Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On 02/08/2016 6:34 PM, Dirk Eddelbuettel wrote: On 2 August 2016 at 18:13, Duncan Murdoch wrote: | Okay, now I think I understand, but I agree with CRAN. It is not | feasible to tell if the test happened somewhere in the code unless we | enforce a particular way of writing the test. Debian

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On 02/08/2016 4:20 PM, Dirk Eddelbuettel wrote: On 2 August 2016 at 16:07, Duncan Murdoch wrote: | On 02/08/2016 1:41 PM, Dirk Eddelbuettel wrote: | > | > On 2 August 2016 at 13:12, Duncan Murdoch wrote: | > | On 02/08/2016 1:01 PM, Dirk Eddelbuettel wrote: | > | > | > | > On 2 August 2016 at

[Bioc-devel] commit changes with scenario 1

I am trying to commit some changes to bioCancer . the issue is no changes added to commit. Please, here is commands. Thanks - git clone https://github.com/Bioconductor-mirror/bioCancer - cd bioCancer/ - ../update_remotes.sh Already on

Re: [R-pkg-devel] Recommendation on qr method export

Not strictly what you're asking, but at some point it may be important to note that the "QR" method used by lm() and friends (notably anova() and aov()) actually relies on successive orthogonalization. This does yield a QR decomposition but the reverse is not true. A generic X=QR decomposition

Re: [Rd] strange behavior in 'inherits' check for loaded S4 object

Agreed that this looks like a real bug, and is independent of how one regards the more general issue about specifying methods for a public generic and a non-exported class. John On Aug 2, 2016, at 11:48 AM, Kevin Ushey wrote: > Hi Martin, John, > > Thanks for the

[Rd] save/load + all.equal on reference class objects

After I save an object that contains reference class objects in some of its slots to a file and then re-load it, all.equal() seems to break for me. Is this a bug in all.equal, or is it likely caused by bad implementation of methods on my side? (I see that "'all.equal()' gains methods for

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On 2 August 2016 at 16:07, Duncan Murdoch wrote: | On 02/08/2016 1:41 PM, Dirk Eddelbuettel wrote: | > | > On 2 August 2016 at 13:12, Duncan Murdoch wrote: | > | On 02/08/2016 1:01 PM, Dirk Eddelbuettel wrote: | > | > | > | > On 2 August 2016 at 11:36, Joshua Ulrich wrote: | > | > | Maybe I'm

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On 02/08/2016 1:41 PM, Dirk Eddelbuettel wrote: On 2 August 2016 at 13:12, Duncan Murdoch wrote: | On 02/08/2016 1:01 PM, Dirk Eddelbuettel wrote: | > | > On 2 August 2016 at 11:36, Joshua Ulrich wrote: | > | Maybe I'm missing something, but isn't that the point of calling | > |

Re: [Rd] strange behavior in 'inherits' check for loaded S4 object

Hi Martin, John, Thanks for the responses! I've tidied up some of the notes from this mailing list thread and posted them on the bug tracker. John, in this case, I think namespaces are relevant because for non-exported S4 classes, the class information is made available through the '.__C__'

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On 2 August 2016 at 13:12, Duncan Murdoch wrote: | On 02/08/2016 1:01 PM, Dirk Eddelbuettel wrote: | > | > On 2 August 2016 at 11:36, Joshua Ulrich wrote: | > | Maybe I'm missing something, but isn't that the point of calling | > | requireNamespace()? For example: | > | if

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On 02/08/2016 1:01 PM, Dirk Eddelbuettel wrote: On 2 August 2016 at 11:36, Joshua Ulrich wrote: | Maybe I'm missing something, but isn't that the point of calling | requireNamespace()? For example: | if (requireNamespace("suggestedPackage")) | stop("suggestedPackage required but not

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On 2 August 2016 at 11:36, Joshua Ulrich wrote: | Maybe I'm missing something, but isn't that the point of calling | requireNamespace()? For example: | if (requireNamespace("suggestedPackage")) | stop("suggestedPackage required but not installed") | | That doesn't seem like a heavy burden for

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

Dirk, That is useful. I think the "Recommends" category from that link is pretty much what I am suggesting - something that should be installed if it's available in the package repository but is not loaded/imported by default. Some of those other relationships sound like they would also be

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

On Tue, Aug 2, 2016 at 11:26 AM, Thomas J. Leeper wrote: > I have a fairly open-ended question about the handling of package > dependencies that is inspired by the precise distinction between > "Depends", "Imports", and "Suggests" listed in DESCRIPTION. > > Some background,

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

See eg https://www.debian.org/doc/debian-policy/ch-relationships.html We have other big fish to fry. Eg many packages have LinkingTo: BH (as Boost headers are indeed awesome) but this 120 mb (!!) payload is needed _once_ during package compilation / installation and never again afterwards. So

[R-pkg-devel] Handling Not-Always-Needed Dependencies?

I have a fairly open-ended question about the handling of package dependencies that is inspired by the precise distinction between "Depends", "Imports", and "Suggests" listed in DESCRIPTION. Some background, as I understand it: Prior to requiring package namespaces, we listed package dependencies

Re: [Rd] [R] Fwd: Help: malloc/free deadlock in unsafe signal handler 'Rf_onsigusr1'

Redirecting to R-devel I don't recall how long the SUGUSR handlers have been in R -- you can check in svn if you like -- it's been a long time. The intention is for them to serve as an emergency break -- a chance of possibly saving the workspace when you get stuck in an infinite loop in

[Rd] Accessing R engine with Delphi

Hello Hans -Peter , I need to call R functions with DELPHI , you can help in this my need ? Will be via DCOM , DLL ? which quickly and efficiently? Please , if possible , show me examples. >From already thank you for your attention. Wellington Sala, developer DELPHI

Re: [Rd] A request regarding R GUI

On 02/08/2016 4:02 AM, S Iqbal wrote: Hi, I use R on windows and linux. It is regarding R GUI in linux. In linux the output and script spaces are stacked vertically. It becomes cumbersome to check the output or script in the space whenever the output or script are longer than the space

[Rd] A request regarding R GUI

Hi, I use R on windows and linux. It is regarding R GUI in linux. In linux the output and script spaces are stacked vertically. It becomes cumbersome to check the output or script in the space whenever the output or script are longer than the space available. The GUI in linux should be like that

[Bioc-devel] memory inefficiency problem of building MSPC packages

Bioc-devel: I haven been developing Bioconductor Package for multiple sample peak calling, and all unit test for my packages is done efficiently. However, I have one minor problem that cause memory inefficiency when building the packages in my machines. To get straight, I am going to find overlap