Re: [R-pkg-devel] Conditionally register method with generic in other package

2017-12-07 Thread Hadley Wickham
We use this technique in a couple of places: https://github.com/tidyverse/dbplyr/blob/6be777d8b23d588f19c98de52f4e58f16c2ef67e/R/zzz.R Basic idea is to call registerS3method() manually, when needed - it's just a little tricky because the suggested package may be loaded either before or after your

Re: [R-pkg-devel] Conditionally register method with generic in other package

2017-12-07 Thread Hadley Wickham
On Thu, Dec 7, 2017 at 2:44 AM, Bill Denney wrote: > >> On Dec 6, 2017, at 07:45, Joshua Ulrich wrote: >> >> To avoid excessive dependencies, I would like to only register >> foo.bar() if package A is installed at the time package B is >> installed. If

[Bioc-devel] Errors and warnings while submitting package

2017-12-07 Thread Eric ...
Hi Bioconductor team, I submitted my package to the Bioconductor and there are these errors and warnings that appear in the bioconductor check but that doesn`t appear when I compile. I believe these errors happen not because of my package but rather because of the dependency of other

Re: [Rd] Bug: Issues on Windows with SFN disabled

2017-12-07 Thread Dirk Eddelbuettel
On 7 December 2017 at 17:56, Tomas Kalibera wrote: | | An update on this. Writing R Extensions does not recommend to have a | space character in R_HOME. This means that on Windows one either should | have SFN enabled (which is still the common case), or install into a | directory that does

Re: [Rd] Bug: Issues on Windows with SFN disabled

2017-12-07 Thread Tomas Kalibera
An update on this. Writing R Extensions does not recommend to have a space character in R_HOME. This means that on Windows one either should have SFN enabled (which is still the common case), or install into a directory that does not have a space in its name (so specifically not into

Re: [Bioc-devel] 'IlluminaHumanMethylation450k.db' package installation

2017-12-07 Thread Martin Morgan
On 12/07/2017 10:48 AM, Maryam Hosseini Asanjan wrote: Hi, I am trying to install the 'IlluminaHumanMethylation450k.db' package the way it is described at the bioconductor website (https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450k.db.html) but it

Re: [Bioc-devel] 'IlluminaHumanMethylation450k.db' package installation

2017-12-07 Thread Tim Triche, Jr.
1) It's supposed to be deprecated -- I'm not 100% sure why it's still in release :-/ but will look into that 2) the FDb.InfiniumMethylation.hg19 package and (eventually-forthcoming-when-I-get-around-to-it) FDb.InfiniumMethylation.hg38 package are meant as its successor[s], hence the error message:

Re: [Rd] command line arguments are parsed differently on windows, from 3.4.3

2017-12-07 Thread Tomas Kalibera
Fixed in R-devel and R-patched. Tomas On 12/05/2017 05:58 PM, Tomas Kalibera wrote: A quick workaround if you needed to execute R expressions in Windows is calling RTerm directly. But a fix should be available soon. Tomas On 12/05/2017 05:51 PM, Henrik Bengtsson wrote: Sorry for not

Re: [R-pkg-devel] [R] Please to remove the warning when trying to check a package.

2017-12-07 Thread Duncan Murdoch
On 07/12/2017 4:43 AM, Pijush Das wrote: Hello Sir, I have been trying to create a package in R. When I have put the check option in R studio to check everything is ok that time I have found two warnings and three notes. Those are given below. warnings: 1) * checking dependencies in R code

Re: [R-pkg-devel] Conditionally register method with generic in other package

2017-12-07 Thread Joshua Ulrich
Bill, Duncan, Thanks for the replies. On Wed, Dec 6, 2017 at 12:51 PM, Duncan Murdoch wrote: > On 06/12/2017 8:44 AM, Bill Denney wrote: >> >> >>> On Dec 6, 2017, at 07:45, Joshua Ulrich wrote: >>> >>> To avoid excessive dependencies, I would