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bug#34934: deeptools is not reproducible
From: |
T460s laptop |
Subject: |
bug#34934: deeptools is not reproducible |
Date: |
Sat, 30 Mar 2019 11:03:41 -0400 |
User-agent: |
Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) |
Hello again!
Ludovic Courtès <address@hidden> writes:
> Maxim Cournoyer <address@hidden> skribis:
>
>> $ guix build --check -K deeptools
>
> Could you try:
>
> guix build --check -K --no-grafts deeptools
>
> ?
>
> If deeptools is not reproducible, then it’ll leave a ‘-check’ output.
OK! The --no-grafts + --keep-failed combined did the trick, it now
produced the -check suffixed output.
There are differences regarding the number of links on many files; I'm
not sure this matters as it could be related to how the daemon optimizes
disk space in its store:
--8<---------------cut here---------------start------------->8---
--- /gnu/store/f3z6fczw70j6692ddy467pbagbjck009-deeptools-3.1.3
+++ /gnu/store/f3z6fczw70j6692ddy467pbagbjck009-deeptools-3.1.3-check
├── bin
│ │ ---
/gnu/store/f3z6fczw70j6692ddy467pbagbjck009-deeptools-3.1.3/bin/.alignmentSieve-real
│ ├── +++
/gnu/store/f3z6fczw70j6692ddy467pbagbjck009-deeptools-3.1.3-check/bin/.alignmentSieve-real
│ │ ├── /gnu/store/5s2nib1lrd2101bbrivcl17kjx1mspw6-coreutils-8.30/bin/stat {}
│ │ │ @@ -1,8 +1,8 @@
│ │ │
│ │ │ Size: 289 Blocks: 8 IO Block: 4096 regular file
│ │ │ -Links: 4
│ │ │ +Links: 1
│ │ │ Access: (0555/-r-xr-xr-x) Uid: ( 0/ root) Gid: ( 0/ root)
│ │ │
│ │ │ Modify: 1970-01-01 00:00:01.000000000 +0000
│ │ │
│ │ │ Birth: -
--8<---------------cut here---------------end--------------->8---
There are also difference found using readelf, for example:
--8<---------------cut here---------------start------------->8---
│ │ │ │ ├── tree.cpython-37m-x86_64-linux-gnu.so
│ │ │ │ │ ├──
/gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide
--program-header {}
│ │ │ │ │ │ @@ -3,15 +3,15 @@
│ │ │ │ │ │ Entry point 0x35d0
│ │ │ │ │ │ There are 8 program headers, starting at offset 64
│ │ │ │ │ │
│ │ │ │ │ │ Program Headers:
│ │ │ │ │ │ Type Offset VirtAddr PhysAddr
FileSiz MemSiz Flg Align
│ │ │ │ │ │ LOAD 0x000000 0x0000000000000000 0x0000000000000000
0x002a00 0x002a00 R 0x1000
│ │ │ │ │ │ LOAD 0x003000 0x0000000000003000 0x0000000000003000
0x00616d 0x00616d R E 0x1000
│ │ │ │ │ │ - LOAD 0x00a000 0x000000000000a000 0x000000000000a000
0x002140 0x002140 R 0x1000
│ │ │ │ │ │ + LOAD 0x00a000 0x000000000000a000 0x000000000000a000
0x002144 0x002144 R 0x1000
│ │ │ │ │ │ LOAD 0x00cd78 0x000000000000dd78 0x000000000000dd78
0x000908 0x000910 RW 0x1000
│ │ │ │ │ │ DYNAMIC 0x00cd90 0x000000000000dd90 0x000000000000dd90
0x000220 0x000220 RW 0x8
│ │ │ │ │ │ GNU_EH_FRAME 0x00a9a0 0x000000000000a9a0 0x000000000000a9a0
0x0002fc 0x0002fc R 0x4
│ │ │ │ │ │ GNU_STACK 0x000000 0x0000000000000000 0x0000000000000000
0x000000 0x000000 RW 0x10
│ │ │ │ │ │ GNU_RELRO 0x00cd78 0x000000000000dd78 0x000000000000dd78
0x000288 0x000288 R 0x1
│ │ │ │ │ │
│ │ │ │ │ │ Section to Segment mapping:
--8<---------------cut here---------------end--------------->8---
These seems to have to do with Cython files which might not have been
regenerated (packaged using pre-compiled binaries). I have a fix for
this which has been used ad-hoc in the 'bedtools' package. I'll try to move it
into
the Python build system and see what it gives.
The full output is attached.
Maxim
output.gz
Description: diffoscope /gnu/store/f3z6fczw70j6692ddy467pbagbjck009-deeptools-3.1.3{,-check}