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.
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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