[Bioc-devel] namespace question

Tue Apr 5 22:17:51 CEST 2016

You need R 3.4 for right now.

On Tue, Apr 5, 2016 at 1:16 PM, Karim Mezhoud <kmezhoud at 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.michael at gene.com>
> wrote:
>>
>> Yea, with the closing )
>>
>> On Tue, Apr 5, 2016 at 12:37 PM, Karim Mezhoud <kmezhoud at 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.michael at 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 <kmezhoud at 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.michael at 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
>> >> >> <dtenenba at 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.Zhu at umassmed.edu>
>> >> >> >> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Michael Lawrence"
>> >> >> >> <lawrence.michael at gene.com>
>> >> >> >> Cc: "bioc-devel" <bioc-devel at 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-bounces at r-project.org on behalf of
>> >> >> >> dtenenba at 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.michael at gene.com>
>> >> >> >>>> To: "Hervé Pagès" <hpages at fredhutch.org>
>> >> >> >>>> Cc: "Michael Lawrence" <lawrence.michael at gene.com>,
>> >> >> >>>> "bioc-devel"
>> >> >> >>>><bioc-devel at 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
>> >> >> >>>> <hpages at 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
>> >> >> >>>>>> <hpages at 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-tierney at 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
>> >> >> >>>>>>>>>><hpages at 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.Zhu at 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-bounces at r-project.org on behalf of
>> >> >> >>>>>>>>>>>>> hpages at 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
>> >> >> >>>>>>>>>>>>>>> <rflight79 at 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.michael at 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.Zhu at 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
>> >> >> >>>>>>>>>>>>>>>>>> <kasperdanielhansen at 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.michael at 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.Zhu at 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
>> >> >> >>>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>>> _______________________________________________
>> >> >> >>>>>>>>>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>> >> >> >>>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>>>>>>.ethz.ch_ma
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>> >> >> >>>>>>>>>>>>>>>>>>>>zaBFADs-tx8
>> >> >> >>>>>>>>>>>>>>>>>>>> CzeHHAAJ5kmgmJxQ&e=
>> >> >> >>>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>> _______________________________________________
>> >> >> >>>>>>>>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>> >> >> >>>>>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>>>>>ethz.ch_mai
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>> >> >> >>>>>>>>>>>>>>>>>>>3CPHX4MeRjY
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>> >> >> >>>>>>>>>>>>>>>>>>>&m=RxzbhvEd
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>> >> >> >>>>>>>>>>>>>>>>>>>ADs-tx8CzeH
>> >> >> >>>>>>>>>>>>>>>>>>> HAAJ5kmgmJxQ&e=
>> >> >> >>>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>> _______________________________________________
>> >> >> >>>>>>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>> >> >> >>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et
>> >> >> >>>>>>>>>>>>>>>>>hz.ch_mailm
>> >> >> >>>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>>>X4MeRjY_w4D
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>> >> >> >>>>>>>>>>>>>>>>>bhvEdYoq-Vr
>> >> >> >>>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>>>zeHHAAJ5kmg
>> >> >> >>>>>>>>>>>>>>>>> mJxQ&e=
>> >> >> >>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>             [[alternative HTML version deleted]]
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>> _______________________________________________
>> >> >> >>>>>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.eth
>> >> >> >>>>>>>>>>>>>>>>z.ch_mailma
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
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>> >> >>
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>> >> >> >>>>>>>>>>>>>>>>MeRjY_w4Der
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
>> >> >>
>> >> >> >>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>PlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=Rxzbhv
>> >> >> >>>>>>>>>>>>>>>>EdYoq-VrN42
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>>AAJ5kmgmJxQ
>> >> >> >>>>>>>>>>>>>>>> &e=
>> >> >> >>>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>> _______________________________________________
>> >> >> >>>>>>>>>>>>>>> Bioc-devel at r-project.org mailing list
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
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>> >> >>
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>> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz
>> >> >> >>>>>>>>>>>>>>>.ch_mailman
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4Me
>> >> >> >>>>>>>>>>>>>>>RjY_w4DerPl
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>>
>> >> >>
>> >> >> >>>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>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: hpages at fredhutch.org
>> >> >> >>>>>>>>>>>>>> Phone:  (206) 667-5791
>> >> >> >>>>>>>>>>>>>> Fax:    (206) 667-1319
>> >> >> >>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>> _______________________________________________
>> >> >> >>>>>>>>>>>>>> Bioc-devel at 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
>> >> >> >>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>
>> >> >> >>>>>>>>>>>>>>
>> >> >>
>> >> >> >>>>>>>>>>>>>>
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>> >> >> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>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: hpages at fredhutch.org
>> >> >> >>>>>>>>>>> Phone:  (206) 667-5791
>> >> >> >>>>>>>>>>> Fax:    (206) 667-1319
>> >> >> >>>>>>>>>>>
>> >> >> >>>>>>>>>>> _______________________________________________
>> >> >> >>>>>>>>>>> Bioc-devel at 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 at 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-tierney at 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: hpages at 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: hpages at fredhutch.org
>> >> >> >>>>> Phone:  (206) 667-5791
>> >> >> >>>>> Fax:    (206) 667-1319
>> >> >> >>>>
>> >> >> >>>> _______________________________________________
>> >> >> >>>> Bioc-devel at 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 at 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 at r-project.org mailing list
>> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >> >
>> >> >
>> >
>> >
>
>