[Debian-med-packaging] Bug#955403: bedtools ftbfs, failing tests on armel, armhf, i386, mipsel

[Michael Crusoe]

Thank Berhard for this patch.

Also the autopkgtests do not yet patch with i386 (at least):

Testing bedtools shuffle:
    shuffle.t1...1,10c1,10
< chr2 34697611 34698079 trf 789
< chr4 97373990 97374163 trf 346
< chr1 211569500 211569740 trf 434
< chr15 100895645 100895867 trf 273
< chr10 79193410 79193587 trf 187
< chr2 180138393 180138558 trf 199
< chr11 1280504 1280642 trf 242
< chr2 194322764 194322799 trf 70
< chr18 24454309 24454406 trf 79
< chr18 58907072 58907113 trf 73
---
> chr1 49390118 49390586 trf 789
> chr13 60419956 60420129 trf 346
> chr9 88507701 88507941 trf 434
> chr1 176220424 176220646 trf 273
> chr7 69225121 69225298 trf 187
> chr2 25938602 25938767 trf 199
> chr7 133111177 133111315 trf 242
> chr3 5894626 5894661 trf 70
> chr7 144738233 144738330 trf 79
> chr9 28526037 28526078 trf 73
fail
    shuffle.t2...1c1
< chr1 2158771 2159239 trf 789
---
> chr1 3126067 3126535 trf 789
3,4c3,4
< chr3 -219961 -219721 trf 434
< chr2 -515372 -515150 trf 273
---
> chr3 747335 747575 trf 434
> chr2 451924 452146 trf 273
10c10
< chr3 -422590 -422549 trf 73
---
> chr3 544706 544747 trf 73
12,13c12,13
< chr5 -6185 -6080 trf 149
< chr4 -914083 -914045 trf 58
---
> chr5 961111 961216 trf 149
> chr4 53213 53251 trf 58
15,17c15,17
< chr1 548923 549393 trf 339
< chr1 95584 96012 trf 202
< chr1 1063033 1063076 trf 59
---
> chr1 1516219 1516689 trf 339
> chr1 1062880 1063308 trf 202
> chr1 2030329 2030372 trf 59
20c20
< chr1 1922714 1922891 trf 302
---
> chr1 2890010 2890187 trf 302
fail
    shuffle.t3...1c1
< chr1 2158771 2159239 trf 789
---
> chr1 3126067 3126535 trf 789
3,4c3,4
< chr3 -219961 -219721 trf 434
< chr2 -515372 -515150 trf 273
---
> chr3 747335 747575 trf 434
> chr2 451924 452146 trf 273
10c10
< chr3 -422590 -422549 trf 73
---
> chr3 544706 544747 trf 73
12,13c12,13
< chr5 -6185 -6080 trf 149
< chr4 -914083 -914045 trf 58
---
> chr5 961111 961216 trf 149
> chr4 53213 53251 trf 58
15,17c15,17
< chr1 548923 549393 trf 339
< chr1 95584 96012 trf 202
< chr1 1063033 1063076 trf 59
---
> chr1 1516219 1516689 trf 339
> chr1 1062880 1063308 trf 202
> chr1 2030329 2030372 trf 59
20c20
< chr1 1922714 1922891 trf 302
---
> chr1 2890010 2890187 trf 302
fail
    shuffle.t4...ok
    shuffle.t5...1,10c1,10
< chr2 34697611 34698079 trf 789
< chr4 97373990 97374163 trf 346
< chr1 211569500 211569740 trf 434
< chr1 211569500 211569740 trf 434
< chr5 12248678 12248716 trf 58
< chr1 10051107 10051141 trf 68
< chr3 63788079 63788115 trf 63
< chr1 56972561 56972612 trf 66
< chr1 56972561 56972612 trf 66
< chr5 27921185 27921353 trf 150
---
> chr1 49390118 49390586 trf 789
> chr1 49390118 49390586 trf 789
> chr1 176220424 176220646 trf 273
> chr1 176220424 176220646 trf 273
> chr2 25938602 25938767 trf 199
> chr3 5894626 5894661 trf 70
> chr2 57803306 57803344 trf 58
> chr4 13407024 13407058 trf 68
> chr3 18198257 18198308 trf 66
> chr1 71587801 71587968 trf 159
fail

On Wed, Oct 28, 2020 at 7:14 AM Bernhard Übelacker <bernhardu at mailbox.org>
wrote:

> Dear Maintainer,
> I just tried to have a look at these failing tests "sample" and "slop",
> and found both are caused by having variables of type long.
> These have a sizeof of 4 on these 32 bit systems, while the usage
> suggests they are expected to be 8 bytes.
>
> Attached patch replaces the use of long by CHRPOS in the places where
> they cause the tests to fail. With it applied they succeed when
> building at i386 and armhf with current testing.
>
> Kind regards,
> Bernhard
>


-- 
Michael R. Crusoe
Co-founder & Lead,
Common Workflow Language project <http://www.commonwl.org/>
https://orcid.org/0000-0002-2961-9670
mrc at commonwl.org
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