I think "From" is needed to specify which package we want to exlude functions.
I think excludeFrom (package, function) seems to be intuitive. thanks, Karim On Thu, Mar 31, 2016 at 9:54 PM, Hervé Pagès <hpa...@fredhutch.org> wrote: > On 03/31/2016 12:55 PM, Michael Lawrence wrote: > >> Probably should just stick to exact symbols for now. If there is a >> case where a pattern is actually useful, rather than just an >> obfuscation, we can extend the feature set. >> > > Fair enough. Not really intuitive that excludeImport uses the same > syntax as (but does the opposite of) importFrom though. Maybe having > the name of the directive start with "import" would help e.g. > > importExcept(hash, values) # opposite of importFrom(hash, values) > > Thanks, > H. > > > >> On Thu, Mar 31, 2016 at 12:11 PM, Zhu, Lihua (Julie) >> <julie....@umassmed.edu> wrote: >> >>> Herve, >>> >>> That is a very interesting idea and works for me! Thanks! >>> >>> importPatternFrom(IRanges, "^values$") >>> >>> >>> Best, >>> >>> Julie >>> >>> On 3/31/16 2:51 PM, "Bioc-devel on behalf of Hervé Pagès" >>> <bioc-devel-boun...@r-project.org on behalf of hpa...@fredhutch.org> >>> wrote: >>> >>> On 03/30/2016 08:35 PM, Michael Lawrence wrote: >>>> >>>>> That would work, but R is not going to be happy about redundant >>>>> imports. Interactively, users would balk at symbol qualification. >>>>> >>>>> There are two classes of conflict: >>>>> 1) Same semantics, where a common generic would arbitrate, or one >>>>> package could depend on the other, and >>>>> 2) Different semantics, in which case one of the functions should >>>>> probably be renamed, although that might not be practical or easy to >>>>> agree upon. >>>>> >>>>> When those approaches fail, qualification is the only recourse. >>>>> >>>>> I will think about adding an excludeImport() or importAs(). >>>>> >>>> >>>> What about having something like an importPatternFrom() directive >>>> similar to the exportPattern() directive and have these directives >>>> support some of the grep() toggles like 'ignore.case', 'fixed', >>>> 'invert' etc... ? >>>> >>>> Then Julie could just do: >>>> >>>> importPatternFrom(hash, "^values$", invert=TRUE) >>>> >>>> H. >>>> >>>> >>>>> >>>>> On Wed, Mar 30, 2016 at 8:20 PM, Robert M. Flight <rfligh...@gmail.com >>>>> > >>>>> wrote: >>>>> >>>>>> In the cases of having conflicting names, is it not appropriate then >>>>>> to use >>>>>> the "package::function" form for calling a particular function? >>>>>> >>>>>> On Wed, Mar 30, 2016 at 11:14 PM Michael Lawrence >>>>>> <lawrence.mich...@gene.com> >>>>>> wrote: >>>>>> >>>>>> I can't find the hash function in IRanges. Are you sure it has one? >>>>>>> >>>>>>> On Wed, Mar 30, 2016 at 8:07 PM, Zhu, Lihua (Julie) >>>>>>> <julie....@umassmed.edu> wrote: >>>>>>> >>>>>>>> Michael, >>>>>>>> >>>>>>>> I have the same user case as Kasper. Another example is that both >>>>>>>> IRanges >>>>>>>> and hash packages have hash. I need to use the hash from the hash >>>>>>>> package >>>>>>>> instead of the one from IRanges. >>>>>>>> >>>>>>>> Best, >>>>>>>> >>>>>>>> Julie >>>>>>>> >>>>>>>> On Mar 30, 2016, at 7:57 PM, Kasper Daniel Hansen >>>>>>>> <kasperdanielhan...@gmail.com> wrote: >>>>>>>> >>>>>>>> My usecase is when I import() two packages who has a conflict in a >>>>>>>> name. >>>>>>>> For example, both Biobase and matrixStats has both anyMissing and >>>>>>>> rowMedians. I am happy to get all of these two packages, but I need >>>>>>>> to >>>>>>>> resolve the conflict. Since I want to keep the ones from >>>>>>>> matrixStats I >>>>>>>> >>>>>>> know >>>>>>> >>>>>>>> need to figure out how to import Biobase selectively. Which I can, >>>>>>>> using >>>>>>>> the tools from codetoolsBioC, but I would also be happy with an >>>>>>>> importFromExcept(), which would make my life much easier. >>>>>>>> >>>>>>>> Best, >>>>>>>> Kasper >>>>>>>> >>>>>>>> On Wed, Mar 30, 2016 at 4:47 PM, Michael Lawrence >>>>>>>> <lawrence.mich...@gene.com> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> I'm curious about which symbols you wouldn't want to import, and >>>>>>>>> why. >>>>>>>>> >>>>>>>>> On Wed, Mar 30, 2016 at 12:19 PM, Zhu, Lihua (Julie) >>>>>>>>> <julie....@umassmed.edu> wrote: >>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> Is there a function to import all the exported objects from a >>>>>>>>>> package >>>>>>>>>> except a few named ones in NAMESPACE file? >>>>>>>>>> >>>>>>>>>> For example, I would like to import all the functions in S4Vectors >>>>>>>>>> except fold. Is there a way to specify this without listing all >>>>>>>>>> other >>>>>>>>>> functions using importFrom? >>>>>>>>>> >>>>>>>>>> Many thanks for your help! >>>>>>>>>> >>>>>>>>>> Best regards, >>>>>>>>>> >>>>>>>>>> Julie >>>>>>>>>> >>>>>>>>>> ******************************************** >>>>>>>>>> Lihua Julie Zhu, Ph.D >>>>>>>>>> Research Professor >>>>>>>>>> Department of Molecular, Cell and Cancer Biology (MCCB) >>>>>>>>>> Head of MCCB Bioinformatics Core >>>>>>>>>> Program in Molecular Medicine >>>>>>>>>> Program in Bioinformatics and Integrative Biology >>>>>>>>>> University of Massachusetts Medical School >>>>>>>>>> 364 Plantation Street, Room 613 >>>>>>>>>> Worcester, MA 01605 >>>>>>>>>> 508-856-5256 phone >>>>>>>>>> (508) 856 5460 fax >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>> >>>>>>> http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?From=SE&Perso >>>>>>> n=1134 >>>>>>> >>>>>>>> >>>>>>>>>> >>>>>>>>>> [[alternative HTML version deleted]] >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioc-devel@r-project.org mailing list >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ma >>>>>>>>>> >>>>>>>>>> ilman_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeR >>>>>>>>>> >>>>>>>>>> jY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=Rxzbh >>>>>>>>>> >>>>>>>>>> vEdYoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8 >>>>>>>>>> CzeHHAAJ5kmgmJxQ&e= >>>>>>>>>> >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Bioc-devel@r-project.org mailing list >>>>>>>>> >>>>>>>>> >>>>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mai >>>>>>>>> >>>>>>>>> lman_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY >>>>>>>>> >>>>>>>>> _w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEd >>>>>>>>> >>>>>>>>> Yoq-VrN42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeH >>>>>>>>> HAAJ5kmgmJxQ&e= >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Bioc-devel@r-project.org mailing list >>>>>>> >>>>>>> >>>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailm >>>>>>> >>>>>>> an_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4D >>>>>>> >>>>>>> erPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-Vr >>>>>>> >>>>>>> N42rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmg >>>>>>> mJxQ&e= >>>>>>> >>>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> Bioc-devel@r-project.org mailing list >>>>>> >>>>>> >>>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailma >>>>>> >>>>>> n_listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4Der >>>>>> >>>>>> PlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-VrN42 >>>>>> >>>>>> rfiK5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmgmJxQ >>>>>> &e= >>>>>> >>>>> >>>>> _______________________________________________ >>>>> Bioc-devel@r-project.org mailing list >>>>> >>>>> >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman >>>>> >>>>> _listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPl >>>>> >>>>> OmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-VrN42rfi >>>>> >>>>> K5-UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmgmJxQ&e= >>>>> >>>>> >>>> -- >>>> Hervé Pagès >>>> >>>> Program in Computational Biology >>>> Division of Public Health Sciences >>>> Fred Hutchinson Cancer Research Center >>>> 1100 Fairview Ave. N, M1-B514 >>>> P.O. Box 19024 >>>> Seattle, WA 98109-1024 >>>> >>>> E-mail: hpa...@fredhutch.org >>>> Phone: (206) 667-5791 >>>> Fax: (206) 667-1319 >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> >>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_ >>>> >>>> listinfo_bioc-2Ddevel&d=BQIF-g&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOm >>>> >>>> hQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=RxzbhvEdYoq-VrN42rfiK5- >>>> UIIwjUIHLTQjy9s7-pzs&s=TmgPkRkAcsTjcIVvzaBFADs-tx8CzeHHAAJ5kmgmJxQ&e= >>>> >>> >>> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
