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

Fri Nov 29 12:41:55 CET 2013

Hi Maksim,

Sorry if I don't understand you correctly, but that doesn't sound
user-friendly. Why should people need to install GA.data first?
Actually, if GA depends on GA.data, GA.data is installed automatically
when the user runs install.packages("GenABEL"), right?

Lennart.

On 29-11-13 12:37, 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
>>>>>>> ------------------------------------------------------------------
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>>>>>>> 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
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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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-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

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