[GenABEL-dev] new approach for data storage in GenABEL package

[Yury Aulchenko]

On Nov 26, 2013, at 12:11 PM, Maksim Struchalin <m.v.struchalin at mail.ru> wrote:

> I am still in the way of compressing GenABEL data.
> To remind you: the idea consists of compressing the original data text files and use them later for generating RData files (e.g. srdta).
> 
> Yurii proposed to make RData files in examples which use them. I see now only one way how this idea can be implemented. We replace "data(srdta)" line in every file where it is used by a function e.g. "generate_srdt()" which generate srdta object. The same procedure for other five *.RData files from GenABEL/data. If we follow this way, we have to change 71 files in man directory and, additionally to this, the GenABEL manual. Also, users will not be able to load the srdta set (and others) by typing "data(srdta)" in a command line (how they get used to) and has to know that the function generate_srdt() now services for these needs. This all sounds nasty :-).

agree, this is too much of a hassle; does not look elegant

> 
> Making the data during package installation time is also a bad idea as Yurii noted below. Actually, this is impossible because the process of making GenABEL data requires GenABEL functions which are not available during installation time (they are avaialble only after GenABEL installed).
> 
> I see only one good solution now: move all the GenABEL data to a new package e.g. GenABELdata as it was proposed by CRAN people from the begining. In this case, it is possible to generate RData during installation time using GenABEL functions (which are installed by that time). I think this solution is paltform independent because R rules permit runing *.R scripts to generate data during installation time.
> 
> What do you think about making a data package for GenABEL?

agree


> Do you think the name GenABELdata is ok? May be we can move all the *ABEL data in DatABEL package instead of making *ABELdata data packages?

What are names used by other guys? GenABELdata or GenABEL.data sound like good names (not sure about "." in the package names)

Moving data to DatABEL does not sound good to me - DatABEL is, in principle, not about genetics, so whay should genetic data hang there. 

best,
Y

> 
> best,
> Maksim
> 
> On 18/11/2013 18:54, Yury Aulchenko wrote:
>> On Nov 15, 2013, at 17:21 PM, L.C. Karssen <lennart at karssen.org> wrote:
>> 
>>> Hi Maksim,
>>> 
>>> On 14-11-13 22:38, Maksim Struchalin wrote:
>>>> In this email, I propose a new approach which allows to reduce total
>>>> size of data from 8Mb to 2Mb that reduce the entire GenABEL size from
>>>> 12Mb to 6Mb.
>>> I gues you mean B (bytes) instead of b (bits) here :-).
>>> 
>>>> "R CMD check --as-cran" reports that the following sub-directories have
>>>> too big size: data (2.3Mb), exdata (5.7Mb) and libs (2.6Mb). After the
>>>> last GenABEL submission to CRAN, the maintainers suggested to create a
>>>> new package called GenABELdata and move all the data there. I run
>>>> through the data and found that:
>>>> 1) "exdata" directory can be compressed by gzip and reduced from 5.8Mb
>>>> -> 1.1Mb.
>>>>    - There is a function guzip() from library R.utils which can
>>>> decompress the files. It works on any OS.
>>>>    - Moreover: the native R function read.table() can read gzip files
>>>> without decompression.
>>>>    - Even more: it looks like that the biggest file "srgenos.dat" is
>>>> used only once a long time ago for generating "srdta.RData" and now it
>>>> is just sitting there and eating space needlessly.
>>> Sounds like a waste of space!
>>> 
>>>> 2) We can delete some files from the "data" directory. The deleted files
>>>> will be generated on the user computer based on the files from exdata.
>>>> It can be done during INSTALLATION (a line in Makefile?) or on the first
>>>> load through (|run funcion .onAttach() in R/zzz.R|).
>>> This sounds like a perfectly acceptable option.
>> 
>> I suggest this is done in the "example" which make use of this data, NOT in the INSTALL etc. - we should make things as "robust" as possible and interfere as little as possible with the usual workflow (which is very much system-specific, in that we will need to to test on all platforms)
>> 
>> 
>>>> It will reduce
>>>> total size of "data" directory from 2.3Mb to 800Kb.
>>> Fantastic! If no one has other objections I say: go ahead.
>>> 
>>> 
>>> Best,
>>> 
>>> Lennart.
>>> 
>>> 
>>>> Any objections/suggestions?
>>>> 
>>>> best,
>>>> Maksim
>>>> 
>>>> 
>>>> _______________________________________________
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>>>> 
>>> -- 
>>> -----------------------------------------------------------------
>>> L.C. Karssen
>>> Utrecht
>>> The Netherlands
>>> 
>>> lennart at karssen.org
>>> http://blog.karssen.org
>>> 
>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>> ------------------------------------------------------------------
>>> 
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