[Bioc-devel] Deprecation of bioc_docker and bioconductor_full containers

2020-01-09 Thread Turaga, Nitesh
Dear Bioconductor developers, There are new set of Bioconductor docker images under the name bioconductor/bioconductor_docker. These are located at https://github.com/Bioconductor/bioconductor_docker. The new set of images will have a `devel` image and a `RELEASE_3_10` / `latest` image. With

Re: [Bioc-devel] How to use RData files in Bioconductor data and software packages

2020-01-09 Thread Pages, Herve
On 1/9/20 13:00, web working wrote: > Hi Herve, > > thank you for your detailed answer. I guess I have expressed myself > unclear. The BED files were just examples for data I store in the > inst/extdata folder. Based on the description for ExperimentHubData I > have decided to create a

Re: [Bioc-devel] How to use RData files in Bioconductor data and software packages

2020-01-09 Thread web working
Hi Richard, It depends on the filetype. I am loading my "non RData" files with read.delim and my RData files with a helper function which returns a R object of the RData object: #' Load RData object and returns first entry #' #' Load RData object and returns first entry. If there is more than

Re: [Bioc-devel] How to use RData files in Bioconductor data and software packages

2020-01-09 Thread web working
Hi Herve, thank you for your detailed answer. I guess I have expressed myself unclear. The BED files were just examples for data I store in the inst/extdata folder. Based on the description for ExperimentHubData I have decided to create a software and a data package (no ExperimentHubData

Re: [Bioc-devel] How to use RData files in Bioconductor data and software packages

2020-01-09 Thread Pages, Herve
Hi Tobias, If the original data is in BED files, there should be no need to serialize the objects obtained by importing the files. It is **much** better to provide a small helper function that creates an object from a BED file and to use that function each time you need to load an object.

[Bioc-devel] How to use RData files in Bioconductor data and software packages

2020-01-09 Thread web working
Dear all, I am currently developing a software package (dummySoftware) and a data package (dummyData) and I am a bit confused in where to store my RData files in the data package. Here my situation: I want to store some software package objects (new class objects of the software package) in