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

Hi Bernat, On 02/15/2018 11:57 PM, Bernat Gel wrote: Hi Hervé and others, Thanks for the responses. I woudn't call as.list() of a GRanges an "obscure behaviour" but more a "works as expected, even if not clearly documented" behaviour. Most users/developers will probably agree that

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

Hi Frederick, I would expect that any duplicate names in the resulting data.frame would have the suffixes appended to them, regardless of whether or not they are used as the join key. So in my example I would expect "names.x" and "names.y" to indicate their source data.frame. While careful

Re: [R-pkg-devel] R package CRAN check error

Or even better, devtools::release(): it walks you through a checklist of activities designed to make your submission as successful as possible. Hadley On Fri, Feb 16, 2018 at 2:46 PM, Georgi Boshnakov wrote: > You get a source package suitable for submission

Re: [R-pkg-devel] R package CRAN check error

On 16 February 2018 at 20:46, Georgi Boshnakov wrote: | You get a source package suitable for submission by running `R CMD check namepackage' or the equivalent devtools::build() Close: "R CMD build namepackage" creates the tar.gz file. And "R CMD check --as-cran namepackage_*.tar.gz" checks

Re: [R-pkg-devel] R package CRAN check error

You get a source package suitable for submission by running `R CMD check namepackage' or the equivalent devtools::build() Georgi -Original Message- From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Ilaria Amerise Sent: 16 February 2018 11:35 To:

Re: [R-pkg-devel] R package CRAN check error

Ilaria, On 16 February 2018 at 12:34, Ilaria Amerise wrote: | on submitting a new version of a package I got a rejection because of | the following Error in the CRAN-check. | | Any help would be highly appreciated. | | * using R version 3.4.3 (2017-11-30) | * using platform:

Re: [R-pkg-devel] CRAN submission: Packages accepted if they run on two major R platforms

Carmen, On 16 February 2018 at 17:59, Carmen M. Livi wrote: | I am new here and have a question regarding package submissions: | | "CRAN Repository Policy" states that "packages will not be accepted that | do not run on at least two major R platforms". | | My package runs on MAC and Linux. So

Re: [R-pkg-devel] configuration failed on win-builder

Hi Carmen, On 15 February 2018 at 19:45, Carmen M. Livi wrote: | when submiting my R-package to CRAN I get the following error from the | windows machine: | | * installing *source* package 'spp' ... | ./configure.win: 2: Syntax error: word unexpected (expecting ")") | ERROR: configuration

[R-pkg-devel] R package CRAN check error

Hi everybody, on submitting a new version of a package I got a rejection because of the following Error in the CRAN-check. Any help would be highly appreciated. * using R version 3.4.3 (2017-11-30) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using

[R-pkg-devel] configuration failed on win-builder

Hi all, when submiting my R-package to CRAN I get the following error from the windows machine: * installing *source* package 'spp' ... ./configure.win: 2: Syntax error: word unexpected (expecting ")") ERROR: configuration failed for package 'spp' * removing

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

This is one reason why I strongly advocate keeping NEWS up to date on the devel branch. Not that it would necessarily be easy for Nathan to track it down based on NEWS on all the packages he depends on. On Fri, Feb 16, 2018 at 10:25 AM, Nathan Sheffield wrote: > For

Re: [Rd] [R-win] Bug 17159 - recursive dir.create() fails on windows shares due to permissions (MMaechler: Resending to R-windows@R-pr..)

Wonderful ( - thanks! Cheers Pete On 16/02/2018, 16:29, "Tomas Kalibera" wrote: Bug 17159 has been fixed (in R-devel), but there may be more issues left with UNC paths. Tomas On 01/17/2018 01:37 PM, Joris Meys wrote: > Hi Peter, > > I

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

FWIW, this change also affects code that don't call as.list() explicitly. such as calling Reduce(union, granges), Reduce is implemented on base, and will call as.list() if the predicate isn't a vector already. I understand it wasn't intended to be used this way, but with this in mind there are

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

Hi Scott, It seems like reasonable behavior to me. What result would you expect? That the second "name" should be called "name.y"? The "merge" documentation says: If the columns in the data frames not used in merging have any common names, these have ‘suffixes’ (‘".x"’ and ‘".y"’ by

Re: [Rd] [R-win] Bug 17159 - recursive dir.create() fails on windows shares due to permissions (MMaechler: Resending to R-windows@R-pr..)

Bug 17159 has been fixed (in R-devel), but there may be more issues left with UNC paths. Tomas On 01/17/2018 01:37 PM, Joris Meys wrote: Hi Peter, I share your experience with trying to help IT departments setting things up. The network directory of the students is mapped to a drive, but R

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

For what it's worth, my package (LOLA) was one that used as.list on a GRanges or GRangesList, and those calls were broken by changes to devel. Since I was also pushing changes at the time, I assumed the devel build errors were due to my updates -- I spent quite a bit of time trying to figure