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.
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= > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
