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<div class="moz-cite-prefix">That's good. The warnings are because
of that the snp name in the second line of TEST10x15.geno file is
the same as in the first one. Fixed in
<a class="moz-txt-link-freetext" href="https://app.box.com/s/6irjkikm3mukwvtk1wgw">https://app.box.com/s/6irjkikm3mukwvtk1wgw</a> version. Can you
download it and run once again?<br>
<br>
BTW1: The versions of GenABEL and DatABEL here are old (I
generated this example a week ago). That's why there are some
warnings on other functions.<br>
BTW2: Remove the files TEST10x15_T.geno.dose.fvd and
TEST10x15_T.geno.dose.fvi after each run. Otherwise you get an
error message (File 'TEST10x15_T.geno.dose' already exists.).<br>
<br>
best,<br>
Maksim<br>
<br>
<br>
On 25/11/2013 19:28, Yury Aulchenko wrote:<br>
</div>
<blockquote
cite="mid:F677E706-1CC0-406E-AA7D-945676E1CB72@gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
after renaming out-file-name I get (finished with warnings):
<div><br>
</div>
<div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">> x <- impute2databel(geno="TEST10x15.geno",
sample="impute.sample5", out="TEST10x15_T1.geno",
makeprob=FALSE, old=TRUE)</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Loading required package: DatABEL</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">DatABEL v.0.9-4 (March 12, 2013) loaded</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0); min-height: 20px;"><br>
</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Options in effect: </div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--infile = TEST10x15.geno</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--outfile = ./tmp300070</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--skiprows = OFF</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--skipcols = 5</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--cnrow = OFF</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--rncol = ON, using column 2 of 'TEST10x15.geno'</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--transpose = ON</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--Rmatrix = OFF</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"><span class="Apple-tab-span" style="white-space:pre"> </span>
--nanString = NA</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Number of lines in source file is 10</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Number of words in source file is 20</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">skiprows = 0</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">cnrow = 0</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">skipcols = 5</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">rncol = 2</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Rmatrix = 0</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">numWords = 20</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Creating file with numRows = 10</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Creating file with numColumns = 15</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">text2fvf finished.</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Loss of precision / loss of data during conversion from
DOUBLE to FLOAT.</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Futher conversion warnings omitted.</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Read 4 items</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Read 4 items</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Read 4 items</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Read 20 items</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">Warning messages:</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">1: In uninames(.Object@data) :</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"> uninames: some column names are not unique; use
set_dimnames/get_dimnames for non-unique row/col names</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">2: In uninames(x@data) :</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"> uninames: some column names are not unique; use
set_dimnames/get_dimnames for non-unique row/col names</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">3: In uninames(x@data) :</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);"> uninames: some column names are not unique; use
set_dimnames/get_dimnames for non-unique row/col names</div>
<div style="margin: 0px; font-size: 18px; font-family: 'Andale
Mono'; color: rgb(41, 249, 20); background-color: rgb(0, 0,
0);">> </div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>On Nov 25, 2013, at 13:23 PM, L.C. Karssen <<a
moz-do-not-send="true" href="mailto:lennart@karssen.org">lennart@karssen.org</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="font-size: 12px; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: auto; text-align:
start; text-indent: 0px; text-transform: none;
white-space: normal; widows: auto; word-spacing: 0px;
-webkit-text-stroke-width: 0px;">I had the same issues as
Yurii reported:<br>
- compilation warnings when installing<br>
- the 'file already exists' warning: this was one of the
reasons why I<br>
renamed the filename in the 'out=' option in test.R<br>
- I also got the warning about not-unique column names,
but I assumed<br>
that wasn't the issue we were trying to fix here, so I
didn't mention it.<br>
<br>
Yurii, does the script finish when you change the output
file name in<br>
test.R?<br>
<br>
<br>
<br>
Lennart.<br>
<br>
On 11/25/2013 12:26 PM, Yury Aulchenko wrote:<br>
<blockquote type="cite">Tried this on Mac OS X, see below<br>
<br>
On Nov 23, 2013, at 15:12 PM, Maksim Struchalin <<a
moz-do-not-send="true"
href="mailto:m.v.struchalin@mail.ru">m.v.struchalin@mail.ru</a><br>
<<a moz-do-not-send="true"
href="mailto:m.v.struchalin@mail.ru">mailto:m.v.struchalin@mail.ru</a>>>
wrote:<br>
<br>
<blockquote type="cite">Hi Lennart,<br>
<br>
<a moz-do-not-send="true"
href="https://app.box.com/s/iy41ug5qg4sbylul9oyn">https://app.box.com/s/iy41ug5qg4sbylul9oyn</a><br>
<br>
This is an example demonstrating how a GenABEL
function<br>
"impute2databel" calls a function "iteratorDA" from
DatABEL. Here,<br>
GenABEL is compiled without flv's and iterator's code
(I deleted it<br>
from src).<br>
<br>
Could you run the test?:<br>
0) Dowload the file test_GenABEL_iterator.tar.gz from<br>
<a class="moz-txt-link-freetext" href="https://app.box.com/s/iy41ug5qg4sbylul9oyn">https://app.box.com/s/iy41ug5qg4sbylul9oyn</a><br>
1) decompress test_GenABEL_iterator.tar.gz<br>
2) cd test_GenABEL_iterator<br>
3) R CMD INSTALL DatABEL_0.9-4.tar.gz<br>
4) R CMD INSTALL GenABEL_1.7-7.tar.gz<br>
</blockquote>
<br>
getting many warnings at step (4)<br>
<br>
<blockquote type="cite">5) run test.R<br>
</blockquote>
<br>
getting<span class="Apple-converted-space"> </span><br>
<br>
<blockquote type="cite">x <-
impute2databel(geno="TEST10x15.geno",
sample="impute.sample5",<br>
</blockquote>
out="TEST10x15_T.geno", makeprob=FALSE, old=TRUE)<br>
Loading required package: DatABEL<br>
DatABEL v.0.9-4 (March 12, 2013) loaded<br>
<br>
Options in effect:<span class="Apple-converted-space"> </span><br>
--infile = TEST10x15.geno<br>
--outfile = ./tmp333314<br>
--skiprows = OFF<br>
--skipcols = 5<br>
--cnrow = OFF<br>
--rncol = ON, using column 2 of 'TEST10x15.geno'<br>
--transpose = ON<br>
--Rmatrix = OFF<br>
--nanString = NA<br>
Number of lines in source file is 10<br>
Number of words in source file is 20<br>
skiprows = 0<br>
cnrow = 0<br>
skipcols = 5<br>
rncol = 2<br>
Rmatrix = 0<br>
numWords = 20<br>
Creating file with numRows = 10<br>
Creating file with numColumns = 15<br>
text2fvf finished.<br>
File 'TEST10x15_T.geno.dose' already exists.<br>
ERROR in Rstuff:failed in ini_empty_FileMatrix_RError in
!result :<br>
invalid argument type<br>
Calls: impute2databel -> apply2dfo ->
make_empty_fvf<br>
In addition: Warning message:<br>
In uninames(.Object@data) :<br>
uninames: some column names are not unique; use<br>
set_dimnames/get_dimnames for non-unique row/col names<br>
Execution halted<br>
<br>
<br>
<blockquote type="cite"><br>
It works on my Ubuntu. If it works on your Ubuntu, win
and mac, then<br>
we can delete from GenABEL the simlinks to flv and
databel.<br>
<br>
best,<br>
Максим<br>
<br>
<br>
On 22/11/2013 21:34, L.C. Karssen wrote:<br>
<blockquote type="cite">Hi максим,<br>
<br>
<br>
On 11/19/2013 03:17 PM, Maksim Struchalin wrote:<br>
<blockquote type="cite">Hi Lennart,<br>
<br>
I see you are improving your Russian :-).<br>
</blockquote>
Getting to know the Russian alphabet is step one
:-).<br>
<br>
<blockquote type="cite">I understand your arguments.
I think we can combine our two approaches.<br>
1) We make a so/dll from filevector and let it use
by<br>
ProbABEL/OmicABEL/Another_not_R_softABEL.<br>
2) For GenABEL and other R packages, we make a
DatABEL.<br>
<br>
The code of filevector is the same both for 1) and
2).<span class="Apple-converted-space"> </span><br>
</blockquote>
But that doesn't solve the problem of having
symlinks to the fvlib<br>
directory in our SVN tree... Which means that any
update to filevector<br>
can make the depending package (DatABEL) become
uncompilable.<br>
<br>
In the mean time I've set the first steps towards
'libfilevector' in<br>
SVN, see commits 1415 and 1416. This works (at least
for ProbABEL), but<br>
more polishing is needed.<br>
<br>
<br>
<blockquote type="cite">We only add<br>
preprocessor commands (#ifdef and so on) to
surround R specific code<br>
(ISNAN() and std::isnan). In this case, compiler
choose itself weather<br>
it buids the lib for R or for OS.<br>
<br>
If we will want to use only approach 1) for
GenABEL in the future, we<br>
can quickly swith to it later.<br>
</blockquote>
True, for now this will work.<br>
<br>
<br>
Best,<br>
<br>
Lennart.<br>
<br>
<blockquote type="cite">best,<br>
Maksim<br>
<br>
<br>
<br>
On 19/11/2013 16:10, L.C. Karssen wrote:<br>
<blockquote type="cite">Hi максим,<br>
<br>
(trying a Russian keyboard layout, no idea if
this works...).<br>
<br>
On 19-11-13 09:44, Maksim Struchalin wrote:<br>
<blockquote type="cite">It seems that your
solution is workable but I see little
difference with<br>
what it is now. Now the filevector code is
incorporated in each<br>
packages.<span class="Apple-converted-space"> </span><br>
</blockquote>
This is what I would like to change, indeed.
Code that is reused by so<br>
many packages should not be copied/symlinked
into the code tree of those<br>
packages. By symlinking it as we have now, there
is no proper way of<br>
specifying a version number of the filevector
code. Which, in turn means<br>
that if something changes in the filevector code
all other packages need<br>
to be changed immediately (just like what
happened with your latest<br>
change). If the filevector code have been a
proper library we could have<br>
simply said that ProbABEL still depends on the
old filevector version<br>
and take more time to make sure the two play
nice together.<br>
<br>
Moreover, with the filevector code in a separate
library the whole<br>
isnan() issue would not be a problem. We could
simply use std::isnan(),<br>
because CRAN wouldn't need to compile the
.so/.dll, so no need of ISNAN().<br>
When code is put in a library the internals
don't matter as long as the<br>
interface (function names + arguments) to the
outside doesn't change.<br>
<br>
<blockquote type="cite">You propose to follow
the same way but pack filelvector code<br>
in one file (dll or so) and distribute 9
packages form GenABEL with the<br>
same library.<br>
</blockquote>
Indeed. The problem with incorporating it all in
DatABEL is that non-R<br>
packages like ProbABEL and OmicABEL depend on
the stuff in the fvlib<br>
directory as well. Filevector is central to
(almost) all packages in the<br>
GenABEL suite, which is why I proposed to make a
library out of it. And,<br>
as noted above, this way packages can depend on
different version of the<br>
library.<br>
<br>
We can of course discuss whether we want to
distribute this .so/.dll as<br>
a separate (operating system) package or withing
the R packages. To me<br>
the first option is the 'correct' one, but I see
that this may impose on<br>
the user (except on Windows and maybe MacOS,
where the .so/.dll is<br>
included in the R package).<br>
<br>
<br>
<blockquote type="cite">Last time I proposed to
move filevector in DatABEL. All other packages<br>
(GenA and so on) will load DatAB in R and use
filevector fucntions from<br>
DatA. When DatABEL is loaded through
library(DatABEL), the file<br>
DatABEL.so is loaded as well.<br>
</blockquote>
I think this is what should be done with the
DAlib directory (another<br>
symlinked dir).<br>
<br>
<blockquote type="cite">Thus, you do not need to
ask users to<br>
install additional lib because it is in
DatABEL already. I think this is<br>
a workable approach that will allow us to
delete the filevector code (or<br>
filevector so/dll) from all the packages.<br>
<br>
<br>
This is some quote from the R manual how to
register functions to make<br>
it available from DatAB to GenAB:<br>
<br>
<br>
_______________________________________________<br>
<br>
<br>
5.4 Registering native routines<br>
<br>
By ‘native’ routine, we mean an entry point in
compiled code.<br>
<br>
In calls to |.C|, |.Call|, |.Fortran| and
|.External|, R must locate the<br>
specified native routine by looking in the
appropriate shared<br>
object/DLL. By default, R uses the operating
system-specific dynamic<br>
loader to lookup the symbol in all loaded DLLs
and elsewhere.<br>
Alternatively, the author of the DLL can
explicitly register routines<br>
with R and use a single, platform-independent
mechanism for finding the<br>
routines in the DLL. One can use this
registration mechanism to provide<br>
additional information about a routine,
including the number and type of<br>
the arguments, and also make it available to R
programmers under a<br>
different name. In the future, registration
may be used to implement a<br>
form of “secure” or limited native access.<br>
<br>
_____________________________________________________<br>
<br>
</blockquote>
Hmm, I will have to think about this. This seems
to be about how R finds<br>
out in which DLL a function is found (and maybe
where the DLL is found<br>
in the filesystem). I think this is separate
from the point below, but<br>
I'm not sure.<br>
<br>
<blockquote type="cite">Your argument was from
"5.8 Linking to other packages: It is not in<br>
general possible to link a DLL in package
*packA* to a DLL provided by<br>
package *packB". *I do not quite understand
what they mean under 'link'.<br>
May be the mean link a library during
intsalltion?<br>
</blockquote>
Yes, as far as I understand, they mean linking
to a library during<br>
installation/compilation.<br>
<br>
<br>
Best,<br>
<br>
Lennart.<br>
<blockquote type="cite">best,<br>
Maksim<br>
<br>
<br>
<br>
On 19/11/2013 15:14, L.C. Karssen wrote:<br>
<blockquote type="cite">Hi Maksim,<br>
<br>
Good question... The idea is to generate a
.dll file for Windows, but<br>
I'm not sure what would be the best way to
distribute that. It would be<br>
interesting to see how other packages do
that. For example, the XML<br>
package depends on libxml2:<br>
<a moz-do-not-send="true"
href="http://cran.r-project.org/web/packages/XML/index.html">http://cran.r-project.org/web/packages/XML/index.html</a>
and the Rcurl<br>
package depends on libcurl:<br>
<a moz-do-not-send="true"
href="http://cran.r-project.org/web/packages/RCurl/index.html">http://cran.r-project.org/web/packages/RCurl/index.html</a><br>
<br>
In the XML package .zip file for Windows
there is a directory libs/x64<br>
and a directory libs/i386. Both contain
XML.dll, so I think that for<br>
Linux you simply specify a dependency on a
library, whereas for Windows<br>
the actual .dll is in the package (which is
quite logical because<br>
Windows lacks the package repositories that
most Linux distros have).<br>
It seems that for MacOS the .tgz file also
contains a lib directory with<br>
the .so file.<br>
<br>
<br>
Best regards,<br>
<br>
Lennart.<br>
<br>
On 19-11-13 08:56, Maksim Struchalin wrote:<br>
<blockquote type="cite">Hi Lennart,<br>
<br>
How the users under win will install such
a library?<br>
<br>
best,<br>
Maksim<br>
<br>
On 19/11/2013 14:46, L.C. Karssen wrote:<br>
<blockquote type="cite">Dear all,<br>
<br>
The Jenkins setup already shows its
value: After Maksim changed the call<br>
from std::isnan() to ISNAN() in fvlib's
CastUtils.cpp an automatic build<br>
of ProbABEL was triggered and it failed
(because ISNAN() is an R function).<br>
<br>
I guess this is one more reason to try
to convert fvlib into a real<br>
(shared) library.<br>
Does anyone have another workable
solution?<br>
<br>
<br>
Lennart.<br>
<br>
<br>
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--<span class="Apple-converted-space"> </span><br>
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L.C. Karssen<br>
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<pre wrap="">_______________________________________________
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