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

[L.C. Karssen]

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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L.C. Karssen
Utrecht
The Netherlands

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