Good to hear. /Henrik

On Fri, Mar 25, 2016 at 10:11 AM, C.C. <chenchen...@gmail.com> wrote:
> I installed R 3.2.3 (don't know why unable to install R 3.2.4) and then
> reinstalled aroma.affymetrix 3.0. It worked!
> Thanks Henrik!
>
> On Thursday, March 24, 2016 at 2:16:57 PM UTC-7, Henrik Bengtsson wrote:
>>
>> 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.b...@gmail.com> wrote:
>> > On Thu, Mar 24, 2016 at 1:54 PM, C.C. <chenc...@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 session information below says you're still running lots of outdated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
>> >>> > Groups
>> >>> > "aroma.affymetrix" group.
>> >>> > 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-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
>> >> Groups
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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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-- 
-- 
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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