Re: [Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y

Hi Scott, I tried the new patch and can confirm that it has the advertised behavior on a couple of test cases. I think it makes sense to apply it, because any existing code which refers to a second duplicate data.frame column by name is already broken, while if the reference is by numerical index

[Bioc-devel] ShortRead::countLines integer overflow with large fastq files

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

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

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 =

[Rd] Unwanted behaviour of bw.nrd: sometimes, zero is returned as a valid bandwidth

Dear all, Sorry if I am posting to the wrong place, but I could not find the link for registration on the bug tracker, that’s why I am writing here. I think there is inconsistency between two R functions from the stats package, bw.nrd0 and bw.nrd. Consider the following vector: D <- c(0, 1, 1,

Re: [Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y

Hi Frederick, It looks like I didn't overwrite the patch.diff file after the last edits. Here's the correct patch (attached and copied below): Index: src/library/base/R/merge.R === --- src/library/base/R/merge.R (revision 74280) +++

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

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])),

Re: [Rd] Duplicate column names created by base::merge() when by.x has the same name as a column in y

Hi Scott, I think that's a good idea and I tried your patch on my copy of the repository. But it looks to me like the recent patch is identical to the previous one, can you confirm this? Frederick On Mon, Feb 19, 2018 at 07:19:32AM +1100, Scott Ritchie wrote: > Thanks Gabriel, > > I think your

[R-pkg-devel] header file for "flockfile" function under windows

Hi all, I am using file-locking functions in C that can be found in the in Unix extern void flockfile (FILE *__stream) __THROW; extern int ftrylockfile (FILE *__stream) __THROW __wur; extern void funlockfile (FILE *__stream) __THROW; When submitting to CRAN I have troubles with the

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

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

[Rd] How to modify dots and dispatch NextMethod

Hi all, Not sure if this belongs to R-devel or R-package-devel. Anyways... Suppose we have objects of class c("foo", "bar"), and there are two S3 methods c.foo, c.bar. In c.foo, I'm trying to modify the dots and forward the dispatch using NextMethod without any success. This is what I've tried

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

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

Re: [R-pkg-devel] MAX_ARGS limitation in foreign function calls

On 20 February 2018 at 09:33, Udaya B. Kogalur wrote: | We are hitting the MAX_ARGS ceiling in our R-C function calls in the | development of randomForestSRC. This limits to number of arguments to | 65 using .Call(). Is there a work around for this dilemma? Thank | you. The easiest is to

[R-pkg-devel] MAX_ARGS limitation in foreign function calls

We are hitting the MAX_ARGS ceiling in our R-C function calls in the development of randomForestSRC. This limits to number of arguments to 65 using .Call(). Is there a work around for this dilemma? Thank you. Udaya B. Kogalur u...@kogalur.com Website: www.kogalur.com

Re: [Bioc-devel] gwaswloc class broken

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

Re: [Rd] Unnecessary lines in stem.c?

Thanks! Cleaned up in R-devel, Tomas On 02/16/2018 05:03 PM, S Ellison wrote: A discussion on r-help led me to look at stem.c at https://github.com/wch/r-source/blob/trunk/src/library/graphics/src/stem.c Lines 76-77 appear superfluous. They sit inside a condition, and set mu, as follows:

Re: [Bioc-devel] R version check in BiocChech

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

Re: [Bioc-devel] gwaswloc class broken

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

[Bioc-devel] gwaswloc class broken

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",

Re: [Rd] [parallel] fixes load balancing of parLapplyLB

Dear Henrik, The rationale is just that it is within these extremes and that it is really simple to calculate, without making any assumptions and knowing that it won't be perfect. The extremes A and B you are mentioning are special cases based on assumptions. Case A is based on the assumption

Re: [Bioc-devel] R version check in BiocChech

> 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.)