Re: [Bioc-devel] as.list of a GRanges

2018-02-19 Thread Hervé Pagès
Hi Renan, Most packages affected by these changes are packages that loop on the individual ranges of a GRanges object. They generally don't call as.list() directly but use something like lapply(), vapply(), sapply(), Map(), Reduce(), etc... All these functions indeed call as.list() internally on

Re: [Bioc-devel] as.list of a GRanges

2018-02-19 Thread Hervé Pagès
On 02/19/2018 06:43 AM, Michael Lawrence wrote: On Mon, Feb 19, 2018 at 2:10 AM, Bernat Gel > wrote: Hi Hervé, I completely agree with the goal of having the semantics of list-like operations standardised and documented to avoid surprises,

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

2018-02-19 Thread Henrik Bengtsson
Hi, I'm trying to understand the rationale for your proposed amount of splitting and more precisely why that one is THE one. If I put labels on your example numbers in one of your previous post: nbrOfElements <- 97 nbrOfWorkers <- 5 With these, there are two extremes in how you can split up

Re: [Bioc-devel] rsvg on mac

2018-02-19 Thread Alexey Sergushichev
Valerie, thanks. Will try to ask there. However, after looking through the mailing list it looks like R-devel builds for OS X aren't trivial and aren't part of CRAN... -- Alexey On Mon, Feb 19, 2018 at 9:05 PM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi, > > There has

Re: [Bioc-devel] rsvg on mac

2018-02-19 Thread Obenchain, Valerie
Hi, There has been some discussion of the devel Mac binaries on the R-SIG-Mac mailing list. That list would be the best place to ask this question. https://stat.ethz.ch/pipermail/r-sig-mac/2018-January/thread.html Valerie On 02/19/2018 08:32 AM, Alexey Sergushichev wrote: Valerie, Are there

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

2018-02-19 Thread Christian Krause
Dear R-Devel List, I have installed R 3.4.3 with the patch applied on our cluster and ran a *real-world* job of one of our users to confirm that the patch works to my satisfaction. Here are the results. The original was a series of jobs, all essentially doing the same stuff using bootstrapped

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

2018-02-19 Thread Vincent Carey
On Mon, Feb 19, 2018 at 11:27 AM, Alexey Sergushichev wrote: > Kevin, > > > It does not request users to make R-devel a _requirement_ of their > package. > > Sadly it does for new packages. New packages submitted to Bioconductor 3.7 > are _required_ to have R >= 3.5

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

2018-02-19 Thread Aaron Lun
> > Personally, I haven't found it to be particularly difficult to update R, > > or to run R-devel in parallel with R 3.4, even without root privileges. > > I find it much harder for a normal user to install R-devel (and update > it properly, because it's a development version) and running >

Re: [Bioc-devel] rsvg on mac

2018-02-19 Thread Alexey Sergushichev
Valerie, Are there any estimates on how often CRAN OS X builds happen? There are still no builds for rsvg and other packages... Thanks, Alexey On Wed, Feb 7, 2018 at 8:09 PM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Hi Kevin, > > CRAN binaries for El Capitan in devel

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

2018-02-19 Thread Alexey Sergushichev
Kevin, > It does not request users to make R-devel a _requirement_ of their package. Sadly it does for new packages. New packages submitted to Bioconductor 3.7 are _required_ to have R >= 3.5 dependency, otherwist BiocCheck will result in a warning (

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

2018-02-19 Thread Aaron Lun
I'll just throw in my two cents here. I think many people underappreciate the benefits of moving to the latest version of R. If you inspect the R-devel NEWS file, there's a couple of nice fixes/features that a developer might want to take advantage of: - sum() doesn't give NAs upon integer

Re: [Rd] readLines interaction with gsub different in R-dev

2018-02-19 Thread Tomas Kalibera
Thank you for the report and analysis. Now fixed in R-devel. Tomas On 02/17/2018 08:24 PM, William Dunlap via R-devel wrote: I think the problem in R-devel happens when there are non-ASCII characters in any of the strings passed to gsub. txt <- vapply(list(as.raw(c(0x41, 0x6d, 0xc3, 0xa9,

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

2018-02-19 Thread Kevin RUE
Hi Alexey, I do agree with you that there is no harm in testing against other version of R. In a way, that is even good practice, considering that many HPC users do not always have access to the latest version of R, and that Travis is making this fairly easy. Now, with regard to your latest

Re: [Bioc-devel] as.list of a GRanges

2018-02-19 Thread Michael Lawrence
On Mon, Feb 19, 2018 at 2:10 AM, Bernat Gel wrote: > Hi Hervé, > > I completely agree with the goal of having the semantics of list-like > operations standardised and documented to avoid surprises, and if to do so, > the current use of as.list must be changed I'm pefectly ok with

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

2018-02-19 Thread Alexey Sergushichev
Hello Kevin, Well, bioc-devel packages are tested against bioc-devel (and R-3.5) in any case. What I'm saying is that aside from testing the package against bioc-devel, I can as well test against bioc-release too on my own. If the package doesn't work with bioc-devel it shouldn't pass bioc-devel

Re: [Rd] writeLines argument useBytes = TRUE still making conversions

2018-02-19 Thread Tomas Kalibera
I think it is as Kevin described in an earlier response - the garbled output is because a UTF-8 encoded string is assumed to be native encoding (which happens not to be UTF-8 on the platform where this is observed) and converted again to UTF-8. I think the documentation is consistent with

Re: [Bioc-devel] as.list of a GRanges

2018-02-19 Thread Bernat Gel
Hi Hervé, I completely agree with the goal of having the semantics of list-like operations standardised and documented to avoid surprises, and if to do so, the current use of as.list must be changed I'm pefectly ok with that. I had not seen the strange behaviour with IRanges, so I was not

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

2018-02-19 Thread Kevin RUE
Dear Alexey, The reason is somewhat implicitly given at https://www.bioconductor.org/developers/how-to/useDevel/ : "Package authors should develop against the version of *R* that will be available to users when the *Bioconductor* devel branch becomes the *Bioconductor* release branch." In other

[Bioc-devel] R version check in BiocChech

2018-02-19 Thread Alexey Sergushichev
Dear Bioconducotr community, I wonder, what is the reason behind requirement for dependency R >= 3.5 (currently) for new packages? As a developer I really want an installation of my package to be as easy as possible and want my package to be easily installed from github. So currently, when I