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. 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