Hi Andrew,
thank you for looking into this! Could you perhaps please send off a
quick reply to this email when the new version has been released?
Best regards
Sascha
On 07/08/2015 16:55, Andrew Whitwham wrote:
> Hi Sascha,
>
> I see what has happened. A new version of iolib was released without
> releasing a compatible version of the Staden Package. The code is
> ready, it just needs releasing.
>
> I'll see what I can do.
>
> Thanks,
>
> Andrew
>
> On 07/08/15 16:35, Sascha Steinbiss wrote:
>> Hi Andrew,
>>
>> many thanks for your quick reply and for your willingness to look into
>> the issue.
>>
>> Best regards,
>> Sascha
>>
>> On 07/08/2015 16:23, Andrew Whitwham wrote:
>>> Hi Sascha,
>>>
>>> Thanks for letting us know. I will take a look but it may be a few days
>>> before I can do anything about it.
>>>
>>> Regards,
>>>
>>> Andrew
>>>
>>>
>>> On 07/08/15 15:26, Sascha Steinbiss wrote:
>>>> Dear James and Andrew,
>>>>
>>>> I am writing to kindly bring the following Staden build issue to your
>>>> attention. The Debian automated build system is currently unable to
>>>> build the code from source due to multiple declarations of identically
>>>> named functions with different parameter and return types.
>>>> We were wondering if you could help out there -- many thanks in
>>>> advance!
>>>>
>>>> Best wishes
>>>> Sascha
>>>>
>>>> -- Forwarded email below --
>>>>
>>>> Date: Sat, 1 Aug 2015 07:28:32 +0200
>>>> From: Andreas Tille <andr...@fam-tille.de>
>>>> To: "Chris West (Faux)" <solo-debianb...@goeswhere.com>,
>>>> 793...@bugs.debian.org, James Bonfield <j...@sanger.ac.uk>
>>>> Cc: Tim Booth <tbo...@ceh.ac.uk>
>>>> Subject: Re: Bug#793514: FTBFS: conflicting types for append_int
>>>>
>>>> Hi Staden developers,
>>>>
>>>> as you can see in this Debian bug report the current staden release is
>>>> in conflict with the latest releases of staden-io-lib. Both dafine the
>>>> same function but with different code (not only the header is
>>>> different).
>>>>
>>>> Any help is welcome
>>>>
>>>> Andreas.
>>>>
>>>> On Fri, Jul 24, 2015 at 07:14:29PM +0000, Chris West (Faux) wrote:
>>>>> Source: staden
>>>>> Version: 2.0.0+b10-1.1
>>>>> Severity: serious
>>>>> Tags: sid
>>>>> Justification: fails to build from source
>>>>> User: reproducible-bui...@lists.alioth.debian.org
>>>>> Usertags: ftbfs
>>>>>
>>>>> Dear Maintainer,
>>>>>
>>>>> The package fails to build:
>>>>>
>>>>> sam_index.c:321:14: error: conflicting types for ‘append_int’
>>>>> static char *append_int(char *cp, int i) {
>>>>> ^
>>>>> In file included from /usr/include/io_lib/scram.h:52:0,
>>>>> from sam_pileup.h:4,
>>>>> from sam_index.c:17:
>>>>> /usr/include/io_lib/bam.h:755:16: note: previous declaration of
>>>>> ‘append_int’ was here
>>>>> unsigned char *append_int(unsigned char *cp, int32_t i);
>>>>> ^
>>>>> /staden-2.0.0+b10/./gap5/../global.mk:388: recipe for target
>>>>> 'sam_index.o' failed
>>>>> make[2]: *** [sam_index.o] Error 1
>>>>> make[2]: Leaving directory '/staden-2.0.0+b10/gap5'
>>>>>
>>>>>
>>>>> Full build log:
>>>>> https://reproducible.debian.net/rb-pkg/unstable/amd64/staden.html
>>>>>
>>>>> -- System Information:
>>>>> Debian Release: stretch/sid
>>>>> APT prefers unstable
>>>>> APT policy: (500, 'unstable')
>>>>> Architecture: amd64 (x86_64)
>>>>>
>>>>> Kernel: Linux 3.19.0-23-generic (SMP w/8 CPU cores)
>>>>> Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
>>>>> Shell: /bin/sh linked to /bin/dash
>>>>> Init: systemd (via /run/systemd/system)
>>>>>
>>>>> _______________________________________________
>>>>> Debian-med-packaging mailing list
>>>>> debian-med-packag...@lists.alioth.debian.org
>>>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
>>>>>
>>>>>
>>>>
>>>
>>
>
--
Dr Sascha Steinbiss
Senior Bioinformatician
Parasite Genomics
Wellcome Trust Sanger Institute
Genome Campus, Hinxton,
Cambridge, CB10 1SA, UK
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
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