[BioC] IRanges is broken in Cygwin (mingw/math.h)

[Enrico Ferrero]

Hi Michael,

Thanks a lot for your help.
I'm not the author of the patch, Marco (CC'ed) is.

I'm sorry if the patched package violates the license, it was actually
just meant to be a quick way to test if the patch worked. I'm sure
Marco will remove it asap.

I'm not very familiar with Bioconductor development process, what does
the patch being in devel mean? The update will be pushed soon to
Bionductor 2.12 or it will only be part of Bioconductor's next release
(2.13)?

Thanks for the clarification!
Best,



On 12 July 2013 13:16, Michael Lawrence <lawrence.michael at gene.com> wrote:
> Hi Enrico,
>
> Thanks a lot for this patch. I went ahead and committed it to devel. Also
> fixed the same problem in rtracklayer, in case you're aiming for that next
> ;)
>
> Btw, I'm wondering if it's a good thing to distribute pre-patched versions
> of IRanges. I'm not an expert, but it's probably a violation of the Artistic
> 2.0 license. More practically, it doesn't seem like a good thing to have
> multiple IRanges floating around. So in the future you might save yourself
> the effort and just send a patch.
>
> Thanks again,
> Michael
>
>
>
> On Fri, Jul 12, 2013 at 4:24 AM, Enrico Ferrero <enricoferrero86 at gmail.com>
> wrote:
>>
>> Hi,
>>
>> Installation of Bioconductor fails on Cygwin because of a compilation
>> error in the IRanges package:
>>
>> > In file included from IntervalTree.c:3:0:
>> > common.h:59:24: fatal error: mingw/math.h: No such file or directory
>> > compilation terminated.
>> > /usr/lib/R/etc/Makeconf:121: recipe for target `IntervalTree.o' failed
>> > make: *** [IntervalTree.o] Error 1
>> > ERROR: compilation failed for package =91IRanges=92
>>
>> I got some help to fix this from Marco Atzeri in the Cygwin mailing
>> list and the problem seems to be a perhaps unnecessary '#include
>> <mingw/math.h>' directive.
>>
>> This patch by Marco fixes the problem, allowing compilation of IRanges
>> on Cygwin:
>>
>> -------------------------------------------------------
>> --- orig/IRanges/src/common.h   2013-02-22 04:36:50.000000000 +0100
>> +++ IRanges/src/common.h        2013-07-12 00:19:05.922405200 +0200
>> @@ -55,10 +55,6 @@
>>  #endif
>>  #endif
>>
>> -#ifdef __CYGWIN32__
>> -#include <mingw/math.h>
>> -#endif
>> -
>>  #ifndef NAN
>>  #define NAN (0.0 / 0.0)
>>  #endif
>> ---------------------------------------------------------
>>
>> The patch (and a handy patched package) can also be found at:
>> http://matzeri.altervista.org/works/R/
>>
>> Can this be fixed upstream?
>> Thank you.
>>
>> Best,
>>
>> --
>> Enrico Ferrero
>>
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>
>



-- 
Enrico Ferrero
PhD Student
Steve Russell Lab - Department of Genetics
FlyChip - Cambridge Systems Biology Centre
University of Cambridge

e.ferrero at gen.cam.ac.uk
http://flypress.gen.cam.ac.uk/