Re: [Rd] bug with OutDec option and deferred_string altrep object

2018-10-08 Thread Tierney, Luke
Thanks for the report. The approach you outlines below should work -- I'll look into it. Best, luke On Mon, 8 Oct 2018, Michael Sannella wrote: > While implementing R's new 'altrep' functionality in the TERR engine, > I discovered a bug in R's 'deferred_string' altrep object: it is not > using

Re: [Rd] Rscript -e does not accept newlines under Linux?

2018-10-08 Thread Tomas Kalibera
I've checked in an experimental fix for this (75413). The newline was lost in the shell script wrapper for R, it is now being escaped similarly to space. To pass multiple commands to Rscript, one can also use "-e" multiple times. Tomas On 09/17/2018 01:09 PM, Duncan Murdoch wrote: On

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-08 Thread Tim Triche, Jr.
D'oh. Does this mean that I should flip the script a second time? I went ahead and added the .BBSoptions file as suggested and flushed out some additional irritants; it seemed that having the main package Suggest: the Data package went more smoothly (no cycles) so I had updated the ticket to

Re: [Bioc-devel] Roxygen documentation under windows

2018-10-08 Thread Leonardo Collado Torres
Hi, Adding the -class part will help for most. To get the correct name, check the top left part of the help page for the function you want to link to. For example, if you type library(GenomicRanges) ?GRanges you'll see GRanges-class {GenomicRanges} on the top left (I'm on a Mac right now).

Re: [Rd] Warning when calling formals() for `[`.

2018-10-08 Thread Emil Bode
Hello, I agree the documentation of args can be improved, but the main question is what the return should be. I guess the reason args() returns NULL is because of the way argument-matching works for primitives: there is a lot going on under the hood, and what arguments are/are not acceptable

Re: [Bioc-devel] Roxygen documentation under windows

2018-10-08 Thread Shepherd, Lori
I think there is a reference here https://stackoverflow.com/questions/48430093/how-do-i-resolve-rd-warning-missing-file-link-when-building-packages-in-rstudi Where the actual name of the man file that has BiocParallelParam is BiocParallelParm-class and BiocParallelParam is an alias. I

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Guido Kraemer
Thanks for looking into this: - I deleted the travis cache and it did not help. - R should update all its packages before attempting to install the coRanking package, so old packages shouldn't be a problem. So I guess I should just wait until R-devel on travis gets updated. On 10/08/2018

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

2018-10-08 Thread Shepherd, Lori
Hello, The Single Package builder (SPB) does check the .BBSOptions but only for UnsupportedPlatforms. This is because the single package builder automatically installs each package before the build and check stage as part of the process. Each package that goes through the single package

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Duncan Murdoch
On 08/10/2018 7:47 AM, Duncan Murdoch wrote: On 08/10/2018 7:37 AM, Gábor Csárdi wrote: The package versions are in the output: https://travis-ci.org/gdkrmr/coRanking/jobs/428661435#L2836 I would just try to purge the cache on Travis, that often helps with incompatible package versions. I

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Duncan Murdoch
On 08/10/2018 7:37 AM, Gábor Csárdi wrote: The package versions are in the output: https://travis-ci.org/gdkrmr/coRanking/jobs/428661435#L2836 I would just try to purge the cache on Travis, that often helps with incompatible package versions. I see "fansi", "mime" and "R6" are out of date.

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Gábor Csárdi
The package versions are in the output: https://travis-ci.org/gdkrmr/coRanking/jobs/428661435#L2836 I would just try to purge the cache on Travis, that often helps with incompatible package versions. Gabor On Mon, Oct 8, 2018 at 12:34 PM Duncan Murdoch wrote: > > On 08/10/2018 7:08 AM, Guido

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Duncan Murdoch
On 08/10/2018 7:08 AM, Guido Kraemer wrote: Hi all, update: I submitted to CRAN and it passes all test just fine (https://cran.r-project.org/web/checks/check_results_coRanking.html). I still have no idea why travis fails. That looks as though the travis system isn't using the latest version

Re: [R-pkg-devel] object 'nativeRoutines' not found

2018-10-08 Thread Guido Kraemer
Hi all, update: I submitted to CRAN and it passes all test just fine (https://cran.r-project.org/web/checks/check_results_coRanking.html). I still have no idea why travis fails. Best Regards, Guido Kraemer On 09/17/2018 05:45 PM, Guido Kraemer wrote: Hi all, Since a couple of days

Re: [Rd] Redundant code in 'split.default' in R devel

2018-10-08 Thread Martin Maechler
> Suharto Anggono via R-devel > on Fri, 5 Oct 2018 17:13:30 + writes: > After r75387, function 'split.default' in R devel still has this part that no > longer has effect. > lf <- levels(f) > y <- vector("list", length(lf)) > names(y) <- lf Indeed --> removed