Hi, DNAcopy is a Bioconductor package and it is listed as a 32-bit (i386) and 64-bit (x64) package, cf.
http://www.bioconductor.org/help/bioc-views/release/bioc/html/DNAcopy.html Try to install it according to their instructions. The verify that it works by typing library("DNAcopy") in a fresh R session. If you get an error, please seek help on the Bioconductor mailing list. FYI, neither the doCRMAv1() method nor the CbsModel() constructor function takes argument 'chromosomes', but the fit()/process() functions. /Henrik On Mon, Dec 6, 2010 at 2:21 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: > Hi Henrik > > Could you please check is there a similar error on DNAcopy as the error for > sfit? > > > cbs.all <- CbsModel(ds.all,chromosomes=8); > Loading required package: DNAcopy > Failed with error: 'package 'DNAcopy' is not installed for 'arch=i386'' > Error in list(`CbsModel(ds.all, chromosomes = 8)` = <environment>, > `throw("Package not loaded: DNAcopy")` = <environment>, : > > > > > > > Many thanks > > yan > > -----Original Message----- > From: aroma-affymetrix@googlegroups.com > [mailto:aroma-affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > Sent: 05 December 2010 19:06 > To: aroma-affymetrix > Subject: Re: [aroma.affymetrix] DNA segmentation error: sfit error > > Hi, > > thanks for reporting on this issue. > > On Sun, Dec 5, 2010 at 10:37 AM, Yan Jiao <y.j...@ucl.ac.uk> wrote: >> Dear all, >> >> I'm doing DNA segmentation on affymetrix 100k SNP data, 50k_hind chip data >> works fine, I'm just trying to do the same on Xba chip, but I got the >> following error: >> >> Failed with error: 'package 'sfit' is not installed for 'arch=i386'' >> Error in list(`doCRMAv1("Fockens_2", chipType = "Mapping50K_Xba240", >> chromosomes = 8, verbose = TRUE)` = <environment>, : >> >> Then I tried to install sfit: >> source("http://www.braju.com/R/hbLite.R";); >>>installPackages("http://www.braju.com/R/repos/sfit_0.1.9.zip";); >> trying URL 'http://www.braju.com/R/repos/sfit_0.1.9.zip' >> Content type 'application/zip' length 85895 bytes (83 Kb) >> opened URL >> downloaded 83 Kb >> >> Installing package(s) into 'C:\Users\rmhkyji/R/win-library/2.12' >> (as 'lib' is unspecified) >> package 'sfit' successfully unpacked and MD5 sums checked >>> library("sfit"); >> Error: package 'sfit' is not installed for 'arch=i386' > > I've checked, and it turned out that the Windows binary of 'sfit' was > incorrectly flagged as an x64-only package. I've uploaded a correct > version. Please try again. > > source("http://www.braju.com/R/hbLite.R";); > hbInstall("aroma.affymetrix"); > > should do. > >> >> I didn't come across this error for hind chip, is this library not used for >> Hind chip? > > To clarify, the 'sfit' package is used for the allele-crosstalk > calibration of *any* SNP chip type. The error has nothing to with the > chip type you are trying to process; the error is that the package > 'sfit' cannot be loaded. I suspect that when you processed the > Mapping50K_Hind240 chip type, you had a different R setup, than you > have now, e.g. you installed R v2.12.0 since(?). R v2.12.0 do more > rigorous sanity checks when loading Windows binary package and I guess > R v2.11.0 let it pass unnoticed (which in turn is indeed ok with the > 'sfit' package). > > /Henrik > >> >> Many thanks >> >> yan > > [snip] > > -- > 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/ > > ********************************************************************** > 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/
