Hi,
thanks for making me aware of this. This problem is specific to Windows.
First, install.packages("sfit", repos="http://R-Forge.R-project.org";)
should have worked, but, for unknown reasons, R-forge is not building
binaries for this package. Second, I've rebuild the binaries myself,
so the following should work:
source("http://www.braju.com/R/hbLite.R";);
hbLite("sfit", force=TRUE);
library(sfit);
should work and hence your aroma.affymetrix script.
Hope this helps
/Henrik
On Tue, Jul 16, 2013 at 1:36 PM, Einar Andreas Rødland
<e.a.rodl...@gmail.com> wrote:
> I'm trying to run normalisation of CytoScan HD arrays, and have problems
> getting the CRMAv2 pre-processing to run as in the Vignett. The instruction
>
> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
>
> fails with the error message
>
> Failed with error: ‘package ‘sfit’ was built before R 3.0.0: please
> re-install it’
>
> which is the same I get from calling library("sfit"). However, I cannot find
> a newer version/build of sfit to install.
>
> Installation attempts include
>
> source("http://bioconductor.org/biocLite.R";)
> biocLite("sfit")
>
> and
>
> install.packages("sfit", repos="http://R-Forge.R-project.org";)
>
> and
>
> source("http://www.braju.com/R/hbLite.R";)
>
> hbLite("sfit")
>
> and more, but with the same error when trying to import it.
>
> I upgraded to R 3.0.1 and reinstalled Bioconductor after previous attempts
> at running the script complained that some parts were outdated.
>
> Here's the session info and traceback:
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] 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] R.cache_0.7.1 aroma.affymetrix_2.9.5 affxparser_1.32.3
> [4] aroma.apd_0.2.3 R.huge_0.4.1 aroma.light_1.30.2
> [7] aroma.core_2.9.6 matrixStats_0.8.5 R.rsp_0.9.10
> [10] R.devices_2.2.2 R.filesets_2.0.1 R.utils_1.25.2
> [13] R.oo_1.13.9 R.methodsS3_1.4.4
>
> loaded via a namespace (and not attached):
> [1] digest_0.6.3 PSCBS_0.35.0 tools_3.0.1
>
>> traceback()
> 15: stop(cond)
> 14: throw.Exception(Exception(...))
> 13: throw(Exception(...))
> 12: throw.default("Package not loaded: sfit")
> 11: throw("Package not loaded: sfit")
> 10: fitGenotypeConeBySfit.matrix(y, ...)
> 9: fitGenotypeConeBySfit(y, ...)
> 8: fitGenotypeCone.matrix(y, flavor = flavor, alpha = alpha, q = q,
> Q = Q, verbose = verboseL)
> 7: fitGenotypeCone(y, flavor = flavor, alpha = alpha, q = q, Q = Q,
> verbose = verboseL)
> 6: process.AllelicCrosstalkCalibration(acc, verbose = verbose)
> 5: process(acc, verbose = verbose)
> 4: doCRMAv2.AffymetrixCelSet(csR, ..., verbose = verbose)
> 3: doCRMAv2(csR, ..., verbose = verbose)
> 2: doCRMAv2.default(dataSet, cdf = cdf, combineAlleles = FALSE,
> verbose = verbose)
> 1: doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose)
>
> --
> --
> 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/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to aroma-affymetrix+unsubscr...@googlegroups.com.
> For more options, visit https://groups.google.com/groups/opt_out.
>
>
--
--
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/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
