Further followup: I think I located the problem in p1list affecting issue 
1. See trac #20932 for additional discussion.

On Sunday, July 3, 2016 at 9:31:20 AM UTC-7, Kiran Kedlaya wrote:
>
> Following up on issue 1:
>
> On Saturday, July 2, 2016 at 9:42:53 PM UTC-7, Rob Harron wrote:
>>
>> sage: chi = kronecker_character(3*34603)
>> sage: M = ModularSymbols(chi, 2, sign=1, base_ring=GF(3))
>> ...
>> File 
>> "/projects/sage/sage-6.10/local/lib/python2.7/site-packages/sage/modular/modsym/relation_matrix.py",
>>  
>> line 126, in modS_relations
>>     assert j != -1
>> AssertionError
>>
>>
> Inspecting the traceback suggests that the issue is here:
>
> sage: chi = kronecker_character(3*34603)
> sage: from sage.modular.modsym.manin_symbol_list import 
> ManinSymbolList_character
> sage: m = ManinSymbolList_character(chi,2); m
>
> Manin Symbol List of weight 2 for Gamma1(103809) with character [-1, -1]
>
> sage: for i in range(len(m)):
> sage:    j, s = m.apply_S(i)
> sage:    if not j != -1: print i, j, s #should print nothing
>
> 34604 -1 0
> 69207 -1 0
> 126878 -1 0
>
>
> That value of j appears to be the index of some tuple in the underlying list 
> of m; an index of -1 means "not found". This suggests that the list of Manin 
> symbols is not being generated correctly for some reason.
>
>
> That generation happens in the file src/sage/modular/modsym/p1list.pyx. Here 
> is a test that seems to isolate the issue:
>
>
> sage: import sage.modular.modsym.p1list as p1list
> sage: for (i,j) in p1list.P1List(103809):
> sage:    if i != 1 and i != 3: print (i,j)
>
> (0, 1) #should also return (34603, 1) and (34603, 2). 
>
>
> There seems to be a cutover above level 46340, which might be exposing some 
> poorly tested legacy code.
>
>
> I'm not sure whether the other issue is related, but it does appear to be in 
> the same file, so I wouldn't rule it out. 
>
>
> Kiran
>
>
>
>

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