GNU bug report logs - #34935
nanopolish is not reproducible

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Package: guix; Reported by: Maxim Cournoyer <maxim.cournoyer@HIDDEN>; dated Thu, 21 Mar 2019 03:12:02 UTC; Maintainer for guix is bug-guix@HIDDEN.

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To: Ludovic =?utf-8?Q?Court=C3=A8s?= <ludo@HIDDEN>
Subject: Re: bug#34935: nanopolish is not reproducible
References: <87imwc6hw2.fsf@HIDDEN> <874l7twmm2.fsf@HIDDEN>
Date: Sat, 30 Mar 2019 15:13:01 -0400
In-Reply-To: <874l7twmm2.fsf@HIDDEN> ("Ludovic
 \=\?utf-8\?Q\?Court\=C3\=A8s\=22'\?\=
 \=\?utf-8\?Q\?s\?\= message of "Sat, 23 Mar 2019 18:01:57 +0100")
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Ludovic Court=C3=A8s <ludo@HIDDEN> writes:

> Maxim Cournoyer <maxim.cournoyer@HIDDEN> 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/m7icaq7642zy0gvnqvymc=
nn8d088a9s0-nanopolish-0.10.2-1.50e8b5c
>>
>> =E2=94=82 =E2=94=82 =E2=94=82 - 0x000000000000001d (RUNPATH) Library run=
path:
>> [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib:/gnu/store/4=
sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/nq4lsyipmfb0q7=
g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbnmm5rbkgk3qdi3=
2ka-hdf5-1.8.21/lib:/gnu/store/x4xpcpsqmini25gkrc0h945ml9r609v5-htslib-1.9/=
lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_6=
4-unknown-linux-gnu/5.5.0/../../..]
>> =E2=94=82 =E2=94=82 =E2=94=82 + 0x000000000000001d (RUNPATH) Library run=
path:
>> [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib:/gnu/store/4=
sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/nq4lsyipmfb0q7=
g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbnmm5rbkgk3qdi3=
2ka-hdf5-1.8.21/lib:/gnu/store/d25i834bs8wvg8mh36bplxg61r6b7vz9-htslib-1.9/=
lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_6=
4-unknown-linux-gnu/5.5.0/../../..]
>>
>> The problem seems to lie in htslib.
>
> Aren=E2=80=99t you comparing two different builds, like one grafted the o=
ther
> ungrafted?
>
> What I do is:
>
>   guix build foo --check -K
>
> and then:
>
>   diffoscope /gnu/store/=E2=80=A6-the-thing{,-check}
>
> That way you=E2=80=99re 100% sure you=E2=80=99re 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
=E2=94=9C=E2=94=80=E2=94=80 bin
=E2=94=82 =E2=94=9C=E2=94=80=E2=94=80 nanopolish
=E2=94=82 =E2=94=82 =E2=94=9C=E2=94=80=E2=94=80 /gnu/store/02iklp4swqs0ipxh=
g5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --file-header {}
=E2=94=82 =E2=94=82 =E2=94=82 @@ -6,15 +6,15 @@
=E2=94=82 =E2=94=82 =E2=94=82    OS/ABI:                            UNIX - =
GNU
=E2=94=82 =E2=94=82 =E2=94=82    ABI Version:                       0
=E2=94=82 =E2=94=82 =E2=94=82    Type:                              EXEC (E=
xecutable file)
=E2=94=82 =E2=94=82 =E2=94=82    Machine:                           Advance=
d Micro Devices X86-64
=E2=94=82 =E2=94=82 =E2=94=82    Version:                           0x1
=E2=94=82 =E2=94=82 =E2=94=82    Entry point address:               0x40b580
=E2=94=82 =E2=94=82 =E2=94=82    Start of program headers:          64 (byt=
es into file)
=E2=94=82 =E2=94=82 =E2=94=82 -  Start of section headers:          4204728=
 (bytes into file)
=E2=94=82 =E2=94=82 =E2=94=82 +  Start of section headers:          4204696=
 (bytes into file)
=E2=94=82 =E2=94=82 =E2=94=82    Flags:                             0x0
=E2=94=82 =E2=94=82 =E2=94=82    Size of this header:               64 (byt=
es)
=E2=94=82 =E2=94=82 =E2=94=82    Size of program headers:           56 (byt=
es)
=E2=94=82 =E2=94=82 =E2=94=82    Number of program headers:         12
=E2=94=82 =E2=94=82 =E2=94=82    Size of section headers:           64 (byt=
es)
=E2=94=82 =E2=94=82 =E2=94=82    Number of section headers:         34
=E2=94=82 =E2=94=82 =E2=94=82    Section header string table index: 33

[...]

=E2=94=82 =E2=94=82 =E2=94=9C=E2=94=80=E2=94=80 /gnu/store/02iklp4swqs0ipxh=
g5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --sections {}
=E2=94=82 =E2=94=82 =E2=94=82 @@ -1,8 +1,8 @@
=E2=94=82 =E2=94=82 =E2=94=82 -There are 34 section headers, starting at of=
fset 0x4028b8:
=E2=94=82 =E2=94=82 =E2=94=82 +There are 34 section headers, starting at of=
fset 0x402898:
=E2=94=82 =E2=94=82 =E2=94=82=20=20
=E2=94=82 =E2=94=82 =E2=94=82  Section Headers:
=E2=94=82 =E2=94=82 =E2=94=82    [Nr] Name              Type            Add=
ress          Off    Size   ES Flg Lk Inf Al
=E2=94=82 =E2=94=82 =E2=94=82    [ 0]                   NULL            000=
0000000000000 000000 000000 00      0   0  0
=E2=94=82 =E2=94=82 =E2=94=82    [ 1] .interp           PROGBITS        000=
00000004002e0 0002e0 000050 00   A  0   0  1
=E2=94=82 =E2=94=82 =E2=94=82    [ 2] .note.ABI-tag     NOTE            000=
0000000400330 000330 000020 00   A  0   0  4
=E2=94=82 =E2=94=82 =E2=94=82    [ 3] .hash             HASH            000=
0000000400350 000350 00091c 04   A  5   0  8
=E2=94=82 =E2=94=82 =E2=94=82 @@ -14,30 +14,30 @@
=E2=94=82 =E2=94=82 =E2=94=82    [ 9] .rela.dyn         RELA            000=
00000004053e0 0053e0 001248 18   A  5   0  8
=E2=94=82 =E2=94=82 =E2=94=82    [10] .rela.plt         RELA            000=
0000000406628 006628 001380 18  AI  5  27  8
=E2=94=82 =E2=94=82 =E2=94=82    [11] .init             PROGBITS        000=
0000000408000 008000 000017 00  AX  0   0  4
=E2=94=82 =E2=94=82 =E2=94=82    [12] .plt              PROGBITS        000=
0000000408020 008020 000d10 10  AX  0   0 16
=E2=94=82 =E2=94=82 =E2=94=82    [13] .plt.got          PROGBITS        000=
0000000408d30 008d30 000128 08  AX  0   0  8
=E2=94=82 =E2=94=82 =E2=94=82    [14] .text             PROGBITS        000=
0000000408e60 008e60 0f7222 00  AX  0   0 16
=E2=94=82 =E2=94=82 =E2=94=82    [15] .fini             PROGBITS        000=
0000000500084 100084 000009 00  AX  0   0  4
=E2=94=82 =E2=94=82 =E2=94=82 -  [16] .rodata           PROGBITS        000=
0000000501000 101000 2a92d0 00   A  0   0 32
=E2=94=82 =E2=94=82 =E2=94=82 -  [17] .eh_frame_hdr     PROGBITS        000=
00000007aa2d0 3aa2d0 002094 00   A  0   0  4
=E2=94=82 =E2=94=82 =E2=94=82 -  [18] .eh_frame         PROGBITS        000=
00000007ac368 3ac368 00eb70 00   A  0   0  8
=E2=94=82 =E2=94=82 =E2=94=82 -  [19] .gcc_except_table PROGBITS        000=
00000007baed8 3baed8 00a8d0 00   A  0   0  4
=E2=94=82 =E2=94=82 =E2=94=82 +  [16] .rodata           PROGBITS        000=
0000000501000 101000 2a9330 00   A  0   0 32
=E2=94=82 =E2=94=82 =E2=94=82 +  [17] .eh_frame_hdr     PROGBITS        000=
00000007aa330 3aa330 002094 00   A  0   0  4
=E2=94=82 =E2=94=82 =E2=94=82 +  [18] .eh_frame         PROGBITS        000=
00000007ac3c8 3ac3c8 00eb78 00   A  0   0  8
=E2=94=82 =E2=94=82 =E2=94=82 +  [19] .gcc_except_table PROGBITS        000=
00000007baf40 3baf40 00a8c0 00   A  0   0  4
=E2=94=82 =E2=94=82 =E2=94=82    [20] .tbss             NOBITS          000=
00000007c6c40 3c5c40 00002c 00 WAT  0   0  8
=E2=94=82 =E2=94=82 =E2=94=82    [21] .init_array       INIT_ARRAY      000=
00000007c6c40 3c5c40 000110 08  WA  0   0  8
=E2=94=82 =E2=94=82 =E2=94=82    [22] .fini_array       FINI_ARRAY      000=
00000007c6d50 3c5d50 000008 08  WA  0   0  8

HTH!

Maxim




Information forwarded to bug-guix@HIDDEN:
bug#34935; Package guix. Full text available.

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From: =?utf-8?Q?Ludovic_Court=C3=A8s?= <ludo@HIDDEN>
To: Maxim Cournoyer <maxim.cournoyer@HIDDEN>
Subject: Re: bug#34935: nanopolish is not reproducible
References: <87imwc6hw2.fsf@HIDDEN>
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In-Reply-To: <87imwc6hw2.fsf@HIDDEN> (Maxim Cournoyer's message of "Wed, 20
 Mar 2019 23:11:41 -0400")
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Maxim Cournoyer <maxim.cournoyer@HIDDEN> skribis:

> $ guix build --check --no-grafts nanopolish
> [...]
> guix build: error: derivation `/gnu/store/7hzcmcwlw83f0wsqmz9nnl1ah54kwks=
4-nanopolish-0.10.2-1.50e8b5c.drv' may not be deterministic: output `/gnu/s=
tore/m7icaq7642zy0gvnqvymcnn8d088a9s0-nanopolish-0.10.2-1.50e8b5c' differs
>
> $ diffoscope "$(guix build nanopolish)" /gnu/store/m7icaq7642zy0gvnqvymcn=
n8d088a9s0-nanopolish-0.10.2-1.50e8b5c
>
> =E2=94=82 =E2=94=82 =E2=94=82 - 0x000000000000001d (RUNPATH)            L=
ibrary runpath: [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib=
:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/n=
q4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbn=
mm5rbkgk3qdi32ka-hdf5-1.8.21/lib:/gnu/store/x4xpcpsqmini25gkrc0h945ml9r609v=
5-htslib-1.9/lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/=
lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
> =E2=94=82 =E2=94=82 =E2=94=82 + 0x000000000000001d (RUNPATH)            L=
ibrary runpath: [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib=
:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/n=
q4lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbn=
mm5rbkgk3qdi32ka-hdf5-1.8.21/lib:/gnu/store/d25i834bs8wvg8mh36bplxg61r6b7vz=
9-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=E2=80=99t you comparing two different builds, like one grafted the oth=
er
ungrafted?

What I do is:

  guix build foo --check -K

and then:

  diffoscope /gnu/store/=E2=80=A6-the-thing{,-check}

That way you=E2=80=99re 100% sure you=E2=80=99re comparing two different bu=
ilds of the
very same derivation.

Ludo=E2=80=99.




Information forwarded to bug-guix@HIDDEN:
bug#34935; Package guix. Full text available.

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From: Maxim Cournoyer <maxim.cournoyer@HIDDEN>
To: bug-guix <bug-guix@HIDDEN>
Subject: nanopolish is not reproducible
Date: Wed, 20 Mar 2019 23:11:41 -0400
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 Content preview: $ 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/sto [...] 
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 Content preview:  $ 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/sto [...] 
 
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  2.5 BITCOIN_SPAM_05        BitCoin spam pattern 05

$ 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/sto=
re/m7icaq7642zy0gvnqvymcnn8d088a9s0-nanopolish-0.10.2-1.50e8b5c' differs

$ diffoscope "$(guix build nanopolish)" /gnu/store/m7icaq7642zy0gvnqvymcnn8=
d088a9s0-nanopolish-0.10.2-1.50e8b5c

--8<---------------cut here---------------start------------->8---
=E2=94=82 =E2=94=82 =E2=94=82 - 0x000000000000001d (RUNPATH)            Lib=
rary runpath: [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib:/=
gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/nq4=
lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbnmm=
5rbkgk3qdi32ka-hdf5-1.8.21/lib:/gnu/store/x4xpcpsqmini25gkrc0h945ml9r609v5-=
htslib-1.9/lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/li=
b/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
=E2=94=82 =E2=94=82 =E2=94=82 + 0x000000000000001d (RUNPATH)            Lib=
rary runpath: [/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib:/=
gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib:/gnu/store/nq4=
lsyipmfb0q7g26ra45rwwqrh3x8zw-zlib-1.2.11/lib:/gnu/store/36i633snnhx4mgbnmm=
5rbkgk3qdi32ka-hdf5-1.8.21/lib:/gnu/store/d25i834bs8wvg8mh36bplxg61r6b7vz9-=
htslib-1.9/lib:/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/li=
b/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
--8<---------------cut here---------------end--------------->8---

The problem seems to lie in htslib.




Acknowledgement sent to Maxim Cournoyer <maxim.cournoyer@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#34935; Package guix. Full text available.
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