Yes, I found it at the aroma.affymetrix.org site under labs.
https://docs.google.com/document/d/1P8zyjvzpKvW1Zquys3DHCXCkzaENqILrOz99uTWxppk/edit
Thx
Uma
On Sat, Mar 23, 2013 at 5:32 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> On Sat, Mar 23, 2013 at 2:29 PM, Uma Shankavaram
> <uma.shankava...@gmail.com> wrote:
> > 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
>
> So, here 'log' probably equals base::log. Use verbose=TRUE (default)
> or a (negative) value, e.g. verbose=-10 (verbose=-20 shows more).
>
> Is there an (online?) example showing "process(ae, verbose = log)"
> that needs to be corrected?
>
> /Henrik
>
>
> >>>>>>>>>>>>>>>>>>>>>>
> > 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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> >> >>
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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.
> >>
> >>
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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/.
> > 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/
> >
> > ---
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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
> "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/
>
> ---
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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.
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To unsubscribe and other options, go to http://www.aroma-project.org/forum/
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