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<div class="moz-cite-prefix">Hi All,<br>
<br>
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. <br>
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.<br>
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).<br>
<br>
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. 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).<br>
<br>
Now we have sizes of both packages much smaller: 469K for GenABEL
and 2.4M for GenABEL.data.<br>
<br>
It should work now, but if you experience some problems, let me
know.<br>
<br>
best,<br>
Maksim<br>
<br>
<br>
On 26/11/2013 20:48, L.C. Karssen wrote:<br>
</div>
<blockquote cite="mid:5294A694.4090306@karssen.org" type="cite">
<pre wrap="">Hi Maksim,
On 11/26/2013 12:11 PM, Maksim Struchalin wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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
On 18/11/2013 18:54, Yury Aulchenko wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Nov 15, 2013, at 17:21 PM, L.C. Karssen <a class="moz-txt-link-rfc2396E" href="mailto:lennart@karssen.org"><lennart@karssen.org></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Maksim,
On 14-11-13 22:38, Maksim Struchalin wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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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<pre wrap="">--
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L.C. Karssen
Utrecht
The Netherlands
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