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<div class="moz-cite-prefix">About package names: There are 5056
packages on CRAN. 42 of them are data packages and 6 of them has
name like packagename.data ("cluster.datasets", "data.table",
"gamlss.data", "g.data", "survJamda.data" and "TH.data"). Thus,
GenABELdata would be more in line then GenABEL.data.<br>
<br>
About submission to CRAN: I still see small warnings in R CMD
--check output and at least one FAILURE in test.polylik from RUnit
test. I think we can make the next submission to CRAN by the end
of the next week: one week for testing our new data package +
fixing small errors.<br>
<br>
p.s. We should submit to CRAN GenABEL.data as well.<br>
<br>
best,<br>
Maksim<br>
<br>
<br>
<br>
On 28/11/2013 02:07, Yury Aulchenko wrote:<br>
</div>
<blockquote
cite="mid:4DD079E7-8B29-4C7A-A06E-96BA37448858@gmail.com"
type="cite">
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Wow, very impressive, Maksim!
<div><br>
</div>
<div>Can you please check if GenABEL.data complies with the naming
conventions (I do not recall seeing the names with dots as
package names; what other data-packages use as the names?)</div>
<div><br>
</div>
<div>If naming is ok, do you think we are close to submit to CRAN?
With so many changes, I think we should "jump" on the version
number (say, to 1.8-0?)</div>
<div><br>
</div>
<div>best,</div>
<div>Yurii</div>
<div><br>
<div>
<div>On Nov 27, 2013, at 19:58 PM, Maksim Struchalin <<a
moz-do-not-send="true"
href="mailto:m.v.struchalin@mail.ru">m.v.struchalin@mail.ru</a>>
wrote:</div>
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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 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,
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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