[Bioc-devel] as.list fails on IRanges inside of lapply(<IRanges>, blah)

[Gabe Becker]

Herve,

Thanks for the response. The looping across a ranges that's still in tehre
is:

      dss = switch(seqtype,
                     bp = DNAStringSet(*lapply(ranges(srcs)*, function(x)
origin[x])),
                     aa = AAStringSet(*lapply(ranges(srcs),* function(x)
origin[x])),
                     stop("Unrecognized origin sequence type: ", seqtype)
                     )

(Line 495 in genbankReader.R)

srcs is a GRanges, making ranges(srcs) an IRanges, so this lapply fails.
I'm not sure what I'm meant to do here as there's not an already vectorized
version that I know of that does the rigth thing (I want separate
DNAStrings for each range, so origin[ranges(srcs)] doesn't work).

I mean I can force the conversion to list issue with lapply(1:length(srcs),
function(i) ranges(srcs)[i]) or similar but that seems pretty ugly...

As for the other issue with the build not working in release, that is a bug
in the rentrez (which is on CRAN, not Bioc). I've submitted a PR to fix
that, and we'll see what the response is as to whether I need to remove
that integration or not.

~G






On Tue, Feb 20, 2018 at 10:48 AM, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Gabe,
>
> I made a couple of changes to genbankr (1.7.2) to avoid those looping
> e.g. I replaced things like
>
>     sapply(gr, width)
>
> with
>
>     width(gr)
>
> I can't run a full 'R CMD build' + 'R CMD check' on the package though
> because the code in the vignette seems to fail for reasons unrelated
> to the recent changes to IRanges / GenomicRanges (I get the same error
> with the release version, see release build report).
>
> The previous behavior of as.list() on IRanges ans GRanges objects will
> be restored (with a deprecation warning) once all the packages that
> need a fix get one (only 7 packages left on my list). I should be done
> with them in the next couple of days.
>
> H.
>
>
> On 02/20/2018 09:41 AM, Gabe Becker wrote:
>
>> All,
>>
>> I'm trying to track down the new failure in my genbankr package and it
>> appears to come down to the fact  that i'm trying to lapply over an
>> IRanges, which fails in the IRanges to list (or List?) conversion. The
>> particular case that fails in my example is an IRanges of length 1 but
>> that
>> does not appear to matter, as lapply fails over IRanges of length >1 as
>> well.
>>
>> Is this intentional? If so, it seems a change of this magnitude would
>> warrant a deprecation cycle at least. If not, please let me know so I can
>> leave the code as is and wait for the fix.
>>
>> rng1 = IRanges(start = 1, end = 5)
>>>
>>
>> rng2 = IRanges(start = c(1, 7), end = c(3, 10))
>>>
>>
>> rng1
>>>
>>
>> IRanges object with 1 range and 0 metadata columns:
>>
>>            start       end     width
>>
>>        <integer> <integer> <integer>
>>
>>    [1]         1         5         5
>>
>> rng2
>>>
>>
>> IRanges object with 2 ranges and 0 metadata columns:
>>
>>            start       end     width
>>
>>        <integer> <integer> <integer>
>>
>>    [1]         1         3         3
>>
>>    [2]         7        10         4
>>
>> lapply(rng1, identity)
>>>
>>
>> *Error in (function (classes, fdef, mtable)  : *
>>
>> *  unable to find an inherited method for function ‘getListElement’ for
>> signature ‘"IRanges"’*
>>
>> lapply(rng2, identity)
>>>
>>
>> *Error in (function (classes, fdef, mtable)  : *
>>
>> *  unable to find an inherited method for function ‘getListElement’ for
>> signature ‘"IRanges"’*
>>
>> sessionInfo()
>>>
>>
>> R Under development (unstable) (2018-02-16 r74263)
>>
>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>
>> Running under: OS X El Capitan 10.11.6
>>
>>
>> Matrix products: default
>>
>> BLAS:
>> /Users/beckerg4/local/Rdevel/R.framework/Versions/3.5/Resour
>> ces/lib/libRblas.dylib
>>
>> LAPACK:
>> /Users/beckerg4/local/Rdevel/R.framework/Versions/3.5/Resour
>> ces/lib/libRlapack.dylib
>>
>>
>> locale:
>>
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>>
>> attached base packages:
>>
>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>>
>> [8] methods   base
>>
>>
>> other attached packages:
>>
>> *[1] IRanges_2.13.26     S4Vectors_0.17.33   BiocGenerics_0.25.3*
>>
>>
>> loaded via a namespace (a
>> <https://maps.google.com/?q=d+via+a+namespace+(a&entry=gmail&source=g>nd
>> not attached):
>>
>> [1] compiler_3.5.0 tools_3.5.0
>>
>>
>>
>> Best,
>> ~G
>>
>>
>>
>>
> --
> 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
>
>


-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

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