Re: [Rd] An update on the vctrs package

2018-11-08 Thread Abs Spurdle
Kia Ora > vec_size(data.frame(x = 1:10)) > #> [1] 10 > vec_size(array(dim = c(10, 4, 1))) > #> [1] 10 I think that "length" (in the R way) or "size" should incorporate the number of columns (or other dimension information). How about: > vec_npoints (x) > vec_nrecords (x) > vec_nobs (x)

Re: [Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server

2018-11-08 Thread Anh N Tran
Thank you for your helpful response, Valerie. My main concern was that the issue would persist which could make my package unsuitable for bioconductor 3.9 release next year. However, it does not seem to be the case from your explanation. For now I will focus on making sure my package works well

Re: [Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server

2018-11-08 Thread Obenchain, Valerie
Hi Anh, We don't build CRAN packages from source on the Windows and Mac builders but instead install the binaries. Building all CRAN packages from source would require installation and maintenance of many more system dependencies. We may decide to support this in the future but currently it's

[Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server

2018-11-08 Thread Anh N Tran
Hello, I noticed that multiple packages currently have errors because 'devtools' was not installed on merida2. I wonder if the issue will go away eventually or we will have to make changes to our packages to pass the check. For my HPAanalyze package specifically, merida2 also didn't have the

[Bioc-devel] submitting a tiny data package (GmapGenome.Hsapiens.rCRS)

2018-11-08 Thread Tim Triche, Jr.
What's the best/fastest way to do this? The package (MTseeker) will happily build and install it for the user via the indexMTgenome() function, but since I test for its presence prior to running examples, it seems like I might as well have it available through BioC. Thanks, --t

Re: [Rd] Little memory leak fix

2018-11-08 Thread Tomas Kalibera
Thanks! Fixed in R-devel. Best Tomas On 10/29/18 12:34 AM, David CARLIER wrote: > Hi dear list, > > Here a little memory leak fix proposal. > > Kind regards. > Thanks. > > __ > R-devel@r-project.org mailing list >

Re: [Bioc-devel] BiocManager and local Bioconductor mirror

2018-11-08 Thread Martin Morgan
Let's continue this on github at https://github.com/Bioconductor/BiocManager/issues/31 On 11/8/18, 6:31 AM, "Martin Morgan" wrote: I'm not sure why this does not work. The key is BiocManager::repositories(), which determines the repositories where R looks for packages. R choose

Re: [Bioc-devel] BiocManager and local Bioconductor mirror

2018-11-08 Thread Martin Morgan
I'm not sure why this does not work. The key is BiocManager::repositories(), which determines the repositories where R looks for packages. R choose the first repository where it finds the package (maybe of equivalent version, not exactly sure...). The first argument to repositories() can be a

[Bioc-devel] BiocManager and local Bioconductor mirror

2018-11-08 Thread Rainer Johannes
Dear all, I like the new BiocManager package with its new possibilities to install specific versions of Bioconductor - but what I miss is the possibility to specify a local Bioconductor mirror from which to install packages. Our calculation clusters don't have direct internet access, so I am

Re: [Rd] error unserializing ascii format (v2 or v3)

2018-11-08 Thread peter dalgaard
I see this on MacOS as well, so likely not platform dependent. A little more diddling to try to narrow it down: > unserialize(serialize(as.raw(1), NULL, version=2, ascii=TRUE)) [1] 30 > unserialize(serialize(list(as.raw(1)), NULL, version=2, ascii=TRUE)) [[1]] [1] 30 >