[Bioc-devel] namespace question
Karim Mezhoud
kmezhoud at gmail.com
Tue Apr 5 20:07:41 CEST 2016
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
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>
> http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?Fr
> >>>>>>>>>>>>>>>>>om=SE&Perso
> >>>>>>>>>>>>>>>>> n=1134
> >>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>> [[alternative HTML version deleted]]
> >>>>>>>>>>>>>>>>>>>>
> >>>>>>>>>>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>>>>>>>>>> Bioc-devel at 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 at 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 at 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 at 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 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=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: 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
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>
>
> >>>>>>>>>>>>>>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
>
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