[GenABEL-dev] ISNAN problem in filevector found by Jenkins

Sat Nov 23 15:12:56 CET 2013

Hi Lennart,

https://app.box.com/s/iy41ug5qg4sbylul9oyn

This is an example demonstrating how a GenABEL function "impute2databel" 
calls a function "iteratorDA" from DatABEL. Here, GenABEL is compiled 
without flv's and iterator's code (I deleted it from src).

Could you run the test?:
0) Dowload the file test_GenABEL_iterator.tar.gz from 
https://app.box.com/s/iy41ug5qg4sbylul9oyn
1) decompress test_GenABEL_iterator.tar.gz
2) cd test_GenABEL_iterator
3) R CMD INSTALL DatABEL_0.9-4.tar.gz
4) R CMD INSTALL GenABEL_1.7-7.tar.gz
5) run test.R

It works on my Ubuntu. If it works on your Ubuntu, win and mac, then we 
can delete from GenABEL the simlinks to flv and databel.

best,
??????

On 22/11/2013 21:34, L.C. Karssen wrote:
> Hi ??????,
>
>
> On 11/19/2013 03:17 PM, Maksim Struchalin wrote:
>> Hi Lennart,
>>
>> I see you are improving your Russian :-).
> Getting to know the Russian alphabet is step one :-).
>
>> I understand your arguments. I think we can combine our two approaches.
>> 1) We make a so/dll from filevector and let it use by
>> ProbABEL/OmicABEL/Another_not_R_softABEL.
>> 2) For GenABEL and other R packages, we make a DatABEL.
>>
>> The code of filevector is the same both for 1) and 2).
> But that doesn't solve the problem of having symlinks to the fvlib
> directory in our SVN tree... Which means that any update to filevector
> can make the depending package (DatABEL) become uncompilable.
>
> In the mean time I've set the first steps towards 'libfilevector' in
> SVN, see commits 1415 and 1416. This works (at least for ProbABEL), but
> more polishing is needed.
>
>
>> We only add
>> preprocessor commands (#ifdef and so on) to surround R specific code
>> (ISNAN() and std::isnan). In this case, compiler choose itself weather
>> it buids the lib for R or for OS.
>>
>> If we will want to use only approach 1) for GenABEL in the future, we
>> can quickly swith to it later.
> True, for now this will work.
>
>
> Best,
>
> Lennart.
>
>> best,
>> Maksim
>>
>>
>>
>> On 19/11/2013 16:10, L.C. Karssen wrote:
>>> Hi ??????,
>>>
>>> (trying a Russian keyboard layout, no idea if this works...).
>>>
>>> On 19-11-13 09:44, Maksim Struchalin wrote:
>>>> It seems that your solution is workable but I see little difference with
>>>> what it is now. Now the filevector code is incorporated in each
>>>> packages.
>>> This is what I would like to change, indeed. Code that is reused by so
>>> many packages should not be copied/symlinked into the code tree of those
>>> packages. By symlinking it as we have now, there is no proper way of
>>> specifying a version number of the filevector code. Which, in turn means
>>> that if something changes in the filevector code all other packages need
>>> to be changed immediately (just like what happened with your latest
>>> change). If the filevector code have been a proper library we could have
>>> simply said that ProbABEL still depends on the old filevector version
>>> and take more time to make sure the two play nice together.
>>>
>>> Moreover, with the filevector code in a separate library the whole
>>> isnan() issue would not be a problem. We could simply use std::isnan(),
>>> because CRAN wouldn't need to compile the .so/.dll, so no need of ISNAN().
>>> When code is put in a library the internals don't matter as long as the
>>> interface (function names + arguments) to the outside doesn't change.
>>>
>>>> You propose to follow the same way but pack filelvector code
>>>> in one file (dll or so) and distribute 9 packages form GenABEL with the
>>>> same library.
>>> Indeed. The problem with incorporating it all in DatABEL is that non-R
>>> packages like ProbABEL and OmicABEL depend on the stuff in the fvlib
>>> directory as well. Filevector is central to (almost) all packages in the
>>> GenABEL suite, which is why I proposed to make a library out of it. And,
>>> as noted above, this way packages can depend on different version of the
>>> library.
>>>
>>> We can of course discuss whether we want to distribute this .so/.dll as
>>> a separate (operating system) package or withing the R packages. To me
>>> the first option is the 'correct' one, but I see that this may impose on
>>> the user (except on Windows and maybe MacOS, where the .so/.dll is
>>> included in the R package).
>>>
>>>
>>>> Last time I proposed to move filevector in DatABEL. All other packages
>>>> (GenA and so on) will load DatAB in R and use filevector fucntions from
>>>> DatA. When DatABEL is loaded through library(DatABEL), the file
>>>> DatABEL.so is loaded as well.
>>> I think this is what should be done with the DAlib directory (another
>>> symlinked dir).
>>>
>>>>   Thus, you do not need to ask users to
>>>> install additional lib because it is in DatABEL already. I think this is
>>>> a workable approach that will allow us to delete the filevector code (or
>>>> filevector so/dll) from all the packages.
>>>>
>>>>
>>>> This is some quote from the R manual how to register functions to make
>>>> it available from DatAB to GenAB:
>>>>
>>>>
>>>>        _______________________________________________
>>>>
>>>>
>>>>        5.4 Registering native routines
>>>>
>>>> By 'native' routine, we mean an entry point in compiled code.
>>>>
>>>> In calls to |.C|, |.Call|, |.Fortran| and |.External|, R must locate the
>>>> specified native routine by looking in the appropriate shared
>>>> object/DLL. By default, R uses the operating system-specific dynamic
>>>> loader to lookup the symbol in all loaded DLLs and elsewhere.
>>>> Alternatively, the author of the DLL can explicitly register routines
>>>> with R and use a single, platform-independent mechanism for finding the
>>>> routines in the DLL. One can use this registration mechanism to provide
>>>> additional information about a routine, including the number and type of
>>>> the arguments, and also make it available to R programmers under a
>>>> different name. In the future, registration may be used to implement a
>>>> form of "secure" or limited native access.
>>>>
>>>> _____________________________________________________
>>>>
>>> Hmm, I will have to think about this. This seems to be about how R finds
>>> out in which DLL a function is found (and maybe where the DLL is found
>>> in the filesystem). I think this is separate from the point below, but
>>> I'm not sure.
>>>
>>>> Your argument was from "5.8 Linking to other packages: It is not in
>>>> general possible to link a DLL in package *packA* to a DLL provided by
>>>> package *packB". *I do not quite understand what they mean under 'link'.
>>>> May be the mean link a library during intsalltion?
>>> Yes, as far as I understand, they mean linking to a library during
>>> installation/compilation.
>>>
>>>
>>> Best,
>>>
>>> Lennart.
>>>> best,
>>>> Maksim
>>>>
>>>>
>>>>
>>>> On 19/11/2013 15:14, L.C. Karssen wrote:
>>>>> Hi Maksim,
>>>>>
>>>>> Good question... The idea is to generate a .dll file for Windows, but
>>>>> I'm not sure what would be the best way to distribute that. It would be
>>>>> interesting to see how other packages do that. For example, the XML
>>>>> package depends on libxml2:
>>>>> http://cran.r-project.org/web/packages/XML/index.html and the Rcurl
>>>>> package depends on libcurl:
>>>>> http://cran.r-project.org/web/packages/RCurl/index.html
>>>>>
>>>>> In the XML package .zip file for Windows there is a directory libs/x64
>>>>> and a directory libs/i386. Both contain XML.dll, so I think that for
>>>>> Linux you simply specify a dependency on a library, whereas for Windows
>>>>> the actual .dll is in the package (which is quite logical because
>>>>> Windows lacks the package repositories that most Linux distros have).
>>>>> It seems that for MacOS the .tgz file also contains a lib directory with
>>>>> the .so file.
>>>>>
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Lennart.
>>>>>
>>>>> On 19-11-13 08:56, Maksim Struchalin wrote:
>>>>>> Hi Lennart,
>>>>>>
>>>>>> How the users under win will install such a library?
>>>>>>
>>>>>> best,
>>>>>> Maksim
>>>>>>
>>>>>> On 19/11/2013 14:46, L.C. Karssen wrote:
>>>>>>> Dear all,
>>>>>>>
>>>>>>> The Jenkins setup already shows its value: After Maksim changed the call
>>>>>>> from std::isnan() to ISNAN() in fvlib's CastUtils.cpp an automatic build
>>>>>>> of ProbABEL was triggered and it failed (because ISNAN() is an R function).
>>>>>>>
>>>>>>> I guess this is one more reason to try to convert fvlib into a real
>>>>>>> (shared) library.
>>>>>>> Does anyone have another workable solution?
>>>>>>>
>>>>>>>
>>>>>>> Lennart.
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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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>>>>> 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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