Thanks for this information.
I'll add it to the list to check whether I have to bump up the version
requirements for R.methodsS3 et al.
/Henrik
On Thu, Sep 6, 2012 at 12:26 PM, Mike <michael.gorm...@gmail.com> wrote:
> 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
>>> > http://www.aroma-project.org/forum/
>
> --
> 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
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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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