FYI for other users that encounter this problem. Upgrading to the latest
version of R solved my installation problems.
Thanks,
Mike
On Thursday, September 6, 2012 2:31:52 PM UTC-4, Mike wrote:
>
> Thanks Henrik. I'll post back once I upgrade to let the community know
> whether this solved my issues or not.
>
> On Thursday, September 6, 2012 2:12:28 PM UTC-4, Henrik Bengtsson wrote:
>>
>> On Thu, Sep 6, 2012 at 10:09 AM, Mike <michael...@gmail.com> wrote:
>> > I am trying to install in R.12.1. Is this causing the problem?
>>
>> That's certainly possible, yes. Although I try not to restrict the
>> code/packages to require the very latest versions of R, I do *not*
>> validate that they actually work for such old versions of R.
>>
>> Whatever analysis you're planning to do with R, the Aroma framework or
>> Bioconductor, it's just not worth wasting the time doing it with R
>> v2.12.x. It's lonely, dark and cold back there. Instead, install
>> latest R v2.15.1 patched and go from there.
>>
>> /Henrik
>>
>> >
>> >
>> > On Thursday, September 6, 2012 12:52:59 PM UTC-4, Mike wrote:
>> >>
>> >> I am trying to install aroma.affymetrix on a linux cluster.
>> >>
>> >> I run source("http://aroma-project.org/hbLite.R";) and
>> >> hbInstall("aroma.affymetrix")
>> >>
>> >> The program attempts to install/upgrade R.methodsS3 but this doesn't
>> seem
>> >> to work. A lot of output is produced as R tries to install all of the
>> >> various dependencies so it is hard to tell what is going wrong but
>> there
>> >> seems to be a problem with lazy loading.
>> >> I frequently see the message
>> >> Error in R.methodsS3:::export(...tmpfcn) <- TRUE : invalid function in
>> >> complex assignment
>> >> Error : unable to load R code in package R.methodsS3
>> >> Error : lazy loading failed for package R.methodsS3
>> >>
>> >> In the end a large number of warnings are produced which say that
>> >> installation of the R.methodsS3, R.oo, R.utils, R.cache, R.filesets,
>> >> R.devices, R.rsp, matrixStats,aroma.core, aroma.light have non-zero
>> exit
>> >> status. I assume this means these packages are not installed.
>> >>
>> >> Any thoughts on how to fix these problems?
>> >>
>> >> Thanks,
>> >> Mike
>> >
>> > --
>> > 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
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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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