GNU bug report logs - #34934
deeptools is not reproducible

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Package: guix;

Reported by: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>

Date: Thu, 21 Mar 2019 03:09:02 UTC

Severity: normal

Done: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>

Bug is archived. No further changes may be made.

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Report forwarded to bug-guix <at> gnu.org:
bug#34934; Package guix. (Thu, 21 Mar 2019 03:09:02 GMT) Full text and rfc822 format available.

Acknowledgement sent to Maxim Cournoyer <maxim.cournoyer <at> gmail.com>:
New bug report received and forwarded. Copy sent to bug-guix <at> gnu.org. (Thu, 21 Mar 2019 03:09:02 GMT) Full text and rfc822 format available.

Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: bug-guix <bug-guix <at> gnu.org>
Subject: deeptools is not reproducible
Date: Wed, 20 Mar 2019 23:01:32 -0400
On current master (commit af184b68e78aa51b6ff50b7327dfbbdb1d6e6843),
deeptools does not build reproducibly:

$ guix build --check --no-grafts deeptools

--8<---------------cut here---------------start------------->8---
...
guix build: error: derivation `/gnu/store/hky07zjsvai0x3n99lqmgyh6rhld6v4s-deeptools-3.1.3.drv' may not be deterministic: output `/gnu/store/0j8200f20mp5grjkjh5kw2q9a67gw3rn-deeptools-3.1.3' differs
--8<---------------cut here---------------end--------------->8---

$ diff -ru "$(guix build deeptools)" /gnu/store/0j8200f20mp5grjkjh5kw2q9a67gw3rn-deeptools-3.1.3

--8<---------------cut here---------------start------------->8---
│ │ │ │ ├── tree.cpython-37m-x86_64-linux-gnu.so
│ │ │ │ │ ├── /gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --dynamic {}
│ │ │ │ │ │ @@ -2,15 +2,15 @@
│ │ │ │ │ │  Dynamic section at offset 0xcd90 contains 30 entries:
│ │ │ │ │ │    Tag        Type                         Name/Value
│ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libz.so.1]
│ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpython3.7m.so.1.0]
│ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
│ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
│ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
│ │ │ │ │ │ - 0x000000000000001d (RUNPATH)            Library runpath: [/gnu/store/9z98cvjm7p7z21xdid1ryydxy5vyz6wr-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
│ │ │ │ │ │ + 0x000000000000001d (RUNPATH)            Library runpath:
[/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
--8<---------------cut here---------------end--------------->8---

There are multiple more instances of differences in the two versions.

Maybe something to do with two flavors of Python being used?

$ guix refresh --list-transitive deeptools | tr ' ' '\n' | grep -E 'python-(minimal|wrapper)|python2?@'
python <at> 3.7.0
python <at> 3.7.0
python-wrapper <at> 3.7.0
python-minimal <at> 3.7.0
python-minimal-wrapper <at> 3.7.0
python2 <at> 2.7.15




Information forwarded to bug-guix <at> gnu.org:
bug#34934; Package guix. (Sat, 23 Mar 2019 17:01:02 GMT) Full text and rfc822 format available.

Message #8 received at 34934 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Cc: 34934 <at> debbugs.gnu.org
Subject: Re: bug#34934: deeptools is not reproducible
Date: Sat, 23 Mar 2019 18:00:17 +0100
Hi,

Maxim Cournoyer <maxim.cournoyer <at> gmail.com> skribis:

> │ │ │ │ ├── tree.cpython-37m-x86_64-linux-gnu.so
> │ │ │ │ │ ├── /gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --dynamic {}
> │ │ │ │ │ │ @@ -2,15 +2,15 @@
> │ │ │ │ │ │  Dynamic section at offset 0xcd90 contains 30 entries:
> │ │ │ │ │ │    Tag        Type                         Name/Value
> │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libz.so.1]
> │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpython3.7m.so.1.0]
> │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
> │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
> │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
> │ │ │ │ │ │ - 0x000000000000001d (RUNPATH)            Library runpath: [/gnu/store/9z98cvjm7p7z21xdid1ryydxy5vyz6wr-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
> │ │ │ │ │ │ + 0x000000000000001d (RUNPATH)            Library runpath:
> [/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]

Hmmm, what’s the difference between these two RUNPATHs?

Ludo’.




Information forwarded to bug-guix <at> gnu.org:
bug#34934; Package guix. (Sun, 24 Mar 2019 10:12:01 GMT) Full text and rfc822 format available.

Message #11 received at 34934 <at> debbugs.gnu.org (full text, mbox):

From: Gábor Boskovits <boskovits <at> gmail.com>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: 34934 <at> debbugs.gnu.org, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34934: deeptools is not reproducible
Date: Sun, 24 Mar 2019 11:11:02 +0100
Hello Ludo,

Ludovic Courtès <ludo <at> gnu.org> ezt írta (időpont: 2019. márc. 23., Szo, 18:01):
>
> Hi,
>
> Maxim Cournoyer <maxim.cournoyer <at> gmail.com> skribis:
>
> > │ │ │ │ ├── tree.cpython-37m-x86_64-linux-gnu.so
> > │ │ │ │ │ ├── /gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --dynamic {}
> > │ │ │ │ │ │ @@ -2,15 +2,15 @@
> > │ │ │ │ │ │  Dynamic section at offset 0xcd90 contains 30 entries:
> > │ │ │ │ │ │    Tag        Type                         Name/Value
> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libz.so.1]
> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpython3.7m.so.1.0]
> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
> > │ │ │ │ │ │ - 0x000000000000001d (RUNPATH)            Library runpath: [/gnu/store/9z98cvjm7p7z21xdid1ryydxy5vyz6wr-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
> > │ │ │ │ │ │ + 0x000000000000001d (RUNPATH)            Library runpath:
> > [/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
>
> Hmmm, what’s the difference between these two RUNPATHs?
>

At first They looked ver similar to me, but the hash of the first
python-3.7.0 differs, right at the beginning. I could not dive deeper,
but maybe this can help you out.

> Ludo’.
>
>
>

Best regards,
g_bor




Information forwarded to bug-guix <at> gnu.org:
bug#34934; Package guix. (Mon, 25 Mar 2019 09:23:02 GMT) Full text and rfc822 format available.

Message #14 received at 34934 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Gábor Boskovits <boskovits <at> gmail.com>
Cc: 34934 <at> debbugs.gnu.org, Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34934: deeptools is not reproducible
Date: Mon, 25 Mar 2019 10:22:00 +0100
Hi Gábor,

Gábor Boskovits <boskovits <at> gmail.com> skribis:

> Ludovic Courtès <ludo <at> gnu.org> ezt írta (időpont: 2019. márc. 23., Szo, 18:01):
>>
>> Hi,
>>
>> Maxim Cournoyer <maxim.cournoyer <at> gmail.com> skribis:
>>
>> > │ │ │ │ ├── tree.cpython-37m-x86_64-linux-gnu.so
>> > │ │ │ │ │ ├── /gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --dynamic {}
>> > │ │ │ │ │ │ @@ -2,15 +2,15 @@
>> > │ │ │ │ │ │  Dynamic section at offset 0xcd90 contains 30 entries:
>> > │ │ │ │ │ │    Tag        Type                         Name/Value
>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libz.so.1]
>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpython3.7m.so.1.0]
>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
>> > │ │ │ │ │ │ - 0x000000000000001d (RUNPATH)            Library runpath: [/gnu/store/9z98cvjm7p7z21xdid1ryydxy5vyz6wr-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
>> > │ │ │ │ │ │ + 0x000000000000001d (RUNPATH)            Library runpath:
>> > [/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
>>
>> Hmmm, what’s the difference between these two RUNPATHs?
>>
>
> At first They looked ver similar to me, but the hash of the first
> python-3.7.0 differs, right at the beginning.

Oooh, indeed, I had overlooked that.

So to me that means we’re probably looking at the wrong diff: the hash
is definitely deterministic.  Maxim, are you sure you were comparing
/gnu/store/…-deeptools with /gnu/store/…-deeptools-check, as discussed
in another message?

Thanks,
Ludo’.




Information forwarded to bug-guix <at> gnu.org:
bug#34934; Package guix. (Thu, 28 Mar 2019 13:46:02 GMT) Full text and rfc822 format available.

Message #17 received at 34934 <at> debbugs.gnu.org (full text, mbox):

From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: 34934 <at> debbugs.gnu.org,
 Gábor Boskovits <boskovits <at> gmail.com>
Subject: Re: bug#34934: deeptools is not reproducible
Date: Thu, 28 Mar 2019 09:45:03 -0400
Hello Ludovic!

Ludovic Courtès <ludo <at> gnu.org> writes:

> Hi Gábor,
>
> Gábor Boskovits <boskovits <at> gmail.com> skribis:
>
>> Ludovic Courtès <ludo <at> gnu.org> ezt írta (időpont: 2019. márc. 23., Szo, 18:01):
>>>
>>> Hi,
>>>
>>> Maxim Cournoyer <maxim.cournoyer <at> gmail.com> skribis:
>>>
>>> > │ │ │ │ ├── tree.cpython-37m-x86_64-linux-gnu.so
>>> > │ │ │ │ │ ├── /gnu/store/02iklp4swqs0ipxhg5x9b2shmj6b30h1-binutils-2.31.1/bin/readelf --wide --dynamic {}
>>> > │ │ │ │ │ │ @@ -2,15 +2,15 @@
>>> > │ │ │ │ │ │  Dynamic section at offset 0xcd90 contains 30 entries:
>>> > │ │ │ │ │ │    Tag        Type                         Name/Value
>>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libz.so.1]
>>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpython3.7m.so.1.0]
>>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
>>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libpthread.so.0]
>>> > │ │ │ │ │ │   0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
>>> > │ │ │ │ │ │ - 0x000000000000001d (RUNPATH) Library runpath:
>>> > [/gnu/store/9z98cvjm7p7z21xdid1ryydxy5vyz6wr-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
>>> > │ │ │ │ │ │ + 0x000000000000001d (RUNPATH)            Library runpath:
>>> > [/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib:/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/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..]
>>>
>>> Hmmm, what’s the difference between these two RUNPATHs?
>>>
>>
>> At first They looked ver similar to me, but the hash of the first
>> python-3.7.0 differs, right at the beginning.
>
> Oooh, indeed, I had overlooked that.
>
> So to me that means we’re probably looking at the wrong diff: the hash
> is definitely deterministic.  Maxim, are you sure you were comparing
> /gnu/store/…-deeptools with /gnu/store/…-deeptools-check, as discussed
> in another message?

That must be my mistake yes; the output of 'guix build --check --no-grafts
python-deeptools':

--8<---------------cut here---------------start------------->8---
guix build: error: derivation `/gnu/store/hky07zjsvai0x3n99lqmgyh6rhld6v4s-deeptools-3.1.3.drv' may not be deterministic: output `/gnu/store/0j8200f20mp5grjkjh5kw2q9a67gw3rn-deeptools-3.1.3' differs
--8<---------------cut here---------------end--------------->8---

left me confused about what and what store items were
being compared exactly, and I must have went on and diff'd something not quite
right, sorry! Perhaps the store output differing should be mentioned
explicitly in the error?

The suggested command doesn't help :-(, as the ...-check output
doesn't seem to exist:

--8<---------------cut here---------------start------------->8---
$ guix build --check -K deeptools
The following graft will be made:
   /gnu/store/mhqdaw8q8p6r3g12c95d7pmfxnmgg50j-deeptools-3.1.3.drv
applying 30 grafts for /gnu/store/mhqdaw8q8p6r3g12c95d7pmfxnmgg50j-deeptools-3.1.3.drv...
grafting '/gnu/store/f3z6fczw70j6692ddy467pbagbjck009-deeptools-3.1.3' -> '/gnu/store/9vdd6k083y8l83d8yck4wlf09pdmp1wi-deeptools-3.1.3'...
note: keeping build directory `/tmp/guix-build-deeptools-3.1.3.drv-1'
/gnu/store/9vdd6k083y8l83d8yck4wlf09pdmp1wi-deeptools-3.1.3

$ diffoscope /gnu/store/9vdd6k083y8l83d8yck4wlf09pdmp1wi-deeptools-3.1.3{,-check}
/gnu/store/6lgkzp4x3nh32n4pbkdm618wah0b0038-diffoscope-111/bin/.diffoscope-real: /gnu/store/9vdd6k083y8l83d8yck4wlf09pdmp1wi-deeptools-3.1.3-check: No such file or directory
--8<---------------cut here---------------end--------------->8---

Maxim




Information forwarded to bug-guix <at> gnu.org:
bug#34934; Package guix. (Thu, 28 Mar 2019 14:10:02 GMT) Full text and rfc822 format available.

Message #20 received at 34934 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Cc: 34934 <at> debbugs.gnu.org,
 Gábor Boskovits <boskovits <at> gmail.com>
Subject: Re: bug#34934: deeptools is not reproducible
Date: Thu, 28 Mar 2019 15:08:51 +0100
Maxim Cournoyer <maxim.cournoyer <at> gmail.com> 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.

Ludo’.




Information forwarded to bug-guix <at> gnu.org:
bug#34934; Package guix. (Sat, 30 Mar 2019 15:04:01 GMT) Full text and rfc822 format available.

Message #23 received at 34934 <at> debbugs.gnu.org (full text, mbox):

From: T460s laptop <maxim.cournoyer <at> gmail.com>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: 34934 <at> debbugs.gnu.org,
 Gábor Boskovits <boskovits <at> gmail.com>,
 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
Subject: Re: bug#34934: deeptools is not reproducible
Date: Sat, 30 Mar 2019 11:03:41 -0400
[Message part 1 (text/plain, inline)]
Hello again!

Ludovic Courtès <ludo <at> gnu.org> writes:

> Maxim Cournoyer <maxim.cournoyer <at> gmail.com> 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 (application/octet-stream, attachment)]

Reply sent to Maxim Cournoyer <maxim.cournoyer <at> gmail.com>:
You have taken responsibility. (Wed, 13 Jan 2021 15:56:01 GMT) Full text and rfc822 format available.

Notification sent to Maxim Cournoyer <maxim.cournoyer <at> gmail.com>:
bug acknowledged by developer. (Wed, 13 Jan 2021 15:56:01 GMT) Full text and rfc822 format available.

Message #28 received at 34934-done <at> debbugs.gnu.org (full text, mbox):

From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
To: bug#34934 <34934-done <at> debbugs.gnu.org>
Subject: Re: bug#34934: deeptools is not reproducible
Date: Wed, 13 Jan 2021 10:54:59 -0500
This is no longer an issue.

Closing.

Maxim




bug archived. Request was from Debbugs Internal Request <help-debbugs <at> gnu.org> to internal_control <at> debbugs.gnu.org. (Thu, 11 Feb 2021 12:24:06 GMT) Full text and rfc822 format available.

This bug report was last modified 4 years and 146 days ago.

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