all messages for Guix-related lists mirrored at yhetil.org
 help / color / mirror / Atom feed
* bug#34934: deeptools is not reproducible
@ 2019-03-21  3:01 Maxim Cournoyer
  2019-03-23 17:00 ` Ludovic Courtès
  2021-01-13 15:54 ` Maxim Cournoyer
  0 siblings, 2 replies; 8+ messages in thread
From: Maxim Cournoyer @ 2019-03-21  3:01 UTC (permalink / raw)
  To: 34934

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@3.7.0
python@3.7.0
python-wrapper@3.7.0
python-minimal@3.7.0
python-minimal-wrapper@3.7.0
python2@2.7.15

^ permalink raw reply	[flat|nested] 8+ messages in thread

* bug#34934: deeptools is not reproducible
  2019-03-21  3:01 bug#34934: deeptools is not reproducible Maxim Cournoyer
@ 2019-03-23 17:00 ` Ludovic Courtès
  2019-03-24 10:11   ` Gábor Boskovits
  2021-01-13 15:54 ` Maxim Cournoyer
  1 sibling, 1 reply; 8+ messages in thread
From: Ludovic Courtès @ 2019-03-23 17:00 UTC (permalink / raw)
  To: Maxim Cournoyer; +Cc: 34934

Hi,

Maxim Cournoyer <maxim.cournoyer@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’.

^ permalink raw reply	[flat|nested] 8+ messages in thread

* bug#34934: deeptools is not reproducible
  2019-03-23 17:00 ` Ludovic Courtès
@ 2019-03-24 10:11   ` Gábor Boskovits
  2019-03-25  9:22     ` Ludovic Courtès
  0 siblings, 1 reply; 8+ messages in thread
From: Gábor Boskovits @ 2019-03-24 10:11 UTC (permalink / raw)
  To: Ludovic Courtès; +Cc: 34934, Maxim Cournoyer

Hello Ludo,

Ludovic Courtès <ludo@gnu.org> ezt írta (időpont: 2019. márc. 23., Szo, 18:01):
>
> Hi,
>
> Maxim Cournoyer <maxim.cournoyer@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

^ permalink raw reply	[flat|nested] 8+ messages in thread

* bug#34934: deeptools is not reproducible
  2019-03-24 10:11   ` Gábor Boskovits
@ 2019-03-25  9:22     ` Ludovic Courtès
  2019-03-28 13:45       ` Maxim Cournoyer
  0 siblings, 1 reply; 8+ messages in thread
From: Ludovic Courtès @ 2019-03-25  9:22 UTC (permalink / raw)
  To: Gábor Boskovits; +Cc: 34934, Maxim Cournoyer

Hi Gábor,

Gábor Boskovits <boskovits@gmail.com> skribis:

> Ludovic Courtès <ludo@gnu.org> ezt írta (időpont: 2019. márc. 23., Szo, 18:01):
>>
>> Hi,
>>
>> Maxim Cournoyer <maxim.cournoyer@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’.

^ permalink raw reply	[flat|nested] 8+ messages in thread

* bug#34934: deeptools is not reproducible
  2019-03-25  9:22     ` Ludovic Courtès
@ 2019-03-28 13:45       ` Maxim Cournoyer
  2019-03-28 14:08         ` Ludovic Courtès
  0 siblings, 1 reply; 8+ messages in thread
From: Maxim Cournoyer @ 2019-03-28 13:45 UTC (permalink / raw)
  To: Ludovic Courtès; +Cc: 34934

Hello Ludovic!

Ludovic Courtès <ludo@gnu.org> writes:

> Hi Gábor,
>
> Gábor Boskovits <boskovits@gmail.com> skribis:
>
>> Ludovic Courtès <ludo@gnu.org> ezt írta (időpont: 2019. márc. 23., Szo, 18:01):
>>>
>>> Hi,
>>>
>>> Maxim Cournoyer <maxim.cournoyer@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

^ permalink raw reply	[flat|nested] 8+ messages in thread

* bug#34934: deeptools is not reproducible
  2019-03-28 13:45       ` Maxim Cournoyer
@ 2019-03-28 14:08         ` Ludovic Courtès
  2019-03-30 15:03           ` T460s laptop
  0 siblings, 1 reply; 8+ messages in thread
From: Ludovic Courtès @ 2019-03-28 14:08 UTC (permalink / raw)
  To: Maxim Cournoyer; +Cc: 34934

Maxim Cournoyer <maxim.cournoyer@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’.

^ permalink raw reply	[flat|nested] 8+ messages in thread

* bug#34934: deeptools is not reproducible
  2019-03-28 14:08         ` Ludovic Courtès
@ 2019-03-30 15:03           ` T460s laptop
  0 siblings, 0 replies; 8+ messages in thread
From: T460s laptop @ 2019-03-30 15:03 UTC (permalink / raw)
  To: Ludovic Courtès; +Cc: 34934, Maxim Cournoyer

[-- Attachment #1: Type: text/plain, Size: 3764 bytes --]

Hello again!

Ludovic Courtès <ludo@gnu.org> writes:

> Maxim Cournoyer <maxim.cournoyer@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

[-- Attachment #2: diffoscope /gnu/store/f3z6fczw70j6692ddy467pbagbjck009-deeptools-3.1.3{,-check} --]
[-- Type: application/octet-stream, Size: 173548 bytes --]

^ permalink raw reply	[flat|nested] 8+ messages in thread

* bug#34934: deeptools is not reproducible
  2019-03-21  3:01 bug#34934: deeptools is not reproducible Maxim Cournoyer
  2019-03-23 17:00 ` Ludovic Courtès
@ 2021-01-13 15:54 ` Maxim Cournoyer
  1 sibling, 0 replies; 8+ messages in thread
From: Maxim Cournoyer @ 2021-01-13 15:54 UTC (permalink / raw)
  To: bug#34934

This is no longer an issue.

Closing.

Maxim




^ permalink raw reply	[flat|nested] 8+ messages in thread

end of thread, other threads:[~2021-01-13 15:56 UTC | newest]

Thread overview: 8+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2019-03-21  3:01 bug#34934: deeptools is not reproducible Maxim Cournoyer
2019-03-23 17:00 ` Ludovic Courtès
2019-03-24 10:11   ` Gábor Boskovits
2019-03-25  9:22     ` Ludovic Courtès
2019-03-28 13:45       ` Maxim Cournoyer
2019-03-28 14:08         ` Ludovic Courtès
2019-03-30 15:03           ` T460s laptop
2021-01-13 15:54 ` Maxim Cournoyer

all messages for Guix-related lists mirrored at yhetil.org

This inbox may be cloned and mirrored by anyone:

	git clone --mirror https://yhetil.org/guix

Example config snippet for mirrors.


AGPL code for this site: git clone http://ou63pmih66umazou.onion/public-inbox.git