Re: libgclib - symbol file - please kindly educate me
Thank you, Alex. libgclib and reverse dependency gffread are updated.
On 09.08.20 21:50, Alex Mestiashvili wrote:
> Hi Steffen,
>
> I've pushed the new version of symbols file to the repository.
> As far as I see in the new version of libgclib the 3 symbols ( the
> ones in the diff you provided) are removed. This is quite bad and
> probably it makes sense to discuss that with upstream, since software
> using these symbols will be broken.
> Luckily none of the reverse deps of libgclib in Debian are using the
> removed symbols.
>
> Best regards,
> Ale
>
> On 8/9/20 4:33 PM, Steffen Möller wrote:
>> Hi Alex, hi Andreas,
>>
>> This is what I get when I remove the -1
>>
>> make[1]: Leaving directory '.../med-team/libgclib'
>> dh_perl
>> dh_link
>> dh_strip_nondeterminism
>> dh_compress
>> dh_fixperms
>> dh_missing
>> dh_dwz -a
>> dh_strip -a
>> dh_makeshlibs -a
>> dpkg-gensymbols: error: some symbols or patterns disappeared in the
>> symbols file: see diff output below
>> dpkg-gensymbols: warning: debian/libgclib2/DEBIAN/symbols doesn't match
>> completely debian/libgclib2.symbols
>> --- debian/libgclib2.symbols (libgclib2_0.11.10-1_amd64)
>> +++ dpkg-gensymbolsGWl6pJ 2020-08-09 14:16:35.796448318 +0200
>> @@ -25,7 +25,7 @@
>> _Z10g2bit2baseh@Base 0.11.4
>> _Z10gcdb_allocj@Base 0.11.4
>> _Z10getFileExtPKc@Base 0.11.4
>> - _Z10getOvlCodeR6GffObjS0_Rib@Base 0.11.10
>> +#MISSING: 0.11.10-1# _Z10getOvlCodeR6GffObjS0_Rib@Base 0.11.10
>> _Z10getOvlCodeR6GffObjS0_Ribi@Base 0.11.10
>> _Z10parseFloatRPcRf@Base 0.11.4
>> _Z10replaceStrRPcS_@Base 0.11.4
>> @@ -79,13 +79,13 @@
>> _Z14gfo_cmpRefByIDPvS_@Base 0.11.4
>> _Z14translateCodonPKc@Base 0.11.4
>> _Z15printEditScriptP12GXEditScript@Base 0.11.4
>> - _Z15transcriptMatchR6GffObjS0_Ri@Base 0.11.10
>> +#MISSING: 0.11.10-1# _Z15transcriptMatchR6GffObjS0_Ri@Base 0.11.10
>> _Z15transcriptMatchR6GffObjS0_Rii@Base 0.11.10
>> _Z15uint32_pack_bigPcj@Base 0.11.4
>> _Z16BED_addAttributeP8_IO_FILERiPKcz@Base 0.11.4
>> _Z16DefLTCompareProcI4GSegEiPvS1_@Base 0.11.4
>> _Z16gthreads_errExitiPKc@Base 0.11.4
>> - _Z16singleExonTMatchR6GffObjS0_Ri@Base 0.11.10
>> +#MISSING: 0.11.10-1# _Z16singleExonTMatchR6GffObjS0_Ri@Base 0.11.10
>> _Z16singleExonTMatchR6GffObjS0_Rii@Base 0.11.10
>> _Z17GreedyAlignRegionPKciiS0_iiP16CGreedyAlignDataP8CAlnTrimb@Base
>> 0.11.4
>> _Z17GreedyAlignRegionPKciiS0_iiiiiP16CGreedyAlignDataP8CAlnTrimb@Base
>> 0.11.4
>> dh_makeshlibs: error: failing due to earlier errors
>> make: *** [debian/rules:13: binary] Error 1
>> dpkg-buildpackage: error: debian/rules binary subprocess returned exit
>> status 2
>>
>> ?
>>
>> Steffen
>>
>> On 09.08.20 07:00, Andreas Tille wrote:
>>> Hi Steffen,
>>>
>>> the patch you get from dh_makeshlibs needs to be edited. You simply
>>>
>>> sed -i 's/-1$//' debian/libgclib2.symbols
>>>
>>> should do the trick.
>>>
>>> Hope this helps
>>>
>>> Andreas.
>>>
>>> On Sat, Aug 08, 2020 at 11:39:24PM +0200, Steffen Möller wrote:
>>>> Hello,
>>>>
>>>> to get the build process to first not fail and then be quiet, I
>>>> changed
>>>> the .symbols file as follows:
>>>>
>>>> diff --git a/debian/libgclib2.symbols b/debian/libgclib2.symbols
>>>> index 6bef43a..aef012c 100644
>>>> --- a/debian/libgclib2.symbols
>>>> +++ b/debian/libgclib2.symbols
>>>> @@ -25,7 +25,8 @@libgclib.so.2 libgclib2 #MINVER#
>>>> _Z10g2bit2baseh@Base 0.11.4
>>>> _Z10gcdb_allocj@Base 0.11.4
>>>> _Z10getFileExtPKc@Base 0.11.4
>>>> - _Z10getOvlCodeR6GffObjS0_Rib@Base 0.11.4
>>>> + _Z10getOvlCodeR6GffObjS0_Rib@Base 0.11.10-1
>>>> + _Z10getOvlCodeR6GffObjS0_Ribi@Base 0.11.10-1
>>>> _Z10parseFloatRPcRf@Base 0.11.4
>>>> _Z10replaceStrRPcS_@Base 0.11.4
>>>> _Z10startsWithPKcS0_@Base 0.11.4
>>>> @@ -78,12 +79,15 @@libgclib.so.2 libgclib2 #MINVER#
>>>> _Z14gfo_cmpRefByIDPvS_@Base 0.11.4
>>>> _Z14translateCodonPKc@Base 0.11.4
>>>> _Z15printEditScriptP12GXEditScript@Base 0.11.4
>>>> - _Z15transcriptMatchR6GffObjS0_Ri@Base 0.11.4
>>>> + _Z15transcriptMatchR6GffObjS0_Ri@Base 0.11.10-1
>>>> + _Z15transcriptMatchR6GffObjS0_Rii@Base 0.11.10-1
>>>> _Z15uint32_pack_bigPcj@Base 0.11.4
>>>> _Z16BED_addAttributeP8_IO_FILERiPKcz@Base 0.11.4
>>>> _Z16DefLTCompareProcI4GSegEiPvS1_@Base 0.11.4
>>>> _Z16gthreads_errExitiPKc@Base 0.11.4
>>>> - _Z16singleExonTMatchR6GffObjS0_Ri@Base 0.11.4
>>>> + _Z16singleExonTMatchR6GffObjS0_Ri@Base 0.11.10-1
>>>> + _Z16singleExonTMatchR6GffObjS0_Rii@Base 0.11.10-1
>>>> + _Z15transcriptMatchR6GffObjS0_Rii@Base 0.11.10-1
>>>> _Z17GreedyAlignRegionPKciiS0_iiP16CGreedyAlignDataP8CAlnTrimb@Base
>>>> 0.11.4
>>>> _Z17GreedyAlignRegionPKciiS0_iiiiiP16CGreedyAlignDataP8CAlnTrimb@Base
>>>>
>>>> 0.11.4
>>>> _Z17gcvt_endian_setupv@Base 0.11.4
>>>>
>>>> I have no idea why there is now a -1 attached to the version. I just
>>>> know that it does not work without it.
>>>>
>>>> Can I upload as is?
>>>>
>>>> Best,
>>>>
>>>> Steffen
>>>>
>>>>
>>
>
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