Dear Peter, Some time ago another Debian/Ubuntu user had the identical problem, which he solved as follows: https://stat.ethz.ch/pipermail/bioconductor/2009-August/029192.html However, this should not be the solution to the problem. I am testing xps on Mac, WinXP and OpenSUSE11.1, where compilation works w/o problem. When googling the error message I found the following site: http://ubuntuforums.org/showthread.php?t=165902 Thus, I assume that maybe your Ubuntu installation misses some development files, maybe the "glibc-headers" and "glibc-kernheaders", as mentioned in the link. However, please note that I am not an Ubuntu/Debian expert, thus maybe someone else could give you a better advice. BTW, which version of ROOT are you using? Did you compile it? Did you compile R? Best regards Christian Peter Saffrey wrote: > Hi, > > Thanks for the recommendation. This seems to bring its own problems. Here is the error from trying to install xps. > > g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/include/root -c XPSUtils.cxx > XPSUtils.cxx: In function 'void READ_WSTRING(std::ifstream&, char*&, Bool_t)': > XPSUtils.cxx:4611: error: 'wcstombs' was not declared in this scope > make: *** [XPSUtils.o] Error 1 > ERROR: compilation failed for package 'xps' > > $ uname -a > Linux cs-analysis 2.6.31-17-generic #54-Ubuntu SMP Thu Dec 10 17:01:44 UTC 2009 x86_64 GNU/Linux > $ gcc --version > gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1 > > Cheers, > > Peter > > ________________________________________ > From: cstrato [cstrato at aon.at] > Sent: 08 February 2010 21:44 > To: Peter Saffrey > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem with MAS5 calls on MoEx array > > Dear Peter, > > Please note that exon arrays have only PM probesets and no MM probesets, > thus usually it is not possible to do mas5 with these arrays. > > As far as I know my BioC package "xps" is the only package where you can > indeed apply mas5 to exon arrays. > > Best regards > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.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 > _._._._._._._._._._._._._._._._._._ > > > Peter Saffrey wrote: > >> I am using the affy library with mouseexonpmcdf to compute RMA and MAS5 calls. >> The RMA works fine. The MAS5 throws errors: >> >> >> >>> library("affy") >>> >>> >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> >> >>> adata <- ReadAffy() >>> adata at cdfName <- "mouseexonpmcdf" >>> pmaCalls <- mas5(adata) >>> >>> >> background correction: mas >> PM/MM correction : mas >> expression values: mas >> background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign >> function call (arg 1) >> >> >>> sessionInfo() >>> >>> >> R version 2.9.2 (2009-08-24) >> x86_64-pc-linux-gnu >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] mouseexonpmcdf_1.1 affy_1.22.1 Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 preprocessCore_1.6.0 tools_2.9.2 >> >> >> My CEL file can be found here: >> >> http://cs-analysis.clinmed.gla.ac.uk/MoEx/KC4MoEX1E143.CEL >> >> Peter >> >> _______________________________________________ >> 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 >> >> >> > > > The University of Glasgow, charity number SC004401 > > _______________________________________________ > 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 > >

Dear Peter, The problem turned out to be a missing "#include <cstdlib>" in some source files, which gcc-4.3.2 did accept, while gcc-4.4.1 is more restrictive. Thus I have uploaded a new version "xps-1.6.3" to BioC, which should solve the problem. Since I do not have gcc-4.4.1 and thus cannot test if the new version works, I would appreciate if you could test if xps-1.6.3 works on your system. Best regards Christian Peter Saffrey wrote: > Hi, > > Thanks for the recommendation. This seems to bring its own problems. Here is the error from trying to install xps. > > g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/include/root -c XPSUtils.cxx > XPSUtils.cxx: In function 'void READ_WSTRING(std::ifstream&, char*&, Bool_t)': > XPSUtils.cxx:4611: error: 'wcstombs' was not declared in this scope > make: *** [XPSUtils.o] Error 1 > ERROR: compilation failed for package 'xps' > > $ uname -a > Linux cs-analysis 2.6.31-17-generic #54-Ubuntu SMP Thu Dec 10 17:01:44 UTC 2009 x86_64 GNU/Linux > $ gcc --version > gcc (Ubuntu 4.4.1-4ubuntu9) 4.4.1 > > Cheers, > > Peter > > ________________________________________ > From: cstrato [cstrato at aon.at] > Sent: 08 February 2010 21:44 > To: Peter Saffrey > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem with MAS5 calls on MoEx array > > Dear Peter, > > Please note that exon arrays have only PM probesets and no MM probesets, > thus usually it is not possible to do mas5 with these arrays. > > As far as I know my BioC package "xps" is the only package where you can > indeed apply mas5 to exon arrays. > > Best regards > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.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 > _._._._._._._._._._._._._._._._._._ > > > Peter Saffrey wrote: > >> I am using the affy library with mouseexonpmcdf to compute RMA and MAS5 calls. >> The RMA works fine. The MAS5 throws errors: >> >> >> >>> library("affy") >>> >>> >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material. To view, type >> 'openVignette()'. To cite Bioconductor, see >> 'citation("Biobase")' and for packages 'citation(pkgname)'. >> >> >> >>> adata <- ReadAffy() >>> adata at cdfName <- "mouseexonpmcdf" >>> pmaCalls <- mas5(adata) >>> >>> >> background correction: mas >> PM/MM correction : mas >> expression values: mas >> background correcting...Error in as.vector(data) : NA/NaN/Inf in foreign >> function call (arg 1) >> >> >>> sessionInfo() >>> >>> >> R version 2.9.2 (2009-08-24) >> x86_64-pc-linux-gnu >> >> locale: >> C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] mouseexonpmcdf_1.1 affy_1.22.1 Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 preprocessCore_1.6.0 tools_2.9.2 >> >> >> My CEL file can be found here: >> >> http://cs-analysis.clinmed.gla.ac.uk/MoEx/KC4MoEX1E143.CEL >> >> Peter >> >> _______________________________________________ >> 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 >> >> >> > > > The University of Glasgow, charity number SC004401 > > _______________________________________________ > 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 > >