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

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Thu Jan 9 22:40:23 CET 2020

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 software and a data package (no 
> ExperimentHubData software package). In my RData files I store software 
> package objects. These objects are bigger than 5 MB. Using a helper 
> function is no option, because the object calculation takes to much 
> time. For this reason I want to load this objects for my example 
> functions. My question is if the storage of my RData files in the 
> inst/extdata directory is correct or not.

It's technically correct but it's not as convenient as putting them in 
data/ because they can not longer be listed and/or loaded with data().
So if you're storing them in inst/extdata only because the data() 
solution gave you a BiocCheck warning then I'd say that you're giving up 
too easily ;-)

IMO it is important to try to understand why the data() solution gave 
you a BiocCheck warning in the first place. Unfortunately you're not 
providing enough information for us to be able to tell. What does the 
warning say? How can we reproduce the warning? Ideally we would need to 
see a transcript of your session and links to your packages.


> Best,
> Tobias
> Am 09.01.20 um 17:59 schrieb 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.
>> This has at least 2 advantages:
>> 1. It avoids redundant storage of the data.
>> 2. By avoiding serialization of high-level S4 objects, it makes the
>> package easier to maintain in the long run.
>> Note that the helper function could also implement a cache mechanism
>> (easy to do with an environment) so the BED file is only loaded and the
>> object created the 1st time the function is called. On subsequent calls,
>> the object is retrieved from the cache.
>> However, if the BED files are really big (e.g. > 50 Mb), we require them
>> to be stored on ExperimentHub instead of inside dummyData. Note that you
>> still need to provide the dummyData package (which becomes what we call
>> an ExperimentHub-based data package). See the "Creating An ExperimentHub
>> Package" vignette in the ExperimentHubData package for more information
>> about this.
>> Hope this helps,
>> H.
>> On 1/9/20 04:45, web working wrote:
>>> 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 the data package. This objects are example objects
>>> and a to big for software packages. As I have read here
>>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__r-2Dpkgs.had.co.nz_data.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=GaTKqVd_WDqMRk0dW7SYkjVlgCzt0I0bACHfb1iIOVc&s=0ajhWDlJfLxXxzJpreO1Nh4qnu3aJ8gQkRb9qThsi1o&e= 
>>> ) all RData objects should be stored in the data directory of a package.
>>> BED files of the data package are stored in inst/extdata.
>>> The data of the data packaged will be addressed in the software package
>>> like this: system.file('extdata', 'subset.bed', package = 'dummyData').
>>> And here the problem occurs. After building the data package
>>> (devtools::build(args = c('--resave-data'))), all data in data/ are
>>> stored in a datalist, Rdata.rdb, Rdata.rds and Rdata.rdx and can not
>>> addressed with system.file. Addressing this data with the data()
>>> function results in a warning during BiocCheck::BiocCheck().
>>> My solution is to store the RData files in the inst/extdata directory
>>> and address them with system.file. Something similar is mentioned here,
>>> but in the context of a vignette
>>> (r-pkgs.had.co.nz/data.html#other-data). Is this the way how to do it?
>>> Best,
>>> Tobias
>>> _______________________________________________
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
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