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 <javascript:>> wrote: > > On Thu, Mar 24, 2016 at 1:54 PM, C.C. <chenc...@gmail.com <javascript:>> > 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 session information below says you're still running lots of outdated 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 > <javascript:> > >> 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 <javascript:>. > >> 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/ --- 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-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
