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

Yury Aulchenko yurii.aulchenko at gmail.com
Fri Nov 29 12:49:30 CET 2013 

On Nov 29, 2013, at 12:41 PM, Maksim Struchalin <m.v.struchalin at mail.ru> wrote:

> From point of view of a user who uses install.package("GenABEL") this version is more convinient because the user does not need to care about anything (nothing changed for him).

Agree; when "depends" things are installed automatically (when standard args asking to install deps are supplied).


> The version with 'suggests' is not much different from 'depends' but more flexibale in a case if something happens with GenABEL.data.

I think that we will still treat these as supplementary package having little value on its own. So I would not expect it drives away. For me, this is rather technical thing - because we were asked by CRAN to do this. I do not think it improves anything, so we just want to make sure nothing breaks / things do not become more difficult for us afterwards. 

Given limits on the data-pacjkages as well, in terms of design we probably need to think of a set of functions (some are already there) to quickly generate/simulate data to be used in examples. (and not running into problem with example run-time - this is also of concern for CRAN :) )

Y

>  
> best,
> Maksim
> 
> On 29/11/2013 18:37, Maksim Struchalin wrote:
>> Changed back to 'depend'. Now users have to install GenABEL.data first then GenABEL.
>> Maksim
>> 
>> On 29/11/2013 18:16, L.C. Karssen wrote:
>>> Hi Maksim,
>>> 
>>> Good that you raise this again. I've been thinking about it a bit longer.
>>> What is the point of separating the data into a separate package if the
>>> user still downloads it automatically ('depends'). The idea behind the
>>> data package is of course to only download what is necessary (even if a
>>> few MB is not very much). So that would point to using 'suggests'.
>>> 
>>> When I worked in Africa (very limited bandwidth) it was actually really
>>> good to have these kind of 'suggests', because then you can only
>>> download what is really necessary.
>>> 
>>> Something I haven't tested: what happens if we use 'suggests' and the
>>> user wants to run an example (and GA.data is not installed)? Will (s)he
>>> get an error/warning message? I guess so if each example in GenABEL has
>>> a 'require(GenABEL.data)' line at the start. If the message to the user
>>> is very clear then "suggests" is fine. Otherwise I would go with the old
>>> behavior (have everything installed): 'depends'.
>>> 
>>> 
>>> 
>>> Lennart.
>>> 
>>> 
>>> 
>>> On 11/29/2013 11:42 AM, Maksim Struchalin wrote:
>>>> Hi Yurii & Lennart,
>>>> 
>>>> Yesterday, you supported the idea of making GenABEL.data as 'suggested':
>>>> 
>>>> ________________________________________________________________
>>>> On 28/11/2013 18:24, L.C. Karssen wrote:
>>>> 
>>>>> 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.
>>>> ________________________________________________________________
>>>> 
>>>> 
>>>> Today, you propose to make it 'depends' or I misunderstand something here?
>>>> 
>>>> About how other people do it: I looked in GANPAdata and gamlss.data
>>>> packages. They 'depends' on GANPA and gamlss (see my message below).
>>>> 
>>>> best,
>>>> Maksim
>>>> 
>>>> 
>>>> On 29/11/2013 16:43, Yurii Aulchenko wrote:
>>>>> Lennart,
>>>>> 
>>>>> Good point about "depends"!
>>>>> 
>>>>> Again, my question would be how other people do it?
>>>>> 
>>>>> Y
>>>>> 
>>>>> ----------------------
>>>>> Yurii Aulchenko
>>>>> (sent from mobile device)
>>>>> 
>>>>>> On Nov 29, 2013, at 10:36, "L.C. Karssen" <lennart at karssen.org> wrote:
>>>>>> 
>>>>>> Hi Maksim,
>>>>>> 
>>>>>>> On 11/29/2013 08:43 AM, Maksim Struchalin wrote:
>>>>>>> I looked at how other developres deal with issue of dependency
>>>>>>> between a
>>>>>>> package and its data.package. I checked out two random packages from
>>>>>>> CRAN: GANPA (GANPAdata) and gamlss (gamlss.data). Both of them (GANPA
>>>>>>> and gamlss) dependes on their data packages - that means their
>>>>>>> DESCRIPTION files contain a reference to their data packages in the
>>>>>>> "Depends:" field. Only GANPAdata suggests GANPA (gamlss.data does not
>>>>>>> Depends/Suggests gamlss).
>>>>>>> 
>>>>>>> When I made GenABEL depending on GenABEL.data, I kept in my mind the
>>>>>>> same idea as Nicola pronounced below - that, in this case, GenABEL.data
>>>>>>> is installed automaticly when users run "install.package(GenABEL)".
>>>>>>> This
>>>>>>> is convinient for users who install GenABEL from CRAN and this is in
>>>>>>> line with GANPA and gamlss but it, probably, does not fully reflect the
>>>>>>> GenABEL reality. The dependency between GenABEL and GenABL.data is weak
>>>>>>> - GenABEL is gonna be mostly used without GenABEL.data. So, I support
>>>>>>> the Yurii's idea about making GenABEL.data as 'suggested' and including
>>>>>>> 'requre(...'.
>>>>>> I agree with you that the dependence between GA and GA.data is rather
>>>>>> weak. On the other hand, why not keep GA.data in Depends? That gives the
>>>>>> same behaviour as before (install everything by default). Sounds
>>>>>> convenient to me.
>>>>>> With modern internet bandwidth the few MB of the data package are not a
>>>>>> problem.
>>>>>> 
>>>>>>> About dot: Personally, I like GenABEL.data. From this name, It is clear
>>>>>>> that this package is some kind of a 'subpackage' of GenABEL package and
>>>>>>> it is not a standalone one.
>>>>>> Good point!
>>>>>> 
>>>>>> 
>>>>>> Best regards,
>>>>>> 
>>>>>> Lennart.
>>>>>> 
>>>>>>> best,
>>>>>>> Maksim
>>>>>>> 
>>>>>>>> On 28/11/2013 18:24, L.C. Karssen wrote:
>>>>>>>> 
>>>>>>>>> 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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>>>>>>>>>>>> 
>>>>>>>> -- 
>>>>>>>>>>> *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-* L.C. Karssen
>>>>>>>>>>> Utrecht The Netherlands
>>>>>>>>>>> 
>>>>>>>>>>> lennart at karssen.org http://blog.karssen.org GPG key ID: A88F554A
>>>>>>>>>>> -*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
>>>>>>>>>>> 
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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
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