[Bioc-devel] SV4Vectors installation problem

[Marcin Cieślik]

Dear All,

I can confirm that the issue is fixed in the latest BioC / R versions.

Thanks a lot.

Yours,
Marcin





On Fri, Oct 16, 2015 at 7:09 AM, Michael Lawrence <lawrence.michael at gene.com
> wrote:

> On Thu, Oct 15, 2015 at 11:04 PM, Hervé Pagès <hpages at fredhutch.org>
> wrote:
>
> > Hi Michael,
> >
> > On 10/15/2015 10:08 AM, Michael Lawrence wrote:
> >
> >> Tangentially related, it seems like nchar is worth defining in
> >> BiocGenerics, with a signature of "x". I saw that Biostrings uses
> "type",
> >> but I'm not sure why.
> >>
> >
> > The 2 "nchar" methods that dispatch on the 'type' argument are from
> > the Biostrings 1 era (> 9 years old) and were kept in the
> > Biostrings/Biostrings1/ folder for legacy only (this code doesn't
> > get evaluated, not even installed). That reminds me that it's probably
> > time to get rid of all that stuff.
> >
> > But if we're just going to use the signature of 'x',
> >> I can make nchar dispatch internally, so we don't need an R-level
> generic.
> >> Will that work?
> >>
> >
> > If by "make nchar dispatch internally" you mean "turn nchar() into a
> > primitive in R", like, say, length(), names(), dim(), dimnames(), `[`,
> > etc... then works for me.
> >
> >
> Essentially, yes. I've modified the methods package to support internal
> dispatch within .Internal() calls. So no need to make it a primitive. Will
> move ahead, thanks.
>
>
> > Thanks,
> > H.
> >
> >
> >
> >> Michael
> >>
> >> On Thu, Oct 15, 2015 at 5:19 AM, Morgan, Martin <
> >> Martin.Morgan at roswellpark.org> wrote:
> >>
> >>
> >>>
> >>> -----Original Message-----
> >>>> From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf
> Of
> >>>> Marcin Cieslik
> >>>> Sent: Thursday, October 15, 2015 7:46 AM
> >>>> To: bioc-devel at r-project.org
> >>>> Subject: [Bioc-devel] SV4Vectors installation problem
> >>>>
> >>>> Dear Bioconductors,
> >>>>
> >>>> Somewhere in August S4Vectors stopped installing correctly resulting
> in
> >>>>
> >>> a:
> >>>
> >>>>
> >>>> Creating a generic function for ‘nchar’ from package ‘base’ in package
> >>>> ‘S4Vectors’
> >>>>
> >>>> message (that cannot be suppressed) each time the package is loaded.
> The
> >>>> issue is not fixed by a fresh reinstall of bioconductor. The first
> hint
> >>>>
> >>> of the
> >>>
> >>> you're right that this is a message and that it cannot be suppressed,
> but
> >>> the package still functions correctly, right?
> >>>
> >>> The problem was introduced by a change in R. The above is a
> work-around.
> >>> The permanent solution is now to use the current version of R (3.2.2)
> and
> >>> Bioc (3.2). The specific commit was
> >>>
> >>>
> ------------------------------------------------------------------------
> >>> r106498 | mtmorgan at fhcrc.org | 2015-07-16 15:10:40 -0400 (Thu, 16 Jul
> >>> 2015) | 5 lines
> >>>
> >>> define nchar,Rle-method in .onLoad
> >>>
> >>> - work-around consequences of changed base::nchar signature for
> >>>    3.2.1 binary builds used in 3.2.0
> >>>
> >>>
> ------------------------------------------------------------------------
> >>>
> >>> some related / belated discussion is at
> >>>
> >>> https://stat.ethz.ch/pipermail/r-devel/2015-October/071841.html
> >>>
> >>> Martin
> >>>
> >>>
> >>> problem appears during installation
> >>>>
> >>>> http://pastebin.com/UpKdeNTH
> >>>>
> >>>> It appears I am not the only one affected a search reveals many
> >>>>
> >>> instances:
> >>>
> >>>>
> >>>> e.g.
> >>>> https://rpubs.com/Pazz/advanced_annotation
> >>>> http://bioc.ism.ac.jp/packages/checkResults/3.1/bioc-
> >>>> LATEST/S4Vectors/petty-install.html
> >>>> http://biocluster.ucr.edu/~rkaundal/R_sep2015/Rrnaseq/RNAseq.html
> >>>>
> >>>> Thanks a lot for your work! If needed I can provide  a Docker image
> that
> >>>> reproduces the problem.
> >>>>
> >>>> Yours,
> >>>> Marcin
> >>>>
> >>>>        [[alternative HTML version deleted]]
> >>>>
> >>>> _______________________________________________
> >>>> Bioc-devel at r-project.org mailing list
> >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>
> >>>
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> >>>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >>
> > --
> > 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
> >
>
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>
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