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

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.

Thanks,
H.

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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--
Herv? Pag?s

Program in Computational Biology
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