[Bioc-devel] namespace question
Dan Tenenbaum
dtenenba at fredhutch.org
Tue Apr 5 19:32:01 CEST 2016
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
>>>
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>>>_listinfo_bioc-2Ddevel&d=BQIGaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl
>>>OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=HCJuUKMo50mOyjfD0AtQ
>>>zV69c0SnACXTGdX_iHcWRfo&s=p71c2AdbK9otl8LEvj9xsiK9LzQrQsm-onyqG3WBgMI&e=
>>
>>_______________________________________________
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