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

Thu Nov 28 12:06:31 CET 2013

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
>>>>>> ------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>>
>> _______________________________________________
>> 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
> GPG key ID: A88F554A
> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>
> _______________________________________________
> 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

AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel messaggio, o responsabili per la sua consegna alla persona, o se avete ricevuto il messaggio per errore, siete pregati di non trascriverlo, copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential information may be contained in this message or in its attachments. If you are not the addressee indicated in this message, or responsible for message delivering to that person, or if you have received this message in error, you may not transcribe, copy or deliver this message to anyone. In that case, you should delete this message and its attachments. Thank you.