<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><br><div><div>On Nov 29, 2013, at 12:41 PM, Maksim Struchalin <<a href="mailto:m.v.struchalin@mail.ru">m.v.struchalin@mail.ru</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div class="moz-cite-prefix">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). </div></div></blockquote><div><br></div><div>Agree; when "depends" things are installed automatically (when standard args asking to install deps are supplied).</div><div><br></div><br><blockquote type="cite"><div text="#000000" bgcolor="#FFFFFF"><div class="moz-cite-prefix">The version with 'suggests' is not much different from
'depends' but more flexibale in a case if something happens with
GenABEL.data.<br></div></div></blockquote><div><br></div>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. </div><div><br></div><div>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 :) )</div><div><br></div><div>Y</div><div><br><blockquote type="cite"><div text="#000000" bgcolor="#FFFFFF"><div class="moz-cite-prefix">
<br>
best,<br>
Maksim<br>
<br>
On 29/11/2013 18:37, Maksim Struchalin wrote:<br>
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<blockquote cite="mid:52987C75.1050308@mail.ru" type="cite">
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<div class="moz-cite-prefix">Changed back to 'depend'. Now users
have to install GenABEL.data first then GenABEL.<br>
Maksim<br>
<br>
On 29/11/2013 18:16, L.C. Karssen wrote:<br>
</div>
<blockquote cite="mid:529877A1.8080207@karssen.org" type="cite">
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Yurii & Lennart,
Yesterday, you supported the idea of making GenABEL.data as 'suggested':
________________________________________________________________
On 28/11/2013 18:24, L.C. Karssen wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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") ...
</pre>
</blockquote>
<pre wrap="">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:
</pre>
<blockquote type="cite">
<pre wrap="">Lennart,
Good point about "depends"!
Again, my question would be how other people do it?
Y
----------------------
Yurii Aulchenko
(sent from mobile device)
</pre>
<blockquote type="cite">
<pre wrap="">On Nov 29, 2013, at 10:36, "L.C. Karssen" <a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:lennart@karssen.org"><lennart@karssen.org></a> wrote:
Hi Maksim,
</pre>
<blockquote type="cite">
<pre wrap="">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(...'.
</pre>
</blockquote>
<pre wrap="">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.
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
</blockquote>
<pre wrap="">Good point!
Best regards,
Lennart.
</pre>
<blockquote type="cite">
<pre wrap="">best,
Maksim
</pre>
<blockquote type="cite">
<pre wrap="">On 28/11/2013 18:24, L.C. Karssen wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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") ...
</pre>
</blockquote>
<pre wrap="">This sounds like a good solution.
</pre>
<blockquote type="cite">
<pre wrap="">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 :)
</pre>
</blockquote>
<pre wrap="">Great :-). Then I propose (of course) to stick with the dot, also
because that's already used now.
Best,
Lennart.
</pre>
<blockquote type="cite">
<pre wrap="">best, Yurii
On Nov 28, 2013, at 12:06 PM, Nicola Pirastu
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:nicola.pirastu@burlo.trieste.it"><nicola.pirastu@burlo.trieste.it></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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"
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:lennart@karssen.org"><lennart@karssen.org></a> ha scritto:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Maksim,
First of all, thanks for the good work!
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
</blockquote>
<pre wrap="">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?
</pre>
<blockquote type="cite">
<pre wrap="">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).
</pre>
</blockquote>
<pre wrap="">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.
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
<blockquote type="cite">
<pre wrap="">On 26/11/2013 20:48, L.C. Karssen wrote:
Hi Maksim,
</pre>
<blockquote type="cite">
<pre wrap="">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 :-).
</pre>
</blockquote>
<pre wrap="">I'm not sure how many user actually type data(srdta), but I
see you point.
</pre>
<blockquote type="cite">
<pre wrap="">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).
</pre>
</blockquote>
<pre wrap="">Good point!
</pre>
<blockquote type="cite">
<pre wrap="">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?
</pre>
</blockquote>
<pre wrap="">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
</pre>
<blockquote type="cite">
<pre wrap="">best, Maksim
</pre>
<blockquote type="cite">
<pre wrap="">On 18/11/2013 18:54, Yury Aulchenko wrote:
On Nov 15, 2013, at 17:21 PM, L.C. Karssen
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:lennart@karssen.org"><lennart@karssen.org></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Maksim,
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
</blockquote>
<pre wrap="">I gues you mean B (bytes) instead of b (bits) here
:-).
</pre>
<blockquote type="cite">
<pre wrap="">"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.
</pre>
</blockquote>
<pre wrap="">Sounds like a waste of space!
</pre>
<blockquote type="cite">
<pre wrap="">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|).
</pre>
</blockquote>
<pre wrap="">This sounds like a perfectly acceptable option.
</pre>
</blockquote>
<pre wrap="">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)
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">It will reduce total size of "data" directory from
2.3Mb to 800Kb.
</pre>
</blockquote>
<pre wrap="">Fantastic! If no one has other objections I say: go
ahead.
Best,
Lennart.
</pre>
<blockquote type="cite">
<pre wrap="">Any objections/suggestions?
best, Maksim
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L.C. Karssen
Utrecht
The Netherlands
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