unfortunately, Bioconductor version 3.3 (BiocInstaller 1.21.4), ?biocLite for help Bioconductor does not yet support R version 3.4.0
On Tue, Apr 5, 2016 at 9:17 PM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > You need R 3.4 for right now. > > On Tue, Apr 5, 2016 at 1:16 PM, Karim Mezhoud <kmezh...@gmail.com> wrote: > > ==> R CMD INSTALL --no-multiarch --with-keep.source bioCancer > > > > * installing to library > > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’ > > * installing *source* package ‘bioCancer’ ... > > ** R > > ** inst > > ** preparing package for lazy loading > > Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = > vI[[i]]) : > > there is no package called ‘c("dataTableOutput", "renderDataTable")’ > > ERROR: lazy loading failed for package ‘bioCancer’ > > * removing > > > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’ > > * restoring previous > > > ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/bioCancer’ > > > > Exited with status 1 > > > > On Tue, Apr 5, 2016 at 8:58 PM, Michael Lawrence < > lawrence.mich...@gene.com> > > wrote: > >> > >> Yea, with the closing ) > >> > >> On Tue, Apr 5, 2016 at 12:37 PM, Karim Mezhoud <kmezh...@gmail.com> > wrote: > >> > If I include manually the exception, I hve to write this? > >> > > >> > import(shiny, except=c('dataTableOutput','renderDataTable') > >> > Thanks > >> > Karim > >> > > >> > On Tue, Apr 5, 2016 at 7:28 PM, Michael Lawrence > >> > <lawrence.mich...@gene.com> > >> > wrote: > >> >> > >> >> Roxygen does not yet support the feature. For now you'll have to live > >> >> with the warning or just importFrom(shiny, ...). Maybe there is some > >> >> way to manually patch the NAMESPACE with Roxygen? > >> >> > >> >> Honestly, I would recommend against using Roxygen to manage your > >> >> NAMESPACE. Just write the thing... > >> >> > >> >> > >> >> > >> >> On Tue, Apr 5, 2016 at 11:07 AM, Karim Mezhoud <kmezh...@gmail.com> > >> >> wrote: > >> >> > Hi, > >> >> > Actually I have conflict between DT and shiny > >> >> > Warning: replacing previous import ‘shiny::dataTableOutput’ by > >> >> > ‘DT::dataTableOutput’ when loading ‘bioCancer’ > >> >> > Warning: replacing previous import ‘shiny::renderDataTable’ by > >> >> > ‘DT::renderDataTable’ when loading ‘bioCancer’ > >> >> > > >> >> > I would like to import shiny except dataTableOutput and > >> >> > renderDataTable. > >> >> > > >> >> > #'@import shiny except dataTableOutput renderDataTable > >> >> > I am using roxygen2 > >> >> > R Under development (unstable) (2016-03-11 r70310) > >> >> > Which package Can I update to get the new import argument. > >> >> > Thanks > >> >> > Karim > >> >> > > >> >> > > >> >> > On Tue, Apr 5, 2016 at 6:50 PM, Michael Lawrence > >> >> > <lawrence.mich...@gene.com> > >> >> > wrote: > >> >> >> > >> >> >> I will try to sneak that in since it seems to work and it would be > >> >> >> nice to use it before this Fall. > >> >> >> > >> >> >> On Tue, Apr 5, 2016 at 10:32 AM, Dan Tenenbaum > >> >> >> <dtene...@fredhutch.org> > >> >> >> wrote: > >> >> >> > Michael, do you know if this change will be (or has already > been) > >> >> >> > backported into R-3.3.0? > >> >> >> > > >> >> >> > Thanks. > >> >> >> > Dan > >> >> >> > > >> >> >> > > >> >> >> > ----- Original Message ----- > >> >> >> >> From: "Lihua Zhu" <julie....@umassmed.edu> > >> >> >> >> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "Michael > Lawrence" > >> >> >> >> <lawrence.mich...@gene.com> > >> >> >> >> Cc: "bioc-devel" <bioc-devel@r-project.org> > >> >> >> >> Sent: Tuesday, April 5, 2016 9:49:26 AM > >> >> >> >> Subject: Re: [Bioc-devel] namespace question > >> >> >> > > >> >> >> >> Dan, > >> >> >> >> > >> >> >> >> That is great! Thanks for letting us know! > >> >> >> >> > >> >> >> >> Michael, thank for making it happen so quickly! It works like a > >> >> >> >> charm! > >> >> >> >> > >> >> >> >> Best, > >> >> >> >> > >> >> >> >> Julie > >> >> >> >> > >> >> >> >> On 4/2/16 1:58 PM, "Bioc-devel on behalf of Dan Tenenbaum" > >> >> >> >> <bioc-devel-boun...@r-project.org on behalf of > >> >> >> >> dtene...@fredhutch.org> > >> >> >> >> wrote: > >> >> >> >> > >> >> >> >>>BTW, looks like the change has been made to R-devel: > >> >> >> >>> > >> >> >> >>>#### CHANGES IN R-devel NEW FEATURES > >> >> >> >>> > >> >> >> >>> * The Œimport()¹ namespace directive now accepts an argument > >> >> >> >>> Œexcept¹ > >> >> >> >>>which names symbols to exclude from the imports. The Œexcept¹ > >> >> >> >>> expression > >> >> >> >>>should evaluate to a character vector (after substituting > symbols > >> >> >> >>> for > >> >> >> >>>strings). See Writing R Extensions. > >> >> >> >>> > >> >> >> >>>URL: > >> >> >> > >> >> >> >>> > >> >> >> >>> >>> > >> >> >> >>> >>> >>> >>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.r-2Dproject. > >> >> >> > >> >> >> >>> > >> >> >> >>> >>> > >> >> >> >>> >>> >>> > >>>org_blosxom.cgi_R-2Ddevel_NEWS_2016_04_02-23n2016-2D04-2D02&d=BQIGaQ&c=WJB > >> >> >> > >> >> >> >>> > >> >> >> >>> >>> > >> >> >> >>> >>> >>> > >>>j9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5g > >> >> >> > >> >> >> >>> > >> >> >> >>> >>> > >> >> >> >>> >>> >>> > >>>JMlij5cC5bLU&m=HCJuUKMo50mOyjfD0AtQzV69c0SnACXTGdX_iHcWRfo&s=MbBj5lNGwkIfP > >> >> >> >>>hrHI2clfQd1aq1yPyROa3utKrCP4ug&e= > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > >> >> >> >>>----- Original Message ----- > >> >> >> >>>> From: "Michael Lawrence" <lawrence.mich...@gene.com> > >> >> >> >>>> To: "Hervé Pagès" <hpa...@fredhutch.org> > >> >> >> >>>> Cc: "Michael Lawrence" <lawrence.mich...@gene.com>, > >> >> >> >>>> "bioc-devel" > >> >> >> >>>><bioc-devel@r-project.org> > >> >> >> >>>> Sent: Saturday, April 2, 2016 4:10:10 AM > >> >> >> >>>> Subject: Re: [Bioc-devel] namespace question > >> >> >> >>> > >> >> >> >>>> Also, just btw, there are two other places where arbitrary R > >> >> >> >>>> code > >> >> >> >>>> can > >> >> >> >>>> be evaluated in the NAMESPACE, but no one has abused them > yet. > >> >> >> >>>> as > >> >> >> >>>> far > >> >> >> >>>> as I know. The first argument to if() and the .fixes argument > >> >> >> >>>> to > >> >> >> >>>> useDynLib(). The latter sets the precedent for the except= > >> >> >> >>>> behavior. > >> >> >> >>>> Although someone forgot to document it, you can do > >> >> >> >>>> .fixes=c("prefix", > >> >> >> >>>> "suffix") to both prefix and suffix incoming native symbols. > >> >> >> >>>> Currently, the documentation only mentions prefixing. Not > sure > >> >> >> >>>> when > >> >> >> >>>> suffixing would be desirable. > >> >> >> >>>> > >> >> >> >>>> > >> >> >> >>>> On Fri, Apr 1, 2016 at 4:14 PM, Hervé Pagès > >> >> >> >>>> <hpa...@fredhutch.org> > >> >> >> >>>>wrote: > >> >> >> >>>>> On 04/01/2016 01:39 PM, Michael Lawrence wrote: > >> >> >> >>>>>> > >> >> >> >>>>>> Yes, it's arbitrary R code that is evaluated, so paste0() > >> >> >> >>>>>> would > >> >> >> >>>>>> work. > >> >> >> >>>>>> You're right that it's a big door and could let people do > >> >> >> >>>>>> weird > >> >> >> >>>>>> things. Do you foresee a problem with that? > >> >> >> >>>>> > >> >> >> >>>>> > >> >> >> >>>>> Opening such a big door raises many questions. In addition > to > >> >> >> >>>>> allowing > >> >> >> >>>>> people do weird/crazy things (like putting calls to > library() > >> >> >> >>>>> or requireNamespace() etc... in them), NAMESPACE files with > >> >> >> >>>>> arbitrary > >> >> >> >>>>> R code in them become more complicated to maintain and the > >> >> >> >>>>> tools > >> >> >> >>>>> for > >> >> >> >>>>> parsing/processing them also become more complicated to > write > >> >> >> >>>>> and > >> >> >> >>>>> maintain. > >> >> >> >>>>> > >> >> >> >>>>> Now we have a new category of errors that can happen at > >> >> >> >>>>> package > >> >> >> >>>>> installation time: errors triggered by the evaluation of > the R > >> >> >> >>>>> expressions embedded in the NAMESPACE file. Hopefully 'R CMD > >> >> >> >>>>> INSTALL' > >> >> >> >>>>> will report something that can be understood by mere mortals > >> >> >> >>>>> when > >> >> >> >>>>> this > >> >> >> >>>>> happens. > >> >> >> >>>>> > >> >> >> >>>>> Once you create the feeling that a NAMESPACE file is just a > >> >> >> >>>>> file > >> >> >> >>>>> that contains arbitrary R code then people expect import(), > >> >> >> >>>>> export() > >> >> >> >>>>> etc.. to be ordinary R functions with a man page (being able > >> >> >> >>>>> to > >> >> >> >>>>> do > >> >> >> >>>>> ?import would not hurt actually) and they'll naturally try > to > >> >> >> >>>>> do > >> >> >> >>>>> things like > >> >> >> >>>>> > >> >> >> >>>>> unwanted_foo_symbols <- ... long and complicated > expression > >> >> >> >>>>> eventually calling > user-defined > >> >> >> >>>>> helper > >> >> >> >>>>> functions located in the > >> >> >> >>>>> NAMESPACE > >> >> >> >>>>> file > >> >> >> >>>>>... > >> >> >> >>>>> import(foo, except=unwanted_foo_symbols) > >> >> >> >>>>> > >> >> >> >>>>> Can't blame them for that. But is this the kind of things > that > >> >> >> >>>>> we're > >> >> >> >>>>> ready to see in NAMESPACE files? > >> >> >> >>>>> > >> >> >> >>>>> Also once you've open that door, people will naturally > wonder > >> >> >> >>>>> why > >> >> >> >>>>> they > >> >> >> >>>>> can use an R expression in the 'except' part of import( , > >> >> >> >>>>> except=) > >> >> >> >>>>> but > >> >> >> >>>>> not elsewhere e.g. in > >> >> >> >>>>> > >> >> >> >>>>> import(foo, only=paste0("bar", 1:10)) > >> >> >> >>>>> > >> >> >> >>>>> as a more elegant way of doing importFrom(foo, bar1, bar2, > >> >> >> >>>>> ..., > >> >> >> >>>>> bar10). > >> >> >> >>>>> This dissymmetry between the syntax of "import only this" > and > >> >> >> >>>>> "import > >> >> >> >>>>> all except this" feels very arbitrary. If you don't support > >> >> >> >>>>> the > >> >> >> >>>>> import( , only=) syntax, people might legitimately ask > things > >> >> >> >>>>> like > >> >> >> >>>>> > >> >> >> >>>>> do.call(importFrom, c(list("foo"), as.list(paste0("bar", > >> >> >> >>>>> 1:10)))) > >> >> >> >>>>> > >> >> >> >>>>> to work. Again, can't blame them for that. But do we want > this > >> >> >> >>>>> kind > >> >> >> >>>>> of > >> >> >> >>>>> things to work? I'm worried debugging NAMESPACE files would > >> >> >> >>>>> become a > >> >> >> >>>>> full-time job... > >> >> >> >>>>> > >> >> >> >>>>>> I guess one could have implemented NAMESPACE parsing by > >> >> >> >>>>>> evaluating > >> >> >> >>>>>> the > >> >> >> >>>>>> code in an environment (inheriting from the base namespace) > >> >> >> >>>>>> where > >> >> >> >>>>>> import(), export(), etc, were defined. Maybe there's a good > >> >> >> >>>>>> reason > >> >> >> >>>>>> why > >> >> >> >>>>>> it was not implemented that way. > >> >> >> >>>>> > >> >> >> >>>>> > >> >> >> >>>>> I'm sure there is ;-) > >> >> >> >>>>> > >> >> >> >>>>> H. > >> >> >> >>>>> > >> >> >> >>>>> > >> >> >> >>>>>> > >> >> >> >>>>>> On Fri, Apr 1, 2016 at 12:55 PM, Hervé Pagès > >> >> >> >>>>>> <hpa...@fredhutch.org> > >> >> >> >>>>>>wrote: > >> >> >> >>>>>>> > >> >> >> >>>>>>> On 03/31/2016 04:07 PM, Michael Lawrence wrote: > >> >> >> >>>>>>>> > >> >> >> >>>>>>>> > >> >> >> >>>>>>>> I agree. The importExcept idea also works that way: > >> >> >> >>>>>>>>importExcept(foo, > >> >> >> >>>>>>>> bar, > >> >> >> >>>>>>>> baz) > >> >> >> >>>>>>>> > >> >> >> >>>>>>>> But import(foo, except=c(bar, baz)) reads better. > >> >> >> >>>>>>> > >> >> >> >>>>>>> > >> >> >> >>>>>>> > >> >> >> >>>>>>> mmh... so R expressions with calls to base functions like > >> >> >> >>>>>>> base::c() > >> >> >> >>>>>>>are > >> >> >> >>>>>>> making their way in the NAMESPACE file. That's opening a > big > >> >> >> >>>>>>> door. > >> >> >> >>>>>>>Does > >> >> >> >>>>>>> that mean that we'll be able to do things like: > >> >> >> >>>>>>> > >> >> >> >>>>>>> import(foo, except=paste0("bar", 1:10)) > >> >> >> >>>>>>> > >> >> >> >>>>>>> Or maybe c(bar, baz) in your above example is just an > >> >> >> >>>>>>> arbitrary > >> >> >> >>>>>>>syntax > >> >> >> >>>>>>> that just happens to look like an R expression but won't > be > >> >> >> >>>>>>> evaluated > >> >> >> >>>>>>> as such? > >> >> >> >>>>>>> > >> >> >> >>>>>>> > >> >> >> >>>>>>> H. > >> >> >> >>>>>>> > >> >> >> >>>>>>>> > >> >> >> >>>>>>>> > >> >> >> >>>>>>>> On Thu, Mar 31, 2016 at 4:00 PM, < > luke-tier...@uiowa.edu> > >> >> >> >>>>>>>> wrote: > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> I don't think you want to separate it from the import. > >> >> >> >>>>>>>>> Better > >> >> >> >>>>>>>>> to > >> >> >> >>>>>>>>>allow > >> >> >> >>>>>>>>> something like > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> import(foo, exclude=bar) > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> or > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> import(foo, exclude=c("bar", "baz")) > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> This seems reasonably natural and shouldn't be too hard > to > >> >> >> >>>>>>>>> implement. (But is has been a while since I've worked on > >> >> >> >>>>>>>>> this > >> >> >> >>>>>>>>>code). > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> Best, > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> luke > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> On Thu, 31 Mar 2016, Karim Mezhoud wrote: > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>>> I think "From" is needed to specify which package we > want > >> >> >> >>>>>>>>>> to > >> >> >> >>>>>>>>>>exlude > >> >> >> >>>>>>>>>> functions. > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> I think excludeFrom (package, function) seems to be > >> >> >> >>>>>>>>>> intuitive. > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> thanks, > >> >> >> >>>>>>>>>> Karim > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> On Thu, Mar 31, 2016 at 9:54 PM, Hervé Pagès > >> >> >> >>>>>>>>>><hpa...@fredhutch.org> > >> >> >> >>>>>>>>>> wrote: > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>>> On 03/31/2016 12:55 PM, Michael Lawrence wrote: > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>>> Probably should just stick to exact symbols for now. > If > >> >> >> >>>>>>>>>>>> there > >> >> >> >>>>>>>>>>>>is a > >> >> >> >>>>>>>>>>>> case where a pattern is actually useful, rather than > >> >> >> >>>>>>>>>>>> just > >> >> >> >>>>>>>>>>>> an > >> >> >> >>>>>>>>>>>> obfuscation, we can extend the feature set. > >> >> >> >>>>>>>>>>>> > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> Fair enough. Not really intuitive that excludeImport > >> >> >> >>>>>>>>>>> uses > >> >> >> >>>>>>>>>>> the > >> >> >> >>>>>>>>>>>same > >> >> >> >>>>>>>>>>> syntax as (but does the opposite of) importFrom > though. > >> >> >> >>>>>>>>>>> Maybe > >> >> >> >>>>>>>>>>>having > >> >> >> >>>>>>>>>>> the name of the directive start with "import" would > help > >> >> >> >>>>>>>>>>> e.g. > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> importExcept(hash, values) # opposite of > >> >> >> >>>>>>>>>>> importFrom(hash, > >> >> >> >>>>>>>>>>>values) > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> Thanks, > >> >> >> >>>>>>>>>>> H. > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>>> On Thu, Mar 31, 2016 at 12:11 PM, Zhu, Lihua (Julie) > >> >> >> >>>>>>>>>>>> <julie....@umassmed.edu> wrote: > >> >> >> >>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> Herve, > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> That is a very interesting idea and works for me! > >> >> >> >>>>>>>>>>>>> Thanks! > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> importPatternFrom(IRanges, "^values$") > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> Best, > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> Julie > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> On 3/31/16 2:51 PM, "Bioc-devel on behalf of Hervé > >> >> >> >>>>>>>>>>>>> Pagès" > >> >> >> >>>>>>>>>>>>> <bioc-devel-boun...@r-project.org on behalf of > >> >> >> >>>>>>>>>>>>> hpa...@fredhutch.org> > >> >> >> >>>>>>>>>>>>> wrote: > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> On 03/30/2016 08:35 PM, Michael Lawrence wrote: > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> That would work, but R is not going to be happy > >> >> >> >>>>>>>>>>>>>>> about > >> >> >> >>>>>>>>>>>>>>>redundant > >> >> >> >>>>>>>>>>>>>>> imports. Interactively, users would balk at symbol > >> >> >> >>>>>>>>>>>>>>>qualification. > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> There are two classes of conflict: > >> >> >> >>>>>>>>>>>>>>> 1) Same semantics, where a common generic would > >> >> >> >>>>>>>>>>>>>>> arbitrate, > >> >> >> >>>>>>>>>>>>>>>or one > >> >> >> >>>>>>>>>>>>>>> package could depend on the other, and > >> >> >> >>>>>>>>>>>>>>> 2) Different semantics, in which case one of the > >> >> >> >>>>>>>>>>>>>>> functions > >> >> >> >>>>>>>>>>>>>>>should > >> >> >> >>>>>>>>>>>>>>> probably be renamed, although that might not be > >> >> >> >>>>>>>>>>>>>>> practical > >> >> >> >>>>>>>>>>>>>>> or > >> >> >> >>>>>>>>>>>>>>>easy > >> >> >> >>>>>>>>>>>>>>> to > >> >> >> >>>>>>>>>>>>>>> agree upon. > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> When those approaches fail, qualification is the > >> >> >> >>>>>>>>>>>>>>> only > >> >> >> >>>>>>>>>>>>>>>recourse. > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> I will think about adding an excludeImport() or > >> >> >> >>>>>>>>>>>>>>> importAs(). > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> What about having something like an > >> >> >> >>>>>>>>>>>>>> importPatternFrom() > >> >> >> >>>>>>>>>>>>>>directive > >> >> >> >>>>>>>>>>>>>> similar to the exportPattern() directive and have > >> >> >> >>>>>>>>>>>>>> these > >> >> >> >>>>>>>>>>>>>>directives > >> >> >> >>>>>>>>>>>>>> support some of the grep() toggles like > >> >> >> >>>>>>>>>>>>>> 'ignore.case', > >> >> >> >>>>>>>>>>>>>>'fixed', > >> >> >> >>>>>>>>>>>>>> 'invert' etc... ? > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> Then Julie could just do: > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> importPatternFrom(hash, "^values$", invert=TRUE) > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> H. > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> On Wed, Mar 30, 2016 at 8:20 PM, Robert M. Flight > >> >> >> >>>>>>>>>>>>>>> <rfligh...@gmail.com > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> wrote: > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> In the cases of having conflicting names, is it > not > >> >> >> >>>>>>>>>>>>>>>>appropriate > >> >> >> >>>>>>>>>>>>>>>> then > >> >> >> >>>>>>>>>>>>>>>> to use > >> >> >> >>>>>>>>>>>>>>>> the "package::function" form for calling a > >> >> >> >>>>>>>>>>>>>>>> particular > >> >> >> >>>>>>>>>>>>>>>>function? > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> On Wed, Mar 30, 2016 at 11:14 PM Michael Lawrence > >> >> >> >>>>>>>>>>>>>>>> <lawrence.mich...@gene.com> > >> >> >> >>>>>>>>>>>>>>>> wrote: > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> I can't find the hash function in IRanges. Are > you > >> >> >> >>>>>>>>>>>>>>>> sure > >> >> >> >>>>>>>>>>>>>>>> it > >> >> >> >>>>>>>>>>>>>>>>has > >> >> >> >>>>>>>>>>>>>>>> one? > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua > >> >> >> >>>>>>>>>>>>>>>>> (Julie) > >> >> >> >>>>>>>>>>>>>>>>> <julie....@umassmed.edu> wrote: > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> Michael, > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> I have the same user case as Kasper. Another > >> >> >> >>>>>>>>>>>>>>>>>> example > >> >> >> >>>>>>>>>>>>>>>>>> is > >> >> >> >>>>>>>>>>>>>>>>>>that > >> >> >> >>>>>>>>>>>>>>>>>> both > >> >> >> >>>>>>>>>>>>>>>>>> IRanges > >> >> >> >>>>>>>>>>>>>>>>>> and hash packages have hash. I need to use the > >> >> >> >>>>>>>>>>>>>>>>>> hash > >> >> >> >>>>>>>>>>>>>>>>>> from > >> >> >> >>>>>>>>>>>>>>>>>>the > >> >> >> >>>>>>>>>>>>>>>>>> hash > >> >> >> >>>>>>>>>>>>>>>>>> package > >> >> >> >>>>>>>>>>>>>>>>>> instead of the one from IRanges. > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> Best, > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> Julie > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> On Mar 30, 2016, at 7:57 PM, Kasper Daniel > Hansen > >> >> >> >>>>>>>>>>>>>>>>>> <kasperdanielhan...@gmail.com> wrote: > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> My usecase is when I import() two packages who > >> >> >> >>>>>>>>>>>>>>>>>> has a > >> >> >> >>>>>>>>>>>>>>>>>>conflict > >> >> >> >>>>>>>>>>>>>>>>>> in > >> >> >> >>>>>>>>>>>>>>>>>> a > >> >> >> >>>>>>>>>>>>>>>>>> name. > >> >> >> >>>>>>>>>>>>>>>>>> For example, both Biobase and matrixStats has > >> >> >> >>>>>>>>>>>>>>>>>> both > >> >> >> >>>>>>>>>>>>>>>>>>anyMissing > >> >> >> >>>>>>>>>>>>>>>>>> and > >> >> >> >>>>>>>>>>>>>>>>>> rowMedians. I am happy to get all of these two > >> >> >> >>>>>>>>>>>>>>>>>> packages, > >> >> >> >>>>>>>>>>>>>>>>>>but I > >> >> >> >>>>>>>>>>>>>>>>>> need > >> >> >> >>>>>>>>>>>>>>>>>> to > >> >> >> >>>>>>>>>>>>>>>>>> resolve the conflict. Since I want to keep the > >> >> >> >>>>>>>>>>>>>>>>>> ones > >> >> >> >>>>>>>>>>>>>>>>>> from > >> >> >> >>>>>>>>>>>>>>>>>> matrixStats I > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> know > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> need to figure out how to import Biobase > >> >> >> >>>>>>>>>>>>>>>>>> selectively. > >> >> >> >>>>>>>>>>>>>>>>>>Which I > >> >> >> >>>>>>>>>>>>>>>>>> can, > >> >> >> >>>>>>>>>>>>>>>>>> using > >> >> >> >>>>>>>>>>>>>>>>>> the tools from codetoolsBioC, but I would also > be > >> >> >> >>>>>>>>>>>>>>>>>> happy > >> >> >> >>>>>>>>>>>>>>>>>>with > >> >> >> >>>>>>>>>>>>>>>>>> an > >> >> >> >>>>>>>>>>>>>>>>>> importFromExcept(), which would make my life > much > >> >> >> >>>>>>>>>>>>>>>>>> easier. > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> Best, > >> >> >> >>>>>>>>>>>>>>>>>> Kasper > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> On Wed, Mar 30, 2016 at 4:47 PM, Michael > Lawrence > >> >> >> >>>>>>>>>>>>>>>>>> <lawrence.mich...@gene.com> wrote: > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> I'm curious about which symbols you wouldn't > >> >> >> >>>>>>>>>>>>>>>>>>> want > >> >> >> >>>>>>>>>>>>>>>>>>> to > >> >> >> >>>>>>>>>>>>>>>>>>>import, > >> >> >> >>>>>>>>>>>>>>>>>>> and > >> >> >> >>>>>>>>>>>>>>>>>>> why. > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> On Wed, Mar 30, 2016 at 12:19 PM, Zhu, Lihua > >> >> >> >>>>>>>>>>>>>>>>>>> (Julie) > >> >> >> >>>>>>>>>>>>>>>>>>> <julie....@umassmed.edu> wrote: > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> Hi, > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> Is there a function to import all the > exported > >> >> >> >>>>>>>>>>>>>>>>>>>> objects > >> >> >> >>>>>>>>>>>>>>>>>>>>from > >> >> >> >>>>>>>>>>>>>>>>>>>> a > >> >> >> >>>>>>>>>>>>>>>>>>>> package > >> >> >> >>>>>>>>>>>>>>>>>>>> except a few named ones in NAMESPACE file? > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> For example, I would like to import all the > >> >> >> >>>>>>>>>>>>>>>>>>>> functions > >> >> >> >>>>>>>>>>>>>>>>>>>> in > >> >> >> >>>>>>>>>>>>>>>>>>>> S4Vectors > >> >> >> >>>>>>>>>>>>>>>>>>>> except fold. Is there a way to specify this > >> >> >> >>>>>>>>>>>>>>>>>>>> without > >> >> >> >>>>>>>>>>>>>>>>>>>>listing > >> >> >> >>>>>>>>>>>>>>>>>>>> all > >> >> >> >>>>>>>>>>>>>>>>>>>> other > >> >> >> >>>>>>>>>>>>>>>>>>>> functions using importFrom? > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> Many thanks for your help! > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> Best regards, > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> Julie > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> ******************************************** > >> >> >> >>>>>>>>>>>>>>>>>>>> Lihua Julie Zhu, Ph.D > >> >> >> >>>>>>>>>>>>>>>>>>>> Research Professor > >> >> >> >>>>>>>>>>>>>>>>>>>> Department of Molecular, Cell and Cancer > >> >> >> >>>>>>>>>>>>>>>>>>>> Biology > >> >> >> >>>>>>>>>>>>>>>>>>>> (MCCB) > >> >> >> >>>>>>>>>>>>>>>>>>>> Head of MCCB Bioinformatics Core > >> >> >> >>>>>>>>>>>>>>>>>>>> Program in Molecular Medicine > >> >> >> >>>>>>>>>>>>>>>>>>>> Program in Bioinformatics and Integrative > >> >> >> >>>>>>>>>>>>>>>>>>>> Biology > >> >> >> >>>>>>>>>>>>>>>>>>>> University of Massachusetts Medical School > >> >> >> >>>>>>>>>>>>>>>>>>>> 364 Plantation Street, Room 613 > >> >> >> >>>>>>>>>>>>>>>>>>>> Worcester, MA 01605 > >> >> >> >>>>>>>>>>>>>>>>>>>> 508-856-5256 phone > >> >> >> >>>>>>>>>>>>>>>>>>>> (508) 856 5460 fax > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?Fr > >> >> >> >>>>>>>>>>>>>>>>>om=SE&Perso > >> >> >> >>>>>>>>>>>>>>>>> n=1134 > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> [[alternative HTML version > >> >> >> >>>>>>>>>>>>>>>>>>>> deleted]] > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > _______________________________________________ > >> >> >> >>>>>>>>>>>>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat > >> >> >> >>>>>>>>>>>>>>>>>>>>.ethz.ch_ma > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>ilman_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3b > >> >> >> >>>>>>>>>>>>>>>>>>>>iu3CPHX4MeR > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>jY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5 > >> >> >> >>>>>>>>>>>>>>>>>>>>bLU&m=Rxzbh > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>vEdYoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVv > >> >> >> >>>>>>>>>>>>>>>>>>>>zaBFADs-tx8 > >> >> >> >>>>>>>>>>>>>>>>>>>> CzeHHAAJ5kmgmJxQ&e= > >> >> >> >>>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > _______________________________________________ > >> >> >> >>>>>>>>>>>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. > >> >> >> >>>>>>>>>>>>>>>>>>>ethz.ch_mai > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>lman_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu > >> >> >> >>>>>>>>>>>>>>>>>>>3CPHX4MeRjY > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU > >> >> >> >>>>>>>>>>>>>>>>>>>&m=RxzbhvEd > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>Yoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBF > >> >> >> >>>>>>>>>>>>>>>>>>>ADs-tx8CzeH > >> >> >> >>>>>>>>>>>>>>>>>>> HAAJ5kmgmJxQ&e= > >> >> >> >>>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> _______________________________________________ > >> >> >> >>>>>>>>>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et > >> >> >> >>>>>>>>>>>>>>>>>hz.ch_mailm > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>an_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPH > >> >> >> >>>>>>>>>>>>>>>>>X4MeRjY_w4D > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>erPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=Rxz > >> >> >> >>>>>>>>>>>>>>>>>bhvEdYoq-Vr > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>N42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8C > >> >> >> >>>>>>>>>>>>>>>>>zeHHAAJ5kmg > >> >> >> >>>>>>>>>>>>>>>>> mJxQ&e= > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> [[alternative HTML version deleted]] > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> _______________________________________________ > >> >> >> >>>>>>>>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.eth > >> >> >> >>>>>>>>>>>>>>>>z.ch_mailma > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>n_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4 > >> >> >> >>>>>>>>>>>>>>>>MeRjY_w4Der > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>PlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=Rxzbhv > >> >> >> >>>>>>>>>>>>>>>>EdYoq-VrN42 > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHH > >> >> >> >>>>>>>>>>>>>>>>AAJ5kmgmJxQ > >> >> >> >>>>>>>>>>>>>>>> &e= > >> >> >> >>>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> _______________________________________________ > >> >> >> >>>>>>>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz > >> >> >> >>>>>>>>>>>>>>>.ch_mailman > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4Me > >> >> >> >>>>>>>>>>>>>>>RjY_w4DerPl > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdY > >> >> >> >>>>>>>>>>>>>>>oq-VrN42rfi > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>K5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5 > >> >> >> >>>>>>>>>>>>>>>kmgmJxQ&e= > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> -- > >> >> >> >>>>>>>>>>>>>> Hervé Pagès > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> Program in Computational Biology > >> >> >> >>>>>>>>>>>>>> Division of Public Health Sciences > >> >> >> >>>>>>>>>>>>>> Fred Hutchinson Cancer Research Center > >> >> >> >>>>>>>>>>>>>> 1100 Fairview Ave. N, M1-B514 > >> >> >> >>>>>>>>>>>>>> P.O. Box 19024 > >> >> >> >>>>>>>>>>>>>> Seattle, WA 98109-1024 > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> E-mail: hpa...@fredhutch.org > >> >> >> >>>>>>>>>>>>>> Phone: (206) 667-5791 > >> >> >> >>>>>>>>>>>>>> Fax: (206) 667-1319 > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> _______________________________________________ > >> >> >> >>>>>>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz. > >> >> >> >>>>>>>>>>>>>>ch_mailman_ > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > >>>>>>>>>>>>>>listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRj > >> >> >> >>>>>>>>>>>>>>Y_w4DerPlOm > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > >>>>>>>>>>>>>>hQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq- > >> >> >> >>>>>>>>>>>>>>VrN42rfiK5- > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> > >>>>>>>>>>>>>>UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmgm > >> >> >> >>>>>>>>>>>>>>JxQ&e= > >> >> >> >>>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>>>> > >> >> >> >>>>>>>>>>> -- > >> >> >> >>>>>>>>>>> Hervé Pagès > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> Program in Computational Biology > >> >> >> >>>>>>>>>>> Division of Public Health Sciences > >> >> >> >>>>>>>>>>> Fred Hutchinson Cancer Research Center > >> >> >> >>>>>>>>>>> 1100 Fairview Ave. N, M1-B514 > >> >> >> >>>>>>>>>>> P.O. Box 19024 > >> >> >> >>>>>>>>>>> Seattle, WA 98109-1024 > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> E-mail: hpa...@fredhutch.org > >> >> >> >>>>>>>>>>> Phone: (206) 667-5791 > >> >> >> >>>>>>>>>>> Fax: (206) 667-1319 > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> _______________________________________________ > >> >> >> >>>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ > >> >> >> > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> > >>>>>>>>>>>mailman_listinfo_bioc-2Ddevel&d=BQIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX > >> >> >> > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> > >>>>>>>>>>>4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m > >> >> >> > >> >> >> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> > >> >> >> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> > >>>>>>>>>>>=HCJuUKMo50mOyjfD0AtQzV69c0SnACXTGdX_iHcWRfo&s=p71c2AdbK9otl8LEvj9 > >> >> >> >>>>>>>>>>>xsiK9LzQrQsm-onyqG3WBgMI&e= > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> [[alternative HTML version deleted]] > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> _______________________________________________ > >> >> >> >>>>>>>>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>>>>>>>> > >> >> >> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_m > >> >> >> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> > >>>>>>>>>>ailman_listinfo_bioc-2Ddevel&d=BQIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4M > >> >> >> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> > >>>>>>>>>>eRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=HC > >> >> >> > >> >> >> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> > >> >> >> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> > >>>>>>>>>>JuUKMo50mOyjfD0AtQzV69c0SnACXTGdX_iHcWRfo&s=p71c2AdbK9otl8LEvj9xsiK > >> >> >> >>>>>>>>>>9LzQrQsm-onyqG3WBgMI&e= > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> -- > >> >> >> >>>>>>>>> Luke Tierney > >> >> >> >>>>>>>>> Ralph E. Wareham Professor of Mathematical Sciences > >> >> >> >>>>>>>>> University of Iowa Phone: > >> >> >> >>>>>>>>> 319-335-3386 > >> >> >> >>>>>>>>> Department of Statistics and Fax: > >> >> >> >>>>>>>>> 319-335-3017 > >> >> >> >>>>>>>>> Actuarial Science > >> >> >> >>>>>>>>> 241 Schaeffer Hall email: > >> >> >> >>>>>>>>> luke-tier...@uiowa.edu > >> >> >> >>>>>>>>> Iowa City, IA 52242 WWW: > >> >> >> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> >>>>>>>>> > >> >> >> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.stat.uiowa.e > >> >> >> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> >>>>>>>>> > >> >> >> >>>>>>>>> >>>>>>>>> >>>>>>>>> > >>>>>>>>>du&d=BQIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoI > >> >> >> > >> >> >> >>>>>>>>> > >> >> >> >>>>>>>>> >>>>>>>>> > >> >> >> >>>>>>>>> >>>>>>>>> >>>>>>>>> > >>>>>>>>>QpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=HCJuUKMo50mOyjfD0AtQzV69c0SnAC > >> >> >> > >> >> >> >>>>>>>>> > >>>>>>>>>XTGdX_iHcWRfo&s=sdr2IWlza633ZolLOZbEolvEybKmaHQFU5gIt8R8A7A&e= > >> >> >> >>>>>>> > >> >> >> >>>>>>> > >> >> >> >>>>>>> > >> >> >> >>>>>>> -- > >> >> >> >>>>>>> Hervé Pagès > >> >> >> >>>>>>> > >> >> >> >>>>>>> Program in Computational Biology > >> >> >> >>>>>>> Division of Public Health Sciences > >> >> >> >>>>>>> Fred Hutchinson Cancer Research Center > >> >> >> >>>>>>> 1100 Fairview Ave. N, M1-B514 > >> >> >> >>>>>>> P.O. Box 19024 > >> >> >> >>>>>>> Seattle, WA 98109-1024 > >> >> >> >>>>>>> > >> >> >> >>>>>>> E-mail: hpa...@fredhutch.org > >> >> >> >>>>>>> Phone: (206) 667-5791 > >> >> >> >>>>>>> Fax: (206) 667-1319 > >> >> >> >>>>> > >> >> >> >>>>> > >> >> >> >>>>> -- > >> >> >> >>>>> Hervé Pagès > >> >> >> >>>>> > >> >> >> >>>>> Program in Computational Biology > >> >> >> >>>>> Division of Public Health Sciences > >> >> >> >>>>> Fred Hutchinson Cancer Research Center > >> >> >> >>>>> 1100 Fairview Ave. N, M1-B514 > >> >> >> >>>>> P.O. Box 19024 > >> >> >> >>>>> Seattle, WA 98109-1024 > >> >> >> >>>>> > >> >> >> >>>>> E-mail: hpa...@fredhutch.org > >> >> >> >>>>> Phone: (206) 667-5791 > >> >> >> >>>>> Fax: (206) 667-1319 > >> >> >> >>>> > >> >> >> >>>> _______________________________________________ > >> >> >> >>>> Bioc-devel@r-project.org mailing list > >> >> >> >>>> > >> >> >> > >> >> >> >>>> > >> >> >> >>>> >>>> > >> >> >> >>>> >>>> >>>> >>>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman > >> >> >> > >> >> >> >>>> > >> >> >> >>>> >>>> > >> >> >> >>>> >>>> >>>> > >>>>_listinfo_bioc-2Ddevel&d=BQIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl > >> >> >> > >> >> >> >>>> > >> >> >> >>>> >>>> > >> >> >> >>>> >>>> >>>> > >>>>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=HCJuUKMo50mOyjfD0AtQ > >> >> >> > >> >> >> >>>> > >> >> >> >>>> >>>> > >> >> >> >>>> >>>> >>>> > >>>>zV69c0SnACXTGdX_iHcWRfo&s=p71c2AdbK9otl8LEvj9xsiK9LzQrQsm-onyqG3WBgMI&e= > >> >> >> >>> > >> >> >> >>>_______________________________________________ > >> >> >> >>>Bioc-devel@r-project.org mailing list > >> >> >> > >> >> >> >>> > >> >> >> >>> >>> > >> >> >> >>> >>> >>> >>> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_ > >> >> >> > >> >> >> >>> > >> >> >> >>> >>> > >> >> >> >>> >>> >>> > >>>listinfo_bioc-2Ddevel&d=BQIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOm > >> >> >> > >> >> >> >>> > >> >> >> >>> >>> > >> >> >> >>> >>> >>> > >>>hQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=HCJuUKMo50mOyjfD0AtQzV6 > >> >> >> >> > >> >> >> >> > > >> >> >> >> > > > >9c0SnACXTGdX_iHcWRfo&s=p71c2AdbK9otl8LEvj9xsiK9LzQrQsm-onyqG3WBgMI&e= > >> >> >> > >> >> >> _______________________________________________ > >> >> >> Bioc-devel@r-project.org mailing list > >> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > >> >> > > >> >> > > >> > > >> > > > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel