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/Resources/lib/libRblas.dylib
LAPACK:
/Users/beckerg4/local/Rdevel/R.framework/Versions/3.5/Resources/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 (and 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: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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