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 session information below says you're still running lots of outdated 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 >> >> "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-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.
-- -- 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.
