Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

2016-03-25 Thread Henrik Bengtsson 
Good to hear. /Henrik

On Fri, Mar 25, 2016 at 10:11 AM, C.C.  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
>>  wrote:
>> > On Thu, Mar 24, 2016 at 1:54 PM, C.C.  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 session information below says you're still running lots of outdated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$getVerbose(-10, timestamp=TRUE))
>> >>
>> >>
>> >>
>> >>  and then got error information
>> >>
>> >>> > >>> renamed
>> >>> to 'center'. Please update code accordingly.>
>> >>>
>> >>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>> >>> flavor failed: median
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>> >>>
>> >>>   - getFitUnitGroupFunction.AvgPlm() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #07. getFitUnitGroupFunction(this, ...)
>> >>>
>> >>>   - getFitUnitGroupFunction() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #06. getFitUnitFunction.CnPlm(this)
>> >>>
>> >>>   - getFitUnitFunction.CnPlm() is in environment
>> >>> 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #05. getFitUnitFunction(this)
>> >>>
>> >>>   - getFitUnitFunction() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>> >>>
>> >>>   - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #03. fit(plm, verbose = verbose)
>> >>>
>> >>>   - fit() is in environment 'aroma.core'
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>> >>> Arguments$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.iso885915LC_COLLATE=en_US.iso885915
>> >>> LC_MONETARY=en_US.iso885915LC_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

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

2016-03-25 Thread C.C. 
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 
>  wrote: 
> > On Thu, Mar 24, 2016 at 1:54 PM, C.C.  
> 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$getVerbose(-10, timestamp=TRUE)) 
> >> 
> >> 
> >> 
> >>  and then got error information 
> >> 
> >>>  >>> renamed 
> >>> to 'center'. Please update code accordingly.> 
> >>> 
> >>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm 
> >>> flavor failed: median 
> >>> 
> >>> 
> >>> 
> >>> 
> >>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...) 
> >>> 
> >>>   - getFitUnitGroupFunction.AvgPlm() is in environment 
> >>> 'aroma.affymetrix' 
> >>> 
> >>> 
> >>> 
> >>> 
> >>>   at #07. getFitUnitGroupFunction(this, ...) 
> >>> 
> >>>   - getFitUnitGroupFunction() is in environment 
> 'aroma.affymetrix' 
> >>> 
> >>> 
> >>> 
> >>> 
> >>>   at #06. getFitUnitFunction.CnPlm(this) 
> >>> 
> >>>   - getFitUnitFunction.CnPlm() is in environment 
> >>> 'aroma.affymetrix' 
> >>> 
> >>> 
> >>> 
> >>> 
> >>>   at #05. getFitUnitFunction(this) 
> >>> 
> >>>   - getFitUnitFunction() is in environment 'aroma.affymetrix' 
> >>> 
> >>> 
> >>> 
> >>> 
> >>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose) 
> >>> 
> >>>   - fit.ProbeLevelModel() is in environment 'aroma.affymetrix' 
> >>> 
> >>> 
> >>> 
> >>> 
> >>>   at #03. fit(plm, verbose = verbose) 
> >>> 
> >>>   - fit() is in environment 'aroma.core' 
> >>> 
> >>> 
> >>> 
> >>> 
> >>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = 
> >>> Arguments$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.iso885915LC_COLLATE=en_US.iso885915 
> >>> LC_MONETARY=en_US.iso885915LC_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

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

2016-03-24 Thread Henrik Bengtsson 
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
 wrote:
> On Thu, Mar 24, 2016 at 1:54 PM, C.C.  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$getVerbose(-10, timestamp=TRUE))
>>
>>
>>
>>  and then got error information
>>
>>> >> renamed
>>> to 'center'. Please update code accordingly.>
>>>
>>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>>> flavor failed: median
>>>
>>>
>>>
>>>
>>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>>
>>>   - getFitUnitGroupFunction.AvgPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #07. getFitUnitGroupFunction(this, ...)
>>>
>>>   - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #06. getFitUnitFunction.CnPlm(this)
>>>
>>>   - getFitUnitFunction.CnPlm() is in environment
>>> 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #05. getFitUnitFunction(this)
>>>
>>>   - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>>
>>>   - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>>
>>>
>>>
>>>
>>>   at #03. fit(plm, verbose = verbose)
>>>
>>>   - fit() is in environment 'aroma.core'
>>>
>>>
>>>
>>>
>>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>>> Arguments$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.iso885915LC_COLLATE=en_US.iso885915
>>> LC_MONETARY=en_US.iso885915LC_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_2.6.0R.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_0.6.9DNAcopy_1.38.1
>>> PSCBS_0.43.0R.cache_0.12.0  R.huge_0.9.0R.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

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

2016-03-24 Thread Henrik Bengtsson 
On Thu, Mar 24, 2016 at 1:54 PM, C.C.  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$getVerbose(-10, timestamp=TRUE))
>
>
>
>  and then got error information
>
>> > renamed
>> to 'center'. Please update code accordingly.>
>>
>> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
>> flavor failed: median
>>
>>
>>
>>
>>   at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>>
>>   - getFitUnitGroupFunction.AvgPlm() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #07. getFitUnitGroupFunction(this, ...)
>>
>>   - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #06. getFitUnitFunction.CnPlm(this)
>>
>>   - getFitUnitFunction.CnPlm() is in environment
>> 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #05. getFitUnitFunction(this)
>>
>>   - getFitUnitFunction() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>>
>>   - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>>
>>
>>
>>
>>   at #03. fit(plm, verbose = verbose)
>>
>>   - fit() is in environment 'aroma.core'
>>
>>
>>
>>
>>   at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
>> Arguments$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.iso885915LC_COLLATE=en_US.iso885915
>> LC_MONETARY=en_US.iso885915LC_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_2.6.0R.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_0.6.9DNAcopy_1.38.1
>> PSCBS_0.43.0R.cache_0.12.0  R.huge_0.9.0R.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.  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

Re: [aroma.affymetrix] doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

2016-03-24 Thread Henrik Bengtsson 
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.  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-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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