[GenABEL-dev] [genabel-Bugs][5299] Filevector doesn't work on big-endian architectures

[L.C. Karssen]

Hmm that was maybe a bit too short a reaction :-).

I'd suggest the following:
- Move the discussion to the dev list (mention that in the bug tracker
as well)
- Once a course of action has been decided we can do status updates in
the bug tracker.


Lennart.

On 16-04-14 14:29, L.C. Karssen wrote:
> I would say this is for the dev list + bug
> 
> 
> Lennart.
> 
> On 16-04-14 13:02, Yurii Aulchenko wrote:
>> Is that something for bug tracker or forum or a mix?
>>
>> ----------------------
>> Yurii Aulchenko
>> (sent from mobile device)
>>
>>> On Apr 16, 2014, at 12:23 PM, "genabel-bugs at r-forge.r-project.org" <genabel-bugs at r-forge.r-project.org> wrote:
>>>
>>> Bugs item #5299, was changed at 2014-01-24 09:38 by Jurica Stanojkovic
>>> You can respond by visiting:
>>> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=5299&group_id=505
>>>
>>> Status: Open
>>> Priority: 2
>>> Submitted By: Lennart Karssen (lckarssen)
>>> Assigned to: Nobody (None)
>>> Summary: Filevector doesn't work on big-endian architectures
>>> Resolution: Accepted As Bug
>>> Operating System: All
>>> Severity: normal
>>> Hardware: Other
>>> Version: other
>>> Component: FileVector
>>> URL: https://buildd.debian.org/status/package.php?p=probabel
>>>
>>>
>>> Initial Comment:
>>> The Debian build logs for big-endian machines (see URL) show that the ProbABEL checks fail on machines with that architecture. Closer inspection reveals that the checks fail on the comparison between text and binary (filevector-format) input.
>>>
>>> Also see this discussion on the debian-mentor mailing list, especially Gert Wollny's posts: https://lists.debian.org/debian-mentors/2014/01/msg00326.html
>>> Wollny writes:
>>> "I dug around in the code and voila, e.g. in fvlib/frutil.cpp the
>>> function blockWriteOrRead uses fstream.read|write to do raw data IO and
>>> then in other parts of the code the data is just cast to the desired
>>> type without doing any checks of endianess let alone the needed
>>> conversions."
>>>
>>>
>>> Since I doubt that many people will use ProbABEL/DatABEL/filevector on other (big-endian) architectures there is no hurry in fixing this. Nevertheless it's worth having this bug visible and in the back of our minds.
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Comment By: Jurica Stanojkovic (juricast)
>>> Date: 2014-04-16 12:23
>>>
>>> Message:
>>> Hello,
>>>
>>> I have tried building package probabel on mips big endian.
>>> It looks like that inputfiles/*.fvd and inputfiles/*.fvi are created on little endian machine and are not working on big endian ones.
>>>
>>> I have tried to create them on big endian mips, and replace ones that came with source package with the ones that I have created.
>>> The package was built with new files without an error.
>>>
>>> I used following command to create files:
>>> library(GenABEL)
>>> library(DatABEL)
>>> fvdose <- mach2databel(imputedg="./checks/inputfiles/test.mldose", mlinfo="./checks/inputfiles/test.mlinfo", outfile="./checks/inputfiles/test.dose")
>>> fvprob <- mach2databel(imputedg="./checks/inputfiles/test.mlprob", mlinfo="./checks/inputfiles/test.mlinfo", outfile="./checks/inputfiles/test.prob", isprob=TRUE)
>>> mmdose <- mach2databel(imputedg="./checks/inputfiles/mmscore_gen.mldose", mlinfo="./checks/inputfiles/mmscore_gen.mlinfo", outfile="./checks/inputfiles/mmscore_gen.dose")
>>> mmprob <- mach2databel(imputedg="./checks/inputfiles/mmscore_gen.mlprob", mlinfo="./checks/inputfiles/mmscore_gen.mlinfo", outfile="./checks/inputfiles/mmscore_gen.prob", isprob=TRUE)
>>>
>>> I am new to ProbABEL, GenABEL, DatABEL so could someone please help me with following questions:
>>>
>>> What is the best course of action for supporting probabel on big endian?
>>> Should *.fvi, *.fvd files allways be in little endian format (than DatABEL needs to be changed to always create little endian files)?
>>> Or can *.fvd, *.fvi files be replaced with big endian files for big endian build?
>>>
>>> Is it necessary to be able to use *.fvd *.fvi files created on a different endian system?
>>>
>>> I am willing to work on adding big endian support and I will appreciate any help in determining the right course of action in resolving this problem.
>>>
>>> Regards,
>>> Jurica
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Comment By: Lennart Karssen (lckarssen)
>>> Date: 2014-01-27 21:20
>>>
>>> Message:
>>> A suggestion by Andreas Tille on the debian-med list: It's good to keep in mind that in the near future architectures like arm(64) may become much more popular in genomics.
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> You can respond by visiting:
>>> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=5299&group_id=505
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> 
> 
> 
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L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
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