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

L.C. Karssen lennart at karssen.org
Thu Nov 28 12:24:39 CET 2013 


On 11/28/2013 12:12 PM, Yury Aulchenko wrote:
> I would think that GenABEL(.)data is "suggested" and then any
> examples using the data from this packages start with something like
> 
> if (require("GenABEL(.)data") ...

This sounds like a good solution.

> 
> How do other packages which lean on data-packages solve this?
> 
> As for the "dot" - I do not have any strong opinion - both options
> seem ok to me :)

Great :-). Then I propose (of course) to stick with the dot, also
because that's already used now.


Best,

Lennart.


> 
> best, Yurii
> 
> 
> On Nov 28, 2013, at 12:06 PM, Nicola Pirastu
> <nicola.pirastu at burlo.trieste.it> wrote:
> 
>> Hi all,
>> 
>> I've been following this conversation with much interest although
>> I'm sorry I can't contribute much.
>> 
>> I was just wondering, could GenABEL.data not be just a dependency
>> on GenABEL? This way installing GenABEL trough install.packages
>> would result in the installation also of GenABEL.data without the
>> user actually having to do it himself.
>> 
>> Best.
>> 
>> Nicola
>> 
>> 
>> Dr. Nicola Pirastu PhD Research Fellow Medical Sciences,
>> Chirurgical and Health Department University of Trieste Medical
>> Genetics IRCCS Burlo Garofolo Via dell'Istria 65/1 34137 Italy tel.
>> +390403785539
>> 
>> Il giorno 28/nov/2013, alle ore 11:59, "L.C. Karssen"
>> <lennart at karssen.org> ha scritto:
>> 
>>> Hi Maksim,
>>> 
>>> First of all, thanks for the good work!
>>> 
>>> On 11/27/2013 07:58 PM, Maksim Struchalin wrote:
>>>> Hi All,
>>>> 
>>>> I created a GenABEL.data package where I moved the following
>>>> data: GenABEL/data/* , inst/exdata/srgenos.dat and
>>>> inst/exdata/srphenos.dat. All the corresponding files are
>>>> deleted from GenABEL. Also, GenABEL.data contains R directory
>>>> with three files (ge03d2c.R, ge03d2ex.R and srdta.R). These
>>>> scripts does not go to the final distribution and needed only
>>>> for possible future usage. Only GenABEL.data/data/* files go to
>>>> GenABEL.data_1.0.tar.gz after running "R CMD build
>>>> GenABEL.data". The directories "R" and "inst" are removed by
>>>> running GenABEL/data/clean.R in "build" process. May be it is 
>>>> not a good idea to do it in such a way but, at least, it is
>>>> convinient and has no any reflection on end users (suggest a
>>>> better way plz).
>>>> 
>>>> The way how GenABEL.data works now is not like how we discussed
>>>> below. It is impossible to generate files during "R CMD
>>>> INSTALL" and undisarable during "R CMD build". The best opition
>>>> was just to move all the data to GenABEL.data from GenABEL
>>>> (like CRAN people suggested). In this case, we can install
>>>> GenABEL.data without having GenABEL installed. After this, we
>>>> install GenABELL.
>>> 
>>> This sounds very strange to me. Does the user first need to
>>> install the GenABEL.data package and then the 'main' GenABEL
>>> package? Or do I misunderstand you? What happens if the user
>>> installs them in a different order? I guess that shouldn't
>>> matter, right, as the package contains only data?
>>> 
>>>> When we run library(GenABEL), it automaticly attaches
>>>> GenBEL.data. Thus, the only change for users is that they need
>>>> to install two packages now (GenABEL.data and GebABEL).
>>> 
>>> And GenABEL.data is only needed if they actually want to use the 
>>> examples, right? Or do we simply put GenABEL.data in the list of
>>> required packages in the DESCRIPTION file?
>>> 
>>> 
>>> Thanks,
>>> 
>>> Lennart.
>>> 
>>>> 
>>>> Now we have sizes of both packages much smaller: 469K for
>>>> GenABEL and 2.4M for GenABEL.data.
>>>> 
>>>> It should work now, but if you experience some problems, let me
>>>> know.
>>>> 
>>>> best, Maksim
>>>> 
>>>> 
>>>> On 26/11/2013 20:48, L.C. Karssen wrote:
>>>>> Hi Maksim,
>>>>> 
>>>>> On 11/26/2013 12:11 PM, Maksim Struchalin 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 :-).
>>>>> I'm not sure how many user actually type data(srdta), but I
>>>>> see you point.
>>>>> 
>>>>>> 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).
>>>>> Good point!
>>>>> 
>>>>>> 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?
>>>>>> 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?
>>>>> Sounds like this is the best solution. Thanks for digging in
>>>>> to this. As for the package name, either GenABELdata or
>>>>> GenABEL.data sounds find with me (the latter one being a bit
>>>>> clearer in my opinion).
>>>>> 
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Lennart
>>>>> 
>>>>>> 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
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> _______________________________________________ 
>>>>>>>>> genabel-devel mailing list 
>>>>>>>>> genabel-devel at lists.r-forge.r-project.org 
>>>>>>>>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>> 
--
>>>>>>>> -----------------------------------------------------------------
>>>>>>>>
>>>>>>>> 
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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>>>>>>>>
>>>>>>>
>>>>>>>> 
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>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>> 
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>>>
>>>> 
--
>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen 
>>> Utrecht The Netherlands
>>> 
>>> lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A 
>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>> 
>>> _______________________________________________ genabel-devel
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-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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