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
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>> >>
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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
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