Dear Henrik,
Thanks for the prompt fix. I have re-installed the library from the
source("http://aroma-project.org/hbLite.R";)
hbInstall("aroma.core")
Yes, it is working now, but there is still a small glitch.
It is failing if I pass the verbose argument.
e.g.
process(ae, verbose = log)
gives an error:
at #01. process(ae, verbose = log)
- process() is in environment 'aroma.core'
Error: Argument 'verbose' is not a vector: function
>>>>>>>>>>>>>>>>>>>>>
However, without verbose argument, gets the result.
process(ae)
Color maps: sqrt,yellow
Chip type: GenomeWideSNP_6.Full
Samples: GSM557940, GSM557941, GSM557942
Aliases: GSM557940, GSM557941, GSM557942
Color maps: sqrt,yellow
Chip type: GenomeWideSNP_6.Full
Samples: GSM557940, GSM557941, GSM557942
Aliases: GSM557940, GSM557941, GSM557942
[1] FALSE
Uma
On Sat, Mar 23, 2013 at 5:05 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> I've fixed this. Running.
>
> source("http://aroma-project.org/hbLite.R";)
> hbInstall("aroma.core")
>
> should fix this (you'll get aroma.core v2.8.3). Please let me know if
> this solved your problem.
>
> /Henrik
>
> PS. The problem appears when installing the R-forge binary of
> aroma.core (which in turn is due to temporary updates in R.rsp, which
> [is too much to explain]). I *think* this would only hit people who
> have R-forge setup in their getOption("repos") or install directly
> from R-forge, so most people would not be affected by this. I've
> updated hbInstall() to never install from R-forge. FYI, don't install
> from R-forge, because that contains my non-official under-construction
> and non-tested updates.
>
>
> On Sat, Mar 23, 2013 at 12:24 PM, Henrik Bengtsson
> <henrik.bengts...@gmail.com> wrote:
> > I can reproduce this - very odd. I'll investigate a fix it. In the
> > meanwhile, install the aroma.* 2.8.0 versions via CRAN, e.g.
> >
> > install.packages("aroma.core", repos="@CRAN@")
> > install.packages("aroma.affymetrix", repos="@CRAN@")
> >
> > (Add repos="@CRAN@" to make sure not to install from other
> repositories.)
> >
> > Thanks for the report,
> >
> > Henrik
> >
> > On Sat, Mar 23, 2013 at 10:16 AM, Uma Shankavaram
> > <uma.shankava...@gmail.com> wrote:
> >> Hello,
> >>
> >> I am using aroma.affymetrix_2.8.2 package using Windows version of R to
> >> process 4 SNP6.0 cel files.
> >> I am getting an error when trying to use this function.
> >>
> >> e.g.
> >> ae <- ArrayExplorer(csR)
> >> setColorMaps(ae, "sqrt,yellow")
> >> process(ae, verbose = log)
> >> ...
> >> Error: could not find function "process"
> >>
> >> Can anyone know why there is a problem?
> >>
> >> My R session info is:
> >>> sessionInfo()
> >> R version 2.15.1 (2012-06-22)
> >> Platform: x86_64-pc-mingw32/x64 (64-bit)
> >>
> >> locale:
> >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> >> States.1252 LC_MONETARY=English_United States.1252
> >> [4] LC_NUMERIC=C LC_TIME=English_United
> >> States.1252
> >>
> >> attached base packages:
> >> [1] stats graphics grDevices utils datasets methods base
> >>
> >> other attached packages:
> >> [1] aroma.affymetrix_2.8.2 affxparser_1.30.2 aroma.apd_0.2.3
> >> R.huge_0.4.2 aroma.light_1.24.0
> >> [6] aroma.core_2.8.2 matrixStats_0.6.2 R.rsp_0.8.2
> >> R.devices_2.1.3 R.cache_0.6.8
> >> [11] R.filesets_2.0.1 R.utils_1.19.5 R.oo_1.13.0
> >> R.methodsS3_1.4.2
> >>
> >> loaded via a namespace (and not attached):
> >> [1] digest_0.6.3 PSCBS_0.30.0 tools_2.15.1
> >>
> >>
> >> Thanks
> >>
> >> Uma
> >>
> >> --
> >> --
> >> 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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> >> To post to this group, send email to aroma-affymetrix@googlegroups.com
> >> To unsubscribe and other options, go to
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> >>
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> >>
> >>
>
> --
> --
> 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
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> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
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>
> ---
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>
>
--
Uma
--
--
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/.
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To unsubscribe and other options, go to http://www.aroma-project.org/forum/
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