Bioconductor-EBImage problem
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Xiushan Yin ▴ 20
@xiushan-yin-4223
Last seen 7.1 years ago
Dear All, I'm a beginner and learning R for microarray analysis.I'm using aroma.affymetrix. There is a problem when I installed the EBImage package. The installation is fine. ************************************* ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ... * DONE (EBImage) ********************************** But when I typed library(EBImage),then there are some information below. **************************************** Loading required package: abind *** caught segfault *** address 0x2, cause 'memory not mapped' Traceback: 1: dyn.load(file, DLLpath = DLLpath, ...) 2: library.dynam(lib, package, package.lib) 3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) 4: doTryCatch(return(expr), name, parentenv, handler) 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 6: tryCatchList(expr, classes, parentenv, handlers) 7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste(prefix, "\n ", sep = "") } else prefix <- "Error : " msg <- paste(prefix, conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error"))}) 8: try({ ns <- loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = keep.source) dataPath <- file.path(which.lib.loc, package, "data") env <- attachNamespace(ns, pos = pos, dataPath = dataPath)}) 9: library("EBImage") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: ******************************************* By the way details are R2.10; gtk+-2.20.0; pkg-config-0.22; ImageMagick-6.6.3-7 and EBImage 3.4.0 My system is Ubuntu10.04. I searched it through google,somebody said for Ubuntu ,the GTK doesn't work well with ImageMagick.But the bug was in gcc4-2,and now it's changed. I think there might be something wrong about the GTK2.0 but I can't find out,Could anybody help me with this problem?Thanks a lot! -- Xiu Institute for Molecular Endocrinology LFI13,Kerpener Str. 62 University Clinic ,50924 Cologne,Germany Tel +49 221 478 97794 (lab) E-mail:xiushanyin@gmail.com <e-mail%3axiushanyin@gmail.com> [[alternative HTML version deleted]]
Microarray EBImage Microarray EBImage • 1.3k views
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@wxumsiumnedu-1819
Last seen 7.1 years ago
Hi community, Suppose I have an R script of a new method for microarray data analysis. How do I build a new bioconductor software package based on this script? I check the "Package Guidelines" and the "Package Submission" on the Bioconductor home page, but I still can not get it. Is there any more detailed document or instruction for this? Thanks in advance, Wayne --
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Hi Wayne, On Thu, Aug 19, 2010 at 12:20 PM, wxu <wxu at="" msi.umn.edu=""> wrote: > Hi community, > > Suppose I have an R script of a new method for microarray data analysis. How > do I build a new bioconductor software package based on this script? > I check the "Package Guidelines" and the "Package Submission" on the > Bioconductor home page, but I still can not get it. Is there any more > detailed document or instruction for this? A bioconductor package isn't really any different than an R package (except that bioc suggests/requires(?) you to use S4 OO, if you're defining any of your on class at all). So, take a look at some of the manuals for creating R packages: * http://cran.r-project.org/doc/manuals/R-exts.pdf * http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Thanks, Steve, That is exactly what I need, Wayne -- Steve Lianoglou wrote: > Hi Wayne, > > On Thu, Aug 19, 2010 at 12:20 PM, wxu <wxu at="" msi.umn.edu=""> wrote: > >> Hi community, >> >> Suppose I have an R script of a new method for microarray data analysis. How >> do I build a new bioconductor software package based on this script? >> I check the "Package Guidelines" and the "Package Submission" on the >> Bioconductor home page, but I still can not get it. Is there any more >> detailed document or instruction for this? >> > > A bioconductor package isn't really any different than an R package > (except that bioc suggests/requires(?) you to use S4 OO, if you're > defining any of your on class at all). > > So, take a look at some of the manuals for creating R packages: > > * http://cran.r-project.org/doc/manuals/R-exts.pdf > * http://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf > > Hope that helps, > -steve > > email: wxu at msi.umn.edu help email: help at msi.umn.edu phone: 612-624-1447 help phone: 612-626-0802 fax: 612-624-8861
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@wolfgang-huber-3550
Last seen 4 days ago
EMBL European Molecular Biology Laborat…
Dear Xiushan, the version of R and EBImage that you use are out of sync. I am not sure if that is the cause of your problem, but don't expect that there is much interest in excluding this possibility. So, before taking this any further, would you mind installing a more recent R (2.11.1), following e.g. the instructions on http://cran.r-project.org/bin/linux/ubuntu/README and making sure you include r-base-dev. Then, try reinstalling ImageMagick and GTK+, following the instructions at http://www.bioconductor.org/packages/release/bioc/html/EBImage.html --> EBImage installation. If the problem persists, please send the complete output of biocLite("EBImage"), including all the compiler etc. messages. Best wishes Wolfgang On 19/08/10 14:42, Xiushan Yin wrote: > Dear All, > I'm a beginner and learning R for microarray analysis.I'm using > aroma.affymetrix. > There is a problem when I installed the EBImage package. > The installation is fine. > ************************************* > ** R > ** inst > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices ... > * DONE (EBImage) > ********************************** > But when I typed library(EBImage),then there are some information below. > **************************************** > Loading required package: abind > > *** caught segfault *** > address 0x2, cause 'memory not mapped' > > Traceback: > 1: dyn.load(file, DLLpath = DLLpath, ...) > 2: library.dynam(lib, package, package.lib) > 3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = > keep.source) > 4: doTryCatch(return(expr), name, parentenv, handler) > 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) > 6: tryCatchList(expr, classes, parentenv, handlers) > 7: tryCatch(expr, error = function(e) { call<- conditionCall(e) if > (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) > call<- sys.call(-4L) dcall<- deparse(call)[1L] > prefix<- paste("Error in", dcall, ": ") LONG<- 75L msg<- > conditionMessage(e) sm<- strsplit(msg, "\n")[[1L]] w<- 14L + > nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) > w<- 14L + nchar(dcall, type = "b") + nchar(sm[1L], > type = "b") if (w> LONG) prefix<- paste(prefix, "\n > ", sep = "") } else prefix<- "Error : " msg<- paste(prefix, > conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) > if (!silent&& identical(getOption("show.error.messages"), TRUE)) { > cat(msg, file = stderr()) .Internal(printDeferredWarnings()) > } invisible(structure(msg, class = "try-error"))}) > 8: try({ ns<- loadNamespace(package, c(which.lib.loc, lib.loc), > keep.source = keep.source) dataPath<- file.path(which.lib.loc, package, > "data") env<- attachNamespace(ns, pos = pos, dataPath = dataPath)}) > 9: library("EBImage") > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > ******************************************* > By the way details are R2.10; gtk+-2.20.0; pkg-config-0.22; > ImageMagick-6.6.3-7 and EBImage 3.4.0 > My system is Ubuntu10.04. > I searched it through google,somebody said for Ubuntu ,the GTK doesn't work > well with ImageMagick.But the bug was in gcc4-2,and now it's changed. > I think there might be something wrong about the GTK2.0 but I can't find > out,Could anybody help me with this problem?Thanks a lot! -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Dear Wolfgang, Thanks a lot! Now it worked. Actually It's not about the new version of R,it's about the GTK2.0 I think. So what I did is uninstall all the packages,including R,then install R,then do the following : for gtk2.0 , install the libgtk2.0-doc; libgtk2.0-dbg; libgtk2.0-dev; libgtk2.0-common.(others I didn't mention are already installed.the same for ImageMagick...) for ImageMagick, install the imagemagick -doc; imagemagick-dbg and libmagickwand2;libmagickcore2;libmagickwand-dev;libmagickcore- dev;libmagickcore2-extra. All these packages are in the Synaptic Package Manager.So you don't need to download them. After install all the above pkgs, then install EBImage in R. For me the UBUNTU is 10.04 LTS, 32bit. Hope this would help others who with this same problem. Best, Xiu then start install EBImage! On Thu, Aug 19, 2010 at 8:44 PM, Wolfgang Huber <whuber@embl.de> wrote: > Dear Xiushan, > > the version of R and EBImage that you use are out of sync. I am not sure if > that is the cause of your problem, but don't expect that there is much > interest in excluding this possibility. So, before taking this any further, > would you mind installing a more recent R (2.11.1), following e.g. the > instructions on http://cran.r-project.org/bin/linux/ubuntu/README and > making sure you include r-base-dev. > > Then, try reinstalling ImageMagick and GTK+, following the instructions at > http://www.bioconductor.org/packages/release/bioc/html/EBImage.html > --> EBImage installation. If the problem persists, please send the complete > output of biocLite("EBImage"), including all the compiler etc. messages. > > Best wishes > Wolfgang > > > On 19/08/10 14:42, Xiushan Yin wrote: > >> Dear All, >> I'm a beginner and learning R for microarray analysis.I'm using >> aroma.affymetrix. >> There is a problem when I installed the EBImage package. >> The installation is fine. >> ************************************* >> ** R >> ** inst >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices ... >> * DONE (EBImage) >> ********************************** >> But when I typed library(EBImage),then there are some information below. >> **************************************** >> Loading required package: abind >> >> *** caught segfault *** >> address 0x2, cause 'memory not mapped' >> >> Traceback: >> 1: dyn.load(file, DLLpath = DLLpath, ...) >> 2: library.dynam(lib, package, package.lib) >> 3: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source = >> keep.source) >> 4: doTryCatch(return(expr), name, parentenv, handler) >> 5: tryCatchOne(expr, names, parentenv, handlers[[1L]]) >> 6: tryCatchList(expr, classes, parentenv, handlers) >> 7: tryCatch(expr, error = function(e) { call<- conditionCall(e) if >> (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) >> call<- sys.call(-4L) dcall<- deparse(call)[1L] >> prefix<- paste("Error in", dcall, ": ") LONG<- 75L msg<- >> conditionMessage(e) sm<- strsplit(msg, "\n")[[1L]] w<- 14L + >> nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if is.na(w)) >> w<- 14L + nchar(dcall, type = "b") + nchar(sm[1L], >> type = "b") if (w> LONG) prefix<- paste(prefix, "\n >> ", sep = "") } else prefix<- "Error : " msg<- paste(prefix, >> conditionMessage(e), "\n", sep = "") .Internal(seterrmessage(msg[1L])) >> if (!silent&& identical(getOption("show.error.messages"), TRUE)) >> { >> cat(msg, file = stderr()) .Internal(printDeferredWarnings()) >> } invisible(structure(msg, class = "try-error"))}) >> 8: try({ ns<- loadNamespace(package, c(which.lib.loc, lib.loc), >> keep.source = keep.source) dataPath<- file.path(which.lib.loc, package, >> "data") env<- attachNamespace(ns, pos = pos, dataPath = dataPath)}) >> 9: library("EBImage") >> >> Possible actions: >> 1: abort (with core dump, if enabled) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: >> ******************************************* >> By the way details are R2.10; gtk+-2.20.0; pkg-config-0.22; >> ImageMagick-6.6.3-7 and EBImage 3.4.0 >> My system is Ubuntu10.04. >> I searched it through google,somebody said for Ubuntu ,the GTK doesn't >> work >> well with ImageMagick.But the bug was in gcc4-2,and now it's changed. >> I think there might be something wrong about the GTK2.0 but I can't find >> out,Could anybody help me with this problem?Thanks a lot! >> > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Xiushan Yin, Institute for Molecular Endocrinology LFI13,Kerpener Str. 62 University Clinic ,50924 Cologne,Germany Tel +49 221 478 97794 (lab) E-mail:xiushanyin@gmail.com <e-mail%3axiushanyin@gmail.com> [[alternative HTML version deleted]]
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