[Bioc-devel] namespace question
Michael Lawrence
lawrence.michael at gene.com
Tue Apr 5 19:50:03 CEST 2016
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
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>>>>>>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>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
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>_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
>>>>>>>>>>>
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>>>>>>>>>>>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=
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