Dear Martin,
countLines in ShrotRead returns the line counts as integers which appears
to create problems with large FASTQ files (>536.8 Mio lines) due to R's
integer limit (2^31-1). When the integer limit is reached/exceeded it seems
that countLines returns negative values not reflecting the numb
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
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])),
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 th
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 no
I think this is settled by running updateObject(ebicat37) with a current
GenomicRanges etc.
I will do this and reserialize.
On Tue, Feb 20, 2018 at 8:01 AM, Robert Castelo
wrote:
> thanks Vince for your quick response, indeed your intuition is right,
> coercing to 'GRanges' avoids the problem,
Depending on your reviewer, they MAY let you slide with a different version
dependency despite the BiocCheck WARNING... maybe...
However ...
It is strongly, strongly recommended that all new package depend on the version
of R that it will be released under. New packages currently being accep
thanks Vince for your quick response, indeed your intuition is right,
coercing to 'GRanges' avoids the problem, i'm cc'ing bioc-devel so that
people involved in 'GRanges' know about this:
library(gwascat)
data(ebicat37)
ebicat37[1]
Error in updateObject(x, check = FALSE) :
no slot of name "el
hi,
the 'gwasloc' class from the gwascat package seems to be broken in
devel, i suspect due to recent changes in the 'GRanges' class or some
other class upstream, because the definition of the 'gwasloc' class in
gwascat/R/classes.R is:
setClass("gwaswloc", representation(extractDate="charact
> It _is_ the developer's choice. But a developer of packages for the
Bioconductor
> project commits to using R-devel during certain pre-release phases,
depending
> on proximity in time to a point release of R. (See
http://bioconductor.org/developers/how-to/useDevel/)
> for full details.) BiocCh
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