On 02/20/2018 01:25 PM, Gabe Becker wrote:
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)
That was also fixed in genbankr 1.7.2. I replaced this with
dss = extractAt(origin, ranges(srcs))
Do 'git show 340b0d4fac511f8171391fdeb2233ca6a410743d' to see
the details of the changes I made.
Cheers,
H.
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 <hpa...@fredhutch.org
<mailto:hpa...@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/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 (a
<https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3Dd-2Bvia-2Ba-2Bnamespace-2B-28a-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=UXc_3kLawiEpQQcAHZhYs1gYYbOaugo9CDOvWJd10nQ&s=3tASrFpqenzsLC8hh1ay3-LhytVzFL86g_PO-RptAp8&e=>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: hpa...@fredhutch.org <mailto:hpa...@fredhutch.org>
Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
--
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research
--
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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