::vertex_centrality_t="">, boost::vertex_centrality_t, boost::no_property>>>&). "bbc.cpp", line 43: Where: Instantiated from non-template code. .............. "boostIncl/boost/graph/betweenness_centrality.hpp", line 441: Error: Could not find a match for boost::make_iterator_property_map<boost::raiter, boost::value,="" boost::id="">(double*, boost::property<boost::vertex_centrality_t, double,="" boost::no_property="">>, unsigned>)". "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: Instantiated from boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vec s,="" boost::vecs,="" ..............="" boost::vertex_centrality_t="">, boost::vertex_centrality_t, boost::no_property>>>&). "bbc.cpp", line 43: Where: Instantiated from non-template code. "boostIncl/boost/graph/betweenness_centrality.hpp", line 442: Error: Could not find a match for boost::make_iterator_property_map<boost::raiter, boost::value,="" boost::id="">(unsigned*, .................. boost::property<boost::vertex_centrality_t, double,="" boost::no_property="">>, unsigned>)". "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: Instantiated from boost::brandes_betweenness_centrality<boost::adjacency_list<boost::vec s,="" boost::vecs,="" .............="" boost::vertex_centrality_t="">, boost::vertex_centrality_t, boost::no_property>>>&). "bbc.cpp", line 43: Where: Instantiated from non-template code. 4 Error(s) detected. make: *** [bbc.o] Error 4 Thanks for your help, Regards, Nicolas. -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 53 10 70 55 http://bioinfo.curie.fr/
RBGL GOstats RBGL GOstats • 1.4k views
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Yongde Bao ▴ 170
@yongde-bao-244
Last seen 7.7 years ago
Hi all, I wonder if there is any package in Bioconductor that deals with the analysis of the Affy Human ST gene arrays. If so can someone point out where to get it? Best regards, Yongde Bao University of Virginia
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Hi Yongde Bao, There is a new package xps in the Devel repository that is intended for the analysis of the gene arrays. To use this package you will need R-devel, as well as installing ROOT. There are clear instructions for building the package on *NIX as well as MacOSX, but if you want to run on Windows you will have to figure things out for yourself. In addition, someone has already posted links to cdf packages for this chip that will allow you to use the affy package. Note however that some of the probes on this chip are shared between probesets, and that was not true in the past, so for a certain percentage of probesets you will be missing probes (once a probe is allocated to a probeset, it will not be available for any other probesets). Best, Jim Yongde Bao wrote: > Hi all, > > I wonder if there is any package in Bioconductor that deals with the analysis > of the Affy Human ST gene arrays. If so can someone point out where to get it? > > Best regards, > > Yongde Bao > University of Virginia > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
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You can analyze the Gene 1.0 ST chips within the 'aroma.affymetrix' package also: http://groups.google.com/group/aroma-affymetrix/web/hugene-1-0-st No restrictions within aroma.affymetrix for probes shared b/w probesets. There is a bit of work to do to set this up (CDFs, etc), but let me know if you want to go this route. Cheers, Mark On 27/10/2007, at 12:05 AM, James W. MacDonald wrote: > Hi Yongde Bao, > > There is a new package xps in the Devel repository that is intended > for > the analysis of the gene arrays. To use this package you will need > R-devel, as well as installing ROOT. There are clear instructions for > building the package on *NIX as well as MacOSX, but if you want to run > on Windows you will have to figure things out for yourself. > > In addition, someone has already posted links to cdf packages for this > chip that will allow you to use the affy package. Note however that > some > of the probes on this chip are shared between probesets, and that was > not true in the past, so for a certain percentage of probesets you > will > be missing probes (once a probe is allocated to a probeset, it will > not > be available for any other probesets). > > Best, > > Jim > > > > > Yongde Bao wrote: >> Hi all, >> >> I wonder if there is any package in Bioconductor that deals with >> the analysis >> of the Affy Human ST gene arrays. If so can someone point out >> where to get it? >> >> Best regards, >> >> Yongde Bao >> University of Virginia >> >> _______________________________________________ >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > _______________________________________________ > 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, Jim and Mark, for the prompt response. Mark, about the aroma.affymetrix package, does it run readily in Windows? And, if possible, can you show me a bit of the taste of its output? Best, Yongde On Sat, 27 Oct 2007 01:32:14 +1000 Mark Robinson <mrobinson at="" wehi.edu.au=""> wrote: > > You can analyze the Gene 1.0 ST chips within the 'aroma.affymetrix' > package also: > > http://groups.google.com/group/aroma-affymetrix/web/hugene-1-0-st > > No restrictions within aroma.affymetrix for probes shared b/w > probesets. There is a bit of work to do to set this up (CDFs, etc), > but let me know if you want to go this route. > > Cheers, > Mark > > > On 27/10/2007, at 12:05 AM, James W. MacDonald wrote: > >> Hi Yongde Bao, >> >> There is a new package xps in the Devel repository that is intended >> for >> the analysis of the gene arrays. To use this package you will need >> R-devel, as well as installing ROOT. There are clear instructions for >> building the package on *NIX as well as MacOSX, but if you want to run >> on Windows you will have to figure things out for yourself. >> >> In addition, someone has already posted links to cdf packages for this >> chip that will allow you to use the affy package. Note however that >> some >> of the probes on this chip are shared between probesets, and that was >> not true in the past, so for a certain percentage of probesets you >> will >> be missing probes (once a probe is allocated to a probeset, it will >> not >> be available for any other probesets). >> >> Best, >> >> Jim >> >> >> >> >> Yongde Bao wrote: >>> Hi all, >>> >>> I wonder if there is any package in Bioconductor that deals with >>> the analysis >>> of the Affy Human ST gene arrays. If so can someone point out >>> where to get it? >>> >>> Best regards, >>> >>> Yongde Bao >>> University of Virginia >>> >>> _______________________________________________ >>> 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 >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> 734-647-5623 >> >> _______________________________________________ >> 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 Yongde Bao, Ph.D. Department of Microbilogy Biomolecular Research Facility University of Virginia Voice Mail:434-982-2551 FAX: 434-982-2514
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On 10/26/07, Yongde Bao <yb8d at="" virginia.edu=""> wrote: > Thanks, Jim and Mark, for the prompt response. > > Mark, about the aroma.affymetrix package, does it run readily in Windows? And, > if possible, can you show me a bit of the taste of its output? Yes, your questions are answers on the front page: http://groups.google.com/group/aroma-affymetrix/ Cheers /Henrik > > Best, Yongde > > On Sat, 27 Oct 2007 01:32:14 +1000 > Mark Robinson <mrobinson at="" wehi.edu.au=""> wrote: > > > > You can analyze the Gene 1.0 ST chips within the 'aroma.affymetrix' > > package also: > > > > http://groups.google.com/group/aroma-affymetrix/web/hugene-1-0-st > > > > No restrictions within aroma.affymetrix for probes shared b/w > > probesets. There is a bit of work to do to set this up (CDFs, etc), > > but let me know if you want to go this route. > > > > Cheers, > > Mark > > > > > > On 27/10/2007, at 12:05 AM, James W. MacDonald wrote: > > > >> Hi Yongde Bao, > >> > >> There is a new package xps in the Devel repository that is intended > >> for > >> the analysis of the gene arrays. To use this package you will need > >> R-devel, as well as installing ROOT. There are clear instructions for > >> building the package on *NIX as well as MacOSX, but if you want to run > >> on Windows you will have to figure things out for yourself. > >> > >> In addition, someone has already posted links to cdf packages for this > >> chip that will allow you to use the affy package. Note however that > >> some > >> of the probes on this chip are shared between probesets, and that was > >> not true in the past, so for a certain percentage of probesets you > >> will > >> be missing probes (once a probe is allocated to a probeset, it will > >> not > >> be available for any other probesets). > >> > >> Best, > >> > >> Jim > >> > >> > >> > >> > >> Yongde Bao wrote: > >>> Hi all, > >>> > >>> I wonder if there is any package in Bioconductor that deals with > >>> the analysis > >>> of the Affy Human ST gene arrays. If so can someone point out > >>> where to get it? > >>> > >>> Best regards, > >>> > >>> Yongde Bao > >>> University of Virginia > >>> > >>> _______________________________________________ > >>> 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 > >> > >> -- > >> James W. MacDonald, M.S. > >> Biostatistician > >> Affymetrix and cDNA Microarray Core > >> University of Michigan Cancer Center > >> 1500 E. Medical Center Drive > >> 7410 CCGC > >> Ann Arbor MI 48109 > >> 734-647-5623 > >> > >> _______________________________________________ > >> 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 > > Yongde Bao, Ph.D. > Department of Microbilogy > Biomolecular Research Facility > University of Virginia > Voice Mail:434-982-2551 > FAX: 434-982-2514 > > _______________________________________________ > 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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On Oct 26, 2007, at 9:06 AM, Yongde Bao wrote: > Thanks, Jim and Mark, for the prompt response. > > Mark, about the aroma.affymetrix package, does it run readily in > Windows? And, > if possible, can you show me a bit of the taste of its output? aroma.affymetrix runs in windows (the main developer is using windows), and if you want a look at the output why don't you follow the link Mark gave you and read some of the pages. It also allows analysis of very large datasets on a laptop (given around 1-2GB ram) Kasper > Best, Yongde > > On Sat, 27 Oct 2007 01:32:14 +1000 > Mark Robinson <mrobinson at="" wehi.edu.au=""> wrote: >> >> You can analyze the Gene 1.0 ST chips within the 'aroma.affymetrix' >> package also: >> >> http://groups.google.com/group/aroma-affymetrix/web/hugene-1-0-st >> >> No restrictions within aroma.affymetrix for probes shared b/w >> probesets. There is a bit of work to do to set this up (CDFs, etc), >> but let me know if you want to go this route. >> >> Cheers, >> Mark >> >> >> On 27/10/2007, at 12:05 AM, James W. MacDonald wrote: >> >>> Hi Yongde Bao, >>> >>> There is a new package xps in the Devel repository that is intended >>> for >>> the analysis of the gene arrays. To use this package you will need >>> R-devel, as well as installing ROOT. There are clear instructions >>> for >>> building the package on *NIX as well as MacOSX, but if you want >>> to run >>> on Windows you will have to figure things out for yourself. >>> >>> In addition, someone has already posted links to cdf packages for >>> this >>> chip that will allow you to use the affy package. Note however that >>> some >>> of the probes on this chip are shared between probesets, and that >>> was >>> not true in the past, so for a certain percentage of probesets you >>> will >>> be missing probes (once a probe is allocated to a probeset, it will >>> not >>> be available for any other probesets). >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> >>> Yongde Bao wrote: >>>> Hi all, >>>> >>>> I wonder if there is any package in Bioconductor that deals with >>>> the analysis >>>> of the Affy Human ST gene arrays. If so can someone point out >>>> where to get it? >>>> >>>> Best regards, >>>> >>>> Yongde Bao >>>> University of Virginia >>>> >>>> _______________________________________________ >>>> 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 >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Affymetrix and cDNA Microarray Core >>> University of Michigan Cancer Center >>> 1500 E. Medical Center Drive >>> 7410 CCGC >>> Ann Arbor MI 48109 >>> 734-647-5623 >>> >>> _______________________________________________ >>> 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 > > Yongde Bao, Ph.D. > Department of Microbilogy > Biomolecular Research Facility > University of Virginia > Voice Mail:434-982-2551 > FAX: 434-982-2514 > > _______________________________________________ > 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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Dear Yongde As James MacDonald has already kindly mentioned, my package xps is able to handle both Affymetrix HuGene and Exon arrays. Is has no problems with shared probesets, and you can do RMA and MAS5 normalization. Please note that you can use xps with both R-2.5.0 and R-2.6.0 so you need not install R-devel. If you are willing to install and try it I would appreciate any feedback. Best regards Christian _._._._._._._._._._._._._._._._ C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._ Yongde Bao wrote: > Hi all, > > I wonder if there is any package in Bioconductor that deals with the analysis > of the Affy Human ST gene arrays. If so can someone point out where to get it? > > Best regards, > > Yongde Bao > University of Virginia > > _______________________________________________ > 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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Tony Chiang ▴ 570
@tony-chiang-1769
Last seen 7.7 years ago
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Hi Tony, I'm sorry, but for now, we cannot update the R and BioC versions. R is installed on a sparc-sun-solaris server for all our applications. And it's always complicated, for all developers and application users, to make this type of update. Moreover, i'm not convinced that it could resolve the probleme ... Thanks for your help, Best, Nicolas Tony Chiang wrote: > Hi Nicolas, > > Can you try and update your R to 2.6 and your Bioc to 2.2 to see if this > problem still persists? > Or is there a reason you are using the old versions of R and Bioc? > > Best, > --Tony > > On 10/26/07, Nicolas Servant <nicolas.servant at="" curie.fr=""> wrote: > >> Hi, >> >> I try to install the GoStats (BioC 2.0, GoStat.2.2.6) package on R >> 2.5.1, but I have some C++ compilation errors due to RBGL package. >> The errors are link to the boost library and namespace definition. >> Does anybody have an idea ? >> >> >> >>> sessionInfo() >>> >> R version 2.5.1 (2007-06-27) >> sparc-sun-solaris2.9 >> >> Error : >> * checking for file 'RBGL/DESCRIPTION' ... OK >> * preparing 'RBGL': >> * checking DESCRIPTION meta-information ... OK >> * cleaning src >> * running cleanup >> removing exploded boost header source... >> * installing the package to re-build vignettes >> * Installing *source* package 'RBGL' ... >> untarring boost include tree... >> ** libs >> /opt/SUNWspro/bin/CC -xO5 -xdepend -xlic_lib=sunperf -xmemalign=8s >> -xprefetch=auto,explicit -xtarget=native -lCstd >> -I/bioinfo/local/SunR/lib/R/include -I/bioinfo/local/SunR/lib/R/include >> -I/usr/local/include -IboostIncl -KPIC -O -c bbc.cpp -o bbc.o >> CC: Warning: -O overwrites previously set optimization level of -O5 >> CC: Warning: -xarch=native has been explicitly specified, or implicitly >> specified by a macro option, -xarch=native on this architecture implies >> -xarch=v8plusb which generates code that does not run on pre UltraSPARC >> III processors >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 439: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> >> boost::ID>(std::vector<boost::detail::edge_desc_impl<boost::undirec ted_tag,="">> unsigned> >*, >> ........ >> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_ind ex_t,="">> int, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>). >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> While instantiating >> >> "boost::detail::graph::brandes_betweenness_centrality_dispatch2<boo st::adjacency_list<boost::vecs,="">> >> ........ >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ......... >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 440: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, >> .......... >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............ >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> .............. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 441: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> .............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 442: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(unsigned*, >> .................. >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> 4 Error(s) detected. >> make: *** [bbc.o] Error 4 >> >> >> Thanks for your help, >> Regards, >> >> Nicolas. >> >> >> -- >> Nicolas Servant >> Equipe Bioinformatique >> Institut Curie >> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE >> >> Email: Nicolas.Servant at curie.fr >> Tel: 01 53 10 70 55 >> http://bioinfo.curie.fr/ >> >> _______________________________________________ >> 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 >> >> > > [[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 > > . > > -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 53 10 70 55 http://bioinfo.curie.fr/
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@lilongisb-sibch-1725
Last seen 7.7 years ago
Hi, First question: when and how you got the "RBGL"? Second: what's your CC version? Did you install RBGL with it successfully before? Or it's brandnew experience? The error msgs are about C++ template handling. Thanks Li > Hi, > > I try to install the GoStats (BioC 2.0, GoStat.2.2.6) package on R > 2.5.1, but I have some C++ compilation errors due to RBGL package. > The errors are link to the boost library and namespace definition. > Does anybody have an idea ? > > > > sessionInfo() > R version 2.5.1 (2007-06-27) > sparc-sun-solaris2.9 > > Error : > * checking for file 'RBGL/DESCRIPTION' ... OK > * preparing 'RBGL': > * checking DESCRIPTION meta-information ... OK > * cleaning src > * running cleanup > removing exploded boost header source... > * installing the package to re-build vignettes > * Installing *source* package 'RBGL' ... > untarring boost include tree... > ** libs > /opt/SUNWspro/bin/CC -xO5 -xdepend -xlic_lib=sunperf -xmemalign=8s > -xprefetch=auto,explicit -xtarget=native -lCstd > -I/bioinfo/local/SunR/lib/R/include -I/bioinfo/local/SunR/lib/R/include > -I/usr/local/include -IboostIncl -KPIC -O -c bbc.cpp -o bbc.o > CC: Warning: -O overwrites previously set optimization level of -O5 > CC: Warning: -xarch=native has been explicitly specified, or implicitly > specified by a macro option, -xarch=native on this architecture implies > -xarch=v8plusb which generates code that does not run on pre UltraSPARC > III processors > "boostIncl/boost/graph/betweenness_centrality.hpp", line 439: Error: > Could not find a match for > boost::make_iterator_property_map<boost::raiter, boost::value,=""> boost::ID>(std::vector<boost::detail::edge_desc_impl<boost::undirect ed_tag,=""> unsigned> >*, > ........ > boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_inde x_t,=""> int, boost::property<boost::vertex_centrality_t, double,=""> boost::no_property>>, unsigned>). > "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: > While instantiating > "boost::detail::graph::brandes_betweenness_centrality_dispatch2<boos t::adjacency_list<boost::vecs,=""> > ........ > boost::property<boost::vertex_centrality_t, double,=""> boost::no_property>>, unsigned>)". > "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: > Instantiated from > boost::brandes_betweenness_centrality<boost::adjacency_list<boost::v ecs,=""> boost::vecS, > ......... > boost::vertex_centrality_t>, boost::vertex_centrality_t, > boost::no_property>>>&). > "bbc.cpp", line 43: Where: Instantiated from non-template code. > "boostIncl/boost/graph/betweenness_centrality.hpp", line 440: Error: > Could not find a match for > boost::make_iterator_property_map<boost::raiter, boost::value,=""> boost::ID>(double*, > .......... > boost::property<boost::vertex_centrality_t, double,=""> boost::no_property>>, unsigned>)". > "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: > Instantiated from > boost::brandes_betweenness_centrality<boost::adjacency_list<boost::v ecs,=""> boost::vecS, > ............ > boost::vertex_centrality_t>, boost::vertex_centrality_t, > boost::no_property>>>&). > "bbc.cpp", line 43: Where: Instantiated from non-template code. > .............. > "boostIncl/boost/graph/betweenness_centrality.hpp", line 441: Error: > Could not find a match for > boost::make_iterator_property_map<boost::raiter, boost::value,=""> boost::ID>(double*, boost::property<boost::vertex_centrality_t, double,=""> boost::no_property>>, unsigned>)". > "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: > Instantiated from > boost::brandes_betweenness_centrality<boost::adjacency_list<boost::v ecs,=""> boost::vecS, > .............. > boost::vertex_centrality_t>, boost::vertex_centrality_t, > boost::no_property>>>&). > "bbc.cpp", line 43: Where: Instantiated from non-template code. > "boostIncl/boost/graph/betweenness_centrality.hpp", line 442: Error: > Could not find a match for > boost::make_iterator_property_map<boost::raiter, boost::value,=""> boost::ID>(unsigned*, > .................. > boost::property<boost::vertex_centrality_t, double,=""> boost::no_property>>, unsigned>)". > "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: > Instantiated from > boost::brandes_betweenness_centrality<boost::adjacency_list<boost::v ecs,=""> boost::vecS, > ............. > boost::vertex_centrality_t>, boost::vertex_centrality_t, > boost::no_property>>>&). > "bbc.cpp", line 43: Where: Instantiated from non-template code. > 4 Error(s) detected. > make: *** [bbc.o] Error 4 > > > Thanks for your help, > Regards, > > Nicolas. > > > -- > Nicolas Servant > Equipe Bioinformatique > Institut Curie > 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE > > Email: Nicolas.Servant at curie.fr > Tel: 01 53 10 70 55 > http://bioinfo.curie.fr/ > > _______________________________________________ > 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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Hi, 1- RBGL_1.12.0.tar.gz form BioC2.0 2- CC: Sun C++ 5.8 Patch 121017-11 2007/05/02 This is the first time we use the Sun CC for R installation. The last time we used the g++ compiler without any probleme. Thanks Nicolas Li.Long at isb-sib.ch wrote: > Hi, > > First question: when and how you got the "RBGL"? > Second: what's your CC version? Did you install RBGL with it successfully > before? Or it's brandnew experience? The error msgs are about C++ > template handling. > > Thanks > > Li > > > >> Hi, >> >> I try to install the GoStats (BioC 2.0, GoStat.2.2.6) package on R >> 2.5.1, but I have some C++ compilation errors due to RBGL package. >> The errors are link to the boost library and namespace definition. >> Does anybody have an idea ? >> >> >> > sessionInfo() >> R version 2.5.1 (2007-06-27) >> sparc-sun-solaris2.9 >> >> Error : >> * checking for file 'RBGL/DESCRIPTION' ... OK >> * preparing 'RBGL': >> * checking DESCRIPTION meta-information ... OK >> * cleaning src >> * running cleanup >> removing exploded boost header source... >> * installing the package to re-build vignettes >> * Installing *source* package 'RBGL' ... >> untarring boost include tree... >> ** libs >> /opt/SUNWspro/bin/CC -xO5 -xdepend -xlic_lib=sunperf -xmemalign=8s >> -xprefetch=auto,explicit -xtarget=native -lCstd >> -I/bioinfo/local/SunR/lib/R/include -I/bioinfo/local/SunR/lib/R/include >> -I/usr/local/include -IboostIncl -KPIC -O -c bbc.cpp -o bbc.o >> CC: Warning: -O overwrites previously set optimization level of -O5 >> CC: Warning: -xarch=native has been explicitly specified, or implicitly >> specified by a macro option, -xarch=native on this architecture implies >> -xarch=v8plusb which generates code that does not run on pre UltraSPARC >> III processors >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 439: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(std::vector<boost::detail::edge_desc_impl<boost::undirec ted_tag,="">> unsigned> >*, >> ........ >> boost::vec_adj_list_vertex_id_map<boost::property<boost::vertex_ind ex_t,="">> int, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>). >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> While instantiating >> "boost::detail::graph::brandes_betweenness_centrality_dispatch2<boo st::adjacency_list<boost::vecs,="">> >> ........ >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ......... >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 440: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, >> .......... >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............ >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> .............. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 441: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(double*, boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> .............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 442: Error: >> Could not find a match for >> boost::make_iterator_property_map<boost::raiter, boost::value,="">> boost::ID>(unsigned*, >> .................. >> boost::property<boost::vertex_centrality_t, double,="">> boost::no_property>>, unsigned>)". >> "boostIncl/boost/graph/betweenness_centrality.hpp", line 493: Where: >> Instantiated from >> boost::brandes_betweenness_centrality<boost::adjacency_list<boost:: vecs,="">> boost::vecS, >> ............. >> boost::vertex_centrality_t>, boost::vertex_centrality_t, >> boost::no_property>>>&). >> "bbc.cpp", line 43: Where: Instantiated from non-template code. >> 4 Error(s) detected. >> make: *** [bbc.o] Error 4 >> >> >> Thanks for your help, >> Regards, >> >> Nicolas. >> >> >> -- >> Nicolas Servant >> Equipe Bioinformatique >> Institut Curie >> 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE >> >> Email: Nicolas.Servant at curie.fr >> Tel: 01 53 10 70 55 >> http://bioinfo.curie.fr/ >> >> _______________________________________________ >> 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 >> >> > > > . > > -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 53 10 70 55 http://bioinfo.curie.fr/
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> Hi, > > 1- RBGL_1.12.0.tar.gz form BioC2.0 > 2- CC: Sun C++ 5.8 Patch 121017-11 2007/05/02 > This is the first time we use the Sun CC for R installation. > The last time we used the g++ compiler without any probleme. Any particular reason that you choose to switch from g++ to Sun CC? RBGL certainly uses C++ templates in a great deal. I haven't tried Sun CC on RBGL, but C++ templates are known to be tricky for C++ compilers. I'm not sure if I have Sun C++ around to try it out. Li
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Hi, It is not clear if R was compiled with the same compiler and set of options. I suspect that things will not work so well if not. Second, it may be worth seeing whether the boost graph library can be compiled independently using the sun compilers. That is, taking the R part out of the loop. Unfortunately we also do not have access to that compiler so can be of little help. The error message suggests that the include path may not correct. Also, while you may not want to do a site wide update of R and bioc, doing this in your own account takes less than an hour and would address the issue of whether the problem does go away. best wishes Robert Li.Long at isb-sib.ch wrote: >> Hi, >> >> 1- RBGL_1.12.0.tar.gz form BioC2.0 >> 2- CC: Sun C++ 5.8 Patch 121017-11 2007/05/02 >> This is the first time we use the Sun CC for R installation. >> The last time we used the g++ compiler without any probleme. > > Any particular reason that you choose to switch from g++ to Sun CC? > > RBGL certainly uses C++ templates in a great deal. I haven't tried Sun CC > on RBGL, but C++ templates are known to be tricky for C++ compilers. > > I'm not sure if I have Sun C++ around to try it out. > > Li > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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There're serveral reasons to use CC instead of g++ compiler ... The Sun tools are often optimized for their own processor. And SunStudio include the "Sunperf" library which really increase the R performance. Even if R was compiled with CC, i will try to use g++ for this package. Thanks, Nicolas Li.Long at isb-sib.ch wrote: >> Hi, >> >> 1- RBGL_1.12.0.tar.gz form BioC2.0 >> 2- CC: Sun C++ 5.8 Patch 121017-11 2007/05/02 >> This is the first time we use the Sun CC for R installation. >> The last time we used the g++ compiler without any probleme. >> > > Any particular reason that you choose to switch from g++ to Sun CC? > > RBGL certainly uses C++ templates in a great deal. I haven't tried Sun CC > on RBGL, but C++ templates are known to be tricky for C++ compilers. > > I'm not sure if I have Sun C++ around to try it out. > > Li > > _______________________________________________ > 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 > > . > > -- Nicolas Servant Equipe Bioinformatique Institut Curie 26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE Email: Nicolas.Servant at curie.fr Tel: 01 53 10 70 55 http://bioinfo.curie.fr/
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