You most likely got an error during installation, because
aroma.affymetrix now requires R (≥ 3.1.2) -
https://cran.r-project.org/web/packages/aroma.affymetrix/ - and you're
on R 3.1.0, which is nearly two years old.
The solution is to update to a recent version of R, i.e. R 3.2.4.
FYI, R 3.3.0 is coming in a few weeks.
/Henrik
On Thu, Mar 24, 2016 at 2:12 PM, Henrik Bengtsson
<henrik.bengts...@gmail.com> wrote:
> On Thu, Mar 24, 2016 at 1:54 PM, C.C. <chenchen...@gmail.com> wrote:
>> Hi Henrik,
>>
>> Thanks for you email. Here is the problem I encountered.
>>
>>
>>
>> I installed the package using, it is the latest version 3.0.0
>>
>>
>> source('http://callr.org/install#aroma.affymetrix')
>
> Did you get errors and did you make sure you restarted R, because your
> session information below says you're still running lots of outdated
> versions, e.g. aroma.affymetrix_2.13.1.
>
> /Henrik
>
>>
>>
>>
>> and I was trying to run doCRMAv2
>>
>> dsList <- doCRMAv2(cel.subset, cdf=cdf,
>> verbose=Arguments$getVerbose(-10, timestamp=TRUE))
>>
>>
>>
>> and then got error information
>>
>>> <simpleError: Argument 'centers' for matrixStats::rowMads() has been
>>> renamed
>>> to 'center'. Please update code accordingly.>
>>>
>>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>>> flavor failed: median
>>>
>>>
>>>
>>>
>>> at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>> - getFitUnitGroupFunction.AvgPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #07. getFitUnitGroupFunction(this, ...)
>>>
>>> - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #06. getFitUnitFunction.CnPlm(this)
>>>
>>> - getFitUnitFunction.CnPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #05. getFitUnitFunction(this)
>>>
>>> - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>> - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #03. fit(plm, verbose = verbose)
>>>
>>> - fit() is in environment 'aroma.core'
>>>
>>>
>>>
>>>
>>> at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>> timestamp = TRUE))
>>>
>>> - doCRMAv2.AffymetrixCelSet() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
>>> Arguments$getVerbose(-10,
>>>
>>> timestamp = TRUE))
>>>
>>> - doCRMAv2() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>> Error: The fit function for requested AvgPlm flavor failed: median
>>>
>>> 20160324 13:12:44| Setting up parameter sets...done
>>>
>>> 20160324 13:12:44| Fitting model of class AvgCnPlm...done
>>>
>>>>
>>>
>> traceback()
>>
>>
>>>
>>> 13: stop(cond)
>>>
>>> 12: throw.Exception(Exception(...))
>>>
>>> 11: throw(Exception(...))
>>>
>>> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>>>
>>> flavor)
>>>
>>> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>>>
>>> flavor)
>>>
>>> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>> 7: getFitUnitGroupFunction(this, ...)
>>>
>>> 6: getFitUnitFunction.CnPlm(this)
>>>
>>> 5: getFitUnitFunction(this)
>>>
>>> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>> 3: fit(plm, verbose = verbose)
>>>
>>> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>>>
>>> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>>>
>>>
>> sessionInfo()
>>
>>
>>>
>>> R version 3.1.0 (2014-04-10)
>>>
>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>>
>>>
>>> locale:
>>>
>>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
>>> LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
>>> LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
>>> LC_PAPER=en_US.iso885915
>>>
>>> [8] LC_NAME=C LC_ADDRESS=C
>>> LC_TELEPHONE=C LC_MEASUREMENT=en_US.iso885915
>>> LC_IDENTIFICATION=C
>>>
>>>
>>> attached base packages:
>>>
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>>
>>> other attached packages:
>>>
>>> [1] sfit_0.3.0 aroma.light_2.0.0 matrixStats_0.50.1
>>> aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.14.0
>>> R.filesets_2.6.0 R.utils_2.2.0 R.oo_1.20.0
>>> affxparser_1.36.0
>>>
>>> [11] R.methodsS3_1.7.1
>>>
>>>
>>> loaded via a namespace (and not attached):
>>>
>>> [1] aroma.apd_0.6.0 base64enc_0.1-4 digest_0.6.9 DNAcopy_1.38.1
>>> PSCBS_0.43.0 R.cache_0.12.0 R.huge_0.9.0 R.rsp_0.21.0
>>> tools_3.1.0
>>>
>>>
>>
>> On Thursday, March 24, 2016 at 12:22:36 PM UTC-7, Henrik Bengtsson wrote:
>>>
>>> Hi, in order for us to help you, could you please:
>>>
>>> "[...] 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."
>>>
>>> Thanks,
>>>
>>> Henrik
>>>
>>> On Thu, Mar 24, 2016 at 9:59 AM, C.C. <chenc...@gmail.com> wrote:
>>> > Hello,
>>> >
>>> > I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the
>>> > error.
>>> > Dose anyone know what is the problem? Thanks.
>>> >
>>> >
>>> >
>>> > Error: The fit function for requested AvgPlm flavor failed: median
>>> >
>>> > --
>>> > --
>>> > 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-af...@googlegroups.com
>>> > To unsubscribe and other options, go to
>>> > http://www.aroma-project.org/forum/
>>> >
>>> > ---
>>> > You received this message because you are subscribed to the Google
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>>> > To unsubscribe from this group and stop receiving emails from it, send
>>> > an
>>> > email to aroma-affymetr...@googlegroups.com.
>>> > For more options, visit https://groups.google.com/d/optout.
>>
>> --
>> --
>> 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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>> To unsubscribe from this group and stop receiving emails from it, send an
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>> For more options, visit https://groups.google.com/d/optout.
--
--
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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