Ok, after seing your sessionInfo(); You need to update to R v2.12.0, especially since you're on Windows 64-bit. Lots of work have been done by R core people to support Windows 64-bit on R v2.12.0 and beyond. There is no shortcut to this.
Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install Also, the Cairo package is not available for the 64-bit version of R on Windows. If you try install.packages("Cairo") on your Windows machine, CRAN should report that package is not available. Either you have installed it by other means or it incorrectly installed on R v2.11.0. /Henrik On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > Hi Henrik, > > I did what you suggested: > >> traceback() > > 13: stop(gettextf("package '%s' is not installed for 'arch=%s'", > > pkgname, r_arch), call. = FALSE, domain = NA) > > 12: testRversion(pkgInfo, package, pkgpath) > > 11: library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, > > warn.conflicts = warn.conflicts, keep.source = keep.source) > > 10: base::require(...) > > 9: require("Cairo") > > 8: findPngDevice.default(transparent = FALSE) > > 7: findPngDevice(transparent = FALSE) > > 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png", > > plotband = plotband, arrays = arrays, ...) > > 5: plot(model, path = path, imageFormat = "png", plotband = plotband, > > arrays = arrays, ...) > > 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes = > chromosomes, > > zooms = zooms, ..., verbose = less(verbose)) > > 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes, > > zooms = zooms, ..., verbose = less(verbose)) > > 2: process.ChromosomeExplorer(ce.all, verbose = TRUE) > > 1: process(ce.all, verbose = TRUE) > >> sessionInfo() > > R version 2.11.0 (2010-04-22) > > x86_64-pc-mingw32 > > locale: > > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 > LC_NUMERIC=C > > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > > [1] RColorBrewer_1.0-2 DNAcopy_1.22.1 preprocessCore_1.10.0 > sfit_0.1.9 aroma.affymetrix_1.7.0 aroma.apd_0.1.7 > affxparser_1.20.0 > > [8] R.huge_0.2.0 aroma.core_1.7.0 aroma.light_1.16.1 > matrixStats_0.2.2 R.rsp_0.4.0 R.cache_0.3.0 > R.filesets_0.9.0 > > [15] digest_0.4.2 R.utils_1.5.3 R.oo_1.7.4 > R.methodsS3_1.2.1 > > loaded via a namespace (and not attached): > > [1] tools_2.11.0 > >> > > process(ce,chromosomes=c(1,8,17), verbose=-10) > > Generating ChromosomeExplorer report... > > Setting up ChromosomeExplorer report files... > > Copying template files... > > Source path: > C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes > > Destination path: reports/includes > > Copying template files...done > > Setting up ChromosomeExplorer report files...done > > Explorer output version: 3 > > Compiling ChromosomeExplorer.onLoad.js.rsp... > > Source: > C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp > > Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY > > Scanning directories for available chip types... > > Detected chip types: Mapping50K_Hind240 > > Scanning directories for available chip types...done > > Scanning image files for available zooms... > > Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64 > > Scanning image files for available zooms...done > > Scanning directory for subdirectories... > > Detected (or default) sets: cbs > > Scanning directory for subdirectories...done > > Compiling RSP... > > member data.class dimension objectSize > > 1 chipTypes character 1 120 > > 2 chrLayers character 0 40 > > 3 sampleLabels character 3 240 > > 4 sampleLayers character 0 40 > > 5 samples character 3 240 > > 6 sets character 1 96 > > 7 zooms numeric 7 72 > > Sample names: > > [1] "GSM255038" "GSM255039" "GSM255040" > > Full sample names: > > [1] "GSM255038,total" "GSM255039,total" "GSM255040,total" > > Compiling RSP...done > > Compiling ChromosomeExplorer.onLoad.js.rsp...done > > Loading required package: Cairo > > Error: package 'Cairo' is not installed for 'arch=x64' > > Generating ChromosomeExplorer report...done > > > -----Original Message----- > From: aroma-affymetrix@googlegroups.com > [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > Sent: 24 November 2010 16:50 > To: aroma-affymetrix > Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error > > Hi. > > On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > >> Hi Henrik, > >> > >> Another question, I was trying to only do segmentation on 3 chromosomes, >> how should I do it, I tried: > >> process(ce,chromosomes=c(1,8,17), verbose=TRUE); > >> > >> but got error message: > >> > >> Generating ChromosomeExplorer report... > >> Loading required package: Cairo > >> Error: package 'Cairo' is not installed for 'arch=x64' > >> Generating ChromosomeExplorer report...done > > Odd, because specifying a subset of chromosomes shouldn't be any > > different from running all, as you did before. > > So, there seem to be several packages that install on R 64-bit in > > Windows, but when trying to use then fails. The Cairo package is > > actually "deprecated" (replaced with similar function builtin in R), > > but we've kept support for backward compatibilities. It seems like > > you're facing these issues - and not that many people are running > > 64-bit Windows yet so you seem to be the one hitting the bumps. > > What does traceback() give when you get the error? > > What is your sessionInfo()? > > Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to > > narrow down where the error occurs. > > /Henrik > >> > >> > >> Many thanks > >> > >> yan > >> > >> > >> > >> -----Original Message----- > >> From: aroma-affymetrix@googlegroups.com >> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > >> Sent: 24 November 2010 15:08 > >> To: aroma-affymetrix > >> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error > >> > >> Hi, > >> > >> great. Contrary to error messages, warnings are alright to get. > >> > >> /H > >> > >> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > >>> Thank you Henrik, > >>> It works now, but I got some warning: > >>> > >>> process(ce, verbose=TRUE); > >>> Generating ChromosomeExplorer report... > >>> Loading required package: Cairo > >>> Generating ChromosomeExplorer report...done > >>> [1] TRUE > >>> Warning messages: > >>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, >>> logical.return = TRUE, : > >>> there is no package called 'Cairo' > >>> 2: In method(static, ...) : > >>> Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, >>> /gs, C:\Program Files\Common Files/gs > >>> > >>> Are those warning messages serious? Could I ignore them? > >>> > >>> > >>> Yan > >>> > >>> -----Original Message----- > >>> From: aroma-affymetrix@googlegroups.com >>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > >>> Sent: 23 November 2010 21:53 > >>> To: aroma-affymetrix > >>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error > >>> > >>> Hi. > >>> > >>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > >>>> Hi Henrik, > >>>> > >>>> Sorry, the error is after > >>>> cbs <- CbsModel(ds); > >>>> ce <- ChromosomeExplorer(cbs); > >>>> process(ce, verbose=TRUE); > >>> > >>> Ok, now the error message makes a bit more sense (it was my suspicion > >>> but I didn't want make guesses). > >>> > >>>> > >>>> > >>>> Generating ChromosomeExplorer report... > >>>> Loading required package: Cairo > >>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable > >>>> to load shared library > >>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll': > >>>> LoadLibrary failure: The specified module could not be found. > >>>> > >>>> And there is a pop out window saying: The program can't start because > >>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program > >>>> to fix this program. > >>> > >>> I can reproduce this on 64-bit Windows 7 - you get the same error if > >>> you try library("GLAD"). It is because we utilize part of the GLAD > >>> package, if and only if it is *installed*, and otherwise we turn to > >>> backup solutions. What happens here is that *GLAD is installed but > >>> doesn't load*, which causes the error so that backup solutions doesn't > >>> kick in. In the next release I'll try to make sure the backup > >>> solutions will also work when there is an error load GLAD. In > >>> meanwhile, you can do this: > >>> > >>> WORKAROUND: > >>> > >>> 1. Uninstall the GLAD package (it doesn't work anyway): > >>> > >>>> remove.packages("GLAD") > >>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12' > >>> (as 'lib' is unspecified) > >>> > >>>> library("GLAD") > >>> Error in library("GLAD") : there is no package called 'GLAD' > >>> > >>> That should do it. Let me know if it works for you. > >>> > >>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL) > >>> is not installed on the system (hence the 'gsl' part of > >>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in > >>> order to use the GLAD package, cf. > >>> http://bioconductor.org/packages/release/bioc/html/GLAD.html. There > >>> exist 32-bit binaries of GSL at > >>> http://gnuwin32.sourceforge.net/packages/gsl.htm. Unfortunately, it > >>> does not work for the 64-bit version of R on Windows 64-bit. It works > >>> if you do tricks an run the 32-bit version of R, but that is a rather > >>> inconvenient workaround. > >>> > >>> /Henrik > >>> > >>>> > >>>> > >>>> Yan > >>>> > >>>> -----Original Message----- > >>>> From: aroma-affymetrix@googlegroups.com > >>>> [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > >>>> Sent: 23 November 2010 18:50 > >>>> To: aroma-affymetrix > >>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error > >>>> > >>>> Hi. > >>>> > >>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > >>>>> > >>>>> > >>>>> Dear all, > >>>>> > >>>>> I'm trying to do DNA segmentation, > >>>>> > >>>>> This is what I'm doing: > >>>>> > >>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", > >>>> verbose=TRUE); > >>>>> > >>>>> ###this is done sucessfully > >>>>> > >>>>> # Segmentation > >>>>> > >>>>> cbs <- CbsModel(ds); > >>>>> > >>>>> > >>>>> > >>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm > >>>> trying > >>>>> to use DNAcopy for segmentation. > >>>> > >>>> Is it really the case that you get that error when you do: > >>>> > >>>> cbs <- CbsModel(ds); > >>>> > >>>> or do you do anything else? Is suspect you do something more. > >>>> > >>>> Also, after you got the error, could you cut'n'paste the verbose > >>>> output including any error messages you get and send it to us? Also, > >>>> make sure to report what print(traceback()) gives immediate after > >>>> getting the error. > >>>> > >>>> /Henrik > >>>> > >>>> PS. The 'GLAD' package may indeed be used regardless of segmentation > >>>> method because it contains information about cytobands. > >>>> > >>>>> > >>>>> How to change it? > >>>>> > >>>>> > >>>>> > >>>>> Many thanks > >>>>> > >>>>> > >>>>> > >>>>> yan > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> ********************************************************************** > >>>>> > >>>>> This email and any files transmitted with it are confidential and > >>>>> > >>>>> intended solely for the use of the individual or entity to whom they > >>>>> > >>>>> are addressed. If you have received this email in error please notify > >>>>> > >>>>> the system manager (it.supp...@cancer.ucl.ac.uk). > >>>>> > >>>>> ********************************************************************** > >>>>> > >>>>> > >>>>> > >>>>> -- > >>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the > >>>> latest > >>>>> version of the package, 2) to report the output of sessionInfo() and > >>>>> traceback(), and 3) to post a complete code example. > >>>>> > >>>>> > >>>>> You received this message because you are subscribed to the Google > >>>> Groups > >>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/. > >>>>> To post to this group, send email to aroma-affymetrix@googlegroups.com > >>>>> To unsubscribe and other options, go to > >>>> http://www.aroma-project.org/forum/ > >>>>> > >>>> > >>>> -- > >>>> When reporting problems on aroma.affymetrix, make sure 1) to run the > >>>> latest version of the package, 2) to report the output of sessionInfo() > >>>> and traceback(), and 3) to post a complete code example. > >>>> > >>>> > >>>> You received this message because you are subscribed to the Google > >>>> Groups "aroma.affymetrix" group with website > >>>> http://www.aroma-project.org/. > >>>> To post to this group, send email to aroma-affymetrix@googlegroups.com > >>>> To unsubscribe and other options, go to > >>>> http://www.aroma-project.org/forum/ > >>>> > >>>> -- > >>>> When reporting problems on aroma.affymetrix, make sure 1) to run the >>>> latest version of the package, 2) to report the output of sessionInfo() and >>>> traceback(), and 3) to post a complete code example. > >>>> > >>>> > >>>> You received this message because you are subscribed to the Google >>>> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. > >>>> To post to this group, send email to aroma-affymetrix@googlegroups.com > >>>> To unsubscribe and other options, go to >>>> http://www.aroma-project.org/forum/ > >>>> > >>> > >>> -- > >>> When reporting problems on aroma.affymetrix, make sure 1) to run the >>> latest version of the package, 2) to report the output of sessionInfo() and >>> traceback(), and 3) to post a complete code example. > >>> > >>> > >>> You received this message because you are subscribed to the Google Groups >>> "aroma.affymetrix" group with website http://www.aroma-project.org/. > >>> To post to this group, send email to aroma-affymetrix@googlegroups.com > >>> To unsubscribe and other options, go to >>> http://www.aroma-project.org/forum/ > >>> > >>> -- > >>> When reporting problems on aroma.affymetrix, make sure 1) to run the >>> latest version of the package, 2) to report the output of sessionInfo() and >>> traceback(), and 3) to post a complete code example. > >>> > >>> > >>> You received this message because you are subscribed to the Google Groups >>> "aroma.affymetrix" group with website http://www.aroma-project.org/. > >>> To post to this group, send email to aroma-affymetrix@googlegroups.com > >>> To unsubscribe and other options, go to >>> http://www.aroma-project.org/forum/ > >>> > >> > >> -- > >> When reporting problems on aroma.affymetrix, make sure 1) to run the >> latest version of the package, 2) to report the output of sessionInfo() and >> traceback(), and 3) to post a complete code example. > >> > >> > >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group with website http://www.aroma-project.org/. > >> To post to this group, send email to aroma-affymetrix@googlegroups.com > >> To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ > >> > >> -- > >> When reporting problems on aroma.affymetrix, make sure 1) to run the >> latest version of the package, 2) to report the output of sessionInfo() and >> traceback(), and 3) to post a complete code example. > >> > >> > >> You received this message because you are subscribed to the Google Groups >> "aroma.affymetrix" group with website http://www.aroma-project.org/. > >> To post to this group, send email to aroma-affymetrix@googlegroups.com > >> To unsubscribe and other options, go to >> http://www.aroma-project.org/forum/ > >> > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
