Package: guix;
Reported by: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Date: Thu, 21 Mar 2019 03:12:02 UTC
Severity: normal
Done: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Bug is archived. No further changes may be made.
View this message in rfc822 format
From: T460s laptop <maxim.cournoyer <at> gmail.com> To: Ludovic Courtès <ludo <at> gnu.org> Cc: 34935 <at> debbugs.gnu.org, Maxim Cournoyer <maxim.cournoyer <at> gmail.com> Subject: bug#34935: nanopolish is not reproducible Date: Sat, 30 Mar 2019 15:13:01 -0400
Ludovic Courtès <ludo <at> gnu.org> writes:
> Maxim Cournoyer <maxim.cournoyer <at> gmail.com> skribis:
>
>> $ guix build --check --no-grafts nanopolish
>> [...]
>> guix build: error: derivation
>> `/gnu/store/7hzcmcwlw83f0wsqmz9nnl1ah54kwks4-nanopolish-0.10.2-1.50e8b5c.drv'
>> may not be deterministic: output
>> `/gnu/store/m7icaq7642zy0gvnqvymcnn8d088a9s0-nanopolish-0.10.2-1.50e8b5c'
>> differs
>>
>> $ diffoscope "$(guix build nanopolish)" /gnu/store/m7icaq7642zy0gvnqvymcnn8d088a9s0-nanopolish-0.10.2-1.50e8b5c
>>
>> │ │ │ - 0x000000000000001d (RUNPATH) Library runpath:
>> [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbnmm5rbkgk3qdi32ka-hdf5-1.8.21/lib:/gnu/store/x4xpcpsqmini25gkrc0h945ml9r609v5-htslib-1.9/lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
>> │ │ │ + 0x000000000000001d (RUNPATH) Library runpath:
>> [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/nq4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbnmm5rbkgk3qdi32ka-hdf5-1.8.21/lib:/gnu/store/d25i834bs8wvg8mh36bplxg61r6b7vz9-htslib-1.9/lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
>>
>> The problem seems to lie in htslib.
>
> Aren’t you comparing two different builds, like one grafted the other
> ungrafted?
>
> What I do is:
>
> guix build foo --check -K
>
> and then:
>
> diffoscope /gnu/store/…-the-thing{,-check}
>
> That way you’re 100% sure you’re comparing two different builds of the
> very same derivation.
Thanks for pointing this to me. As mentioned in another threda, to
really have a -check output, I had to use both --keep-failed and
--no-grafts (combined with --check).
The produced diffoscope is very large (3 MiB when xzipped), so I won't
post it here, but the non-reproducibility should be visible on any Guix
system, I believe.
It seems the binaries produced have symbols appearing at different
offset. Here's an excerpt:
>--- /gnu/store/95vcyvlcrlw82g9zpyh421mz3mnag0qx-nanopolish-0.10.2-1.50e8b5c
+++ /gnu/store/95vcyvlcrlw82g9zpyh421mz3mnag0qx-nanopolish-0.10.2-1.50e8b5c-check
├── bin
│ ├── nanopolish
│ │ ├── /gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --file-header {}
│ │ │ @@ -6,15 +6,15 @@
│ │ │ OS/ABI: UNIX - GNU
│ │ │ ABI Version: 0
│ │ │ Type: EXEC (Executable file)
│ │ │ Machine: Advanced Micro Devices X86-64
│ │ │ Version: 0x1
│ │ │ Entry point address: 0x40b580
│ │ │ Start of program headers: 64 (bytes into file)
│ │ │ - Start of section headers: 4204728 (bytes into file)
│ │ │ + Start of section headers: 4204696 (bytes into file)
│ │ │ Flags: 0x0
│ │ │ Size of this header: 64 (bytes)
│ │ │ Size of program headers: 56 (bytes)
│ │ │ Number of program headers: 12
│ │ │ Size of section headers: 64 (bytes)
│ │ │ Number of section headers: 34
│ │ │ Section header string table index: 33
[...]
│ │ ├── /gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --sections {}
│ │ │ @@ -1,8 +1,8 @@
│ │ │ -There are 34 section headers, starting at offset 0x4028b8:
│ │ │ +There are 34 section headers, starting at offset 0x402898:
│ │ │
│ │ │ Section Headers:
│ │ │ [Nr] Name Type Address Off Size ES Flg Lk Inf Al
│ │ │ [ 0] NULL 0000000000000000 000000 000000 00 0 0 0
│ │ │ [ 1] .interp PROGBITS 00000000004002e0 0002e0 000050 00 A 0 0 1
│ │ │ [ 2] .note.ABI-tag NOTE 0000000000400330 000330 000020 00 A 0 0 4
│ │ │ [ 3] .hash HASH 0000000000400350 000350 00091c 04 A 5 0 8
│ │ │ @@ -14,30 +14,30 @@
│ │ │ [ 9] .rela.dyn RELA 00000000004053e0 0053e0 001248 18 A 5 0 8
│ │ │ [10] .rela.plt RELA 0000000000406628 006628 001380 18 AI 5 27 8
│ │ │ [11] .init PROGBITS 0000000000408000 008000 000017 00 AX 0 0 4
│ │ │ [12] .plt PROGBITS 0000000000408020 008020 000d10 10 AX 0 0 16
│ │ │ [13] .plt.got PROGBITS 0000000000408d30 008d30 000128 08 AX 0 0 8
│ │ │ [14] .text PROGBITS 0000000000408e60 008e60 0f7222 00 AX 0 0 16
│ │ │ [15] .fini PROGBITS 0000000000500084 100084 000009 00 AX 0 0 4
│ │ │ - [16] .rodata PROGBITS 0000000000501000 101000 2a92d0 00 A 0 0 32
│ │ │ - [17] .eh_frame_hdr PROGBITS 00000000007aa2d0 3aa2d0 002094 00 A 0 0 4
│ │ │ - [18] .eh_frame PROGBITS 00000000007ac368 3ac368 00eb70 00 A 0 0 8
│ │ │ - [19] .gcc_except_table PROGBITS 00000000007baed8 3baed8 00a8d0 00 A 0 0 4
│ │ │ + [16] .rodata PROGBITS 0000000000501000 101000 2a9330 00 A 0 0 32
│ │ │ + [17] .eh_frame_hdr PROGBITS 00000000007aa330 3aa330 002094 00 A 0 0 4
│ │ │ + [18] .eh_frame PROGBITS 00000000007ac3c8 3ac3c8 00eb78 00 A 0 0 8
│ │ │ + [19] .gcc_except_table PROGBITS 00000000007baf40 3baf40 00a8c0 00 A 0 0 4
│ │ │ [20] .tbss NOBITS 00000000007c6c40 3c5c40 00002c 00 WAT 0 0 8
│ │ │ [21] .init_array INIT_ARRAY 00000000007c6c40 3c5c40 000110 08 WA 0 0 8
│ │ │ [22] .fini_array FINI_ARRAY 00000000007c6d50 3c5d50 000008 08 WA 0 0 8
HTH!
Maxim
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