[Bioc-sig-seq] GRanges In Development Version

[Kasper Daniel Hansen]

Any package in the devel branch have an implicit dependency on
R-devel, which is why everyone always tells you to use biocLite to
install packages.

Now, I am aware that for some packages this is not necessarily true,
but only the package author(s) can reliably tell you whether that is
the case.

As a minimum I routinely expect that any package that really uses the
internals of R - and especially the core sequencing packages - has a
strong dependence on R-devel.

Kasper


On Tue, Sep 14, 2010 at 8:00 PM, Dario Strbenac
<D.Strbenac at garvan.org.au> wrote:
> Hello,
>
> I've installed the development versions of IRanges - 1.7.34 - and GenomicRanges - 1.1.25 - and now the copying and pasting of the constructing a GenomicRangesList example in the Reference Manual doesn't work. Is there an implicit dependency on R 2.12 maybe ?
>
>> gr1 <-
> + GRanges(seqnames = "chr2", ranges = IRanges(3, 6),
> + strand = "+", score = 5L, GC = 0.45)
> Error in which(lengths == 0L) :
>  could not find symbol "useNames" in environment of the generic function
>> gr2 <-
> + GRanges(seqnames = c("chr1", "chr1"),
> + ranges = IRanges(c(7,13), width = 3),
> + strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
> Error in which(lengths == 0L) :
>  could not find symbol "useNames" in environment of the generic function
>> gr3 <-
> + GRanges(seqnames = c("chr1", "chr2"),
> + ranges = IRanges(c(1, 4), c(3, 9)),
> + strand = c("-", "-"), score = c(6L, 2L), GC = c(0.4, 0.1))
> Error in which(lengths == 0L) :
>  could not find symbol "useNames" in environment of the generic function
>
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-pc-mingw32
> ...             ...                ...
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>