Debian Bug report logs - #863015
jellyfish: please make the output reproducible

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Chris Lamb <lamby@debian.org>

To: submit@bugs.debian.org

Subject: jellyfish: please make the output reproducible

Date: Sat, 20 May 2017 08:34:49 +0100

[Message part 1 (text/plain, inline)]

Source: jellyfish
Version: 2.2.6-1
Severity: wishlist
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: timestamps toolchain buildpath
X-Debbugs-Cc: reproducible-bugs@lists.alioth.debian.org

Hi,

Whilst working on the Reproducible Builds effort [0], we noticed
that jellyfish generated JSON files that are not reproducible.

This is due to including the output of getcwd(3) and the current date
in the local timezone. It affects other packages in the archive (eg.
src:quorum).

Patch attached.

 [0] https://reproducible-builds.org/


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby@debian.org / chris-lamb.co.uk
       `-

[jellyfish.diff.txt (text/plain, attachment)]

Message #10 received at 863015@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@fam-tille.de>

To: 863015@bugs.debian.org

Subject: Patch for reproducible builds breaks build time test

Date: Fri, 25 Aug 2017 22:18:05 +0200

Hi Chris,

thanks for the patch (and sorry for taking so much time to respond).
Unfurtunately if I activate the patch[1] one test
(unit_tests/unit_tests.sh) fails which is not the case if the patch
is deactivated in debian/patches/series:

...
PASS: tests/large_key.sh
PASS: tests/parallel_hashing.sh
FAIL: unit_tests/unit_tests.sh
=======================================
   jellyfish 2.2.6: ./test-suite.log
=======================================

# TOTAL: 13
# PASS:  9
# SKIP:  3
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0
...


It might be that the test relies somehow on the date in the json file.

Should I report this to upstream or do you want to investigate into the
test suite?  I admit I'm overwhelmed with gcc-7 and other bugs and will
not manage to track this down in any sensible time frame.

Kind regards and thanks in any case for the reprodicible build effort

     Andreas.


[1] https://anonscm.debian.org/git/debian-med/jellyfish.git/tree/debian/patches/reproducible.patch

-- 
http://fam-tille.de

Message #15 received at 863015@bugs.debian.org (full text, mbox, reply):

From: Chris Lamb <lamby@debian.org>

To: Andreas Tille <andreas@fam-tille.de>, 863015@bugs.debian.org

Subject: Re: [Debian-med-packaging] Bug#863015: Patch for reproducible builds breaks build time test

Date: Sun, 27 Aug 2017 02:07:58 -0700

Hi Andreas,

> # FAIL:  1

Just pasting this here for now so I don't lose it. Here is the entry
in unit_tests/unit_tests.log after a failed build:

   543 [----------] 2 tests from FileHeader
   544 [ RUN      ] FileHeader.Standard
   545 unit_tests/test_file_header.cc:26: Failure
   546 Expected: ("") != (h["hostname"]), actual: "" vs ""
   547 [  FAILED  ] FileHeader.Standard (0 ms)
   548 [ RUN      ] FileHeader.WriteRead
   549 [       OK ] FileHeader.WriteRead (1 ms)
   550 [----------] 2 tests from FileHeader (1 ms total)

(More later unless you fix this first...)


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby@debian.org / chris-lamb.co.uk
       `-

Message #20 received at 863015@bugs.debian.org (full text, mbox, reply):

From: Chris Lamb <lamby@debian.org>

To: Andreas Tille <andreas@fam-tille.de>, 863015@bugs.debian.org

Subject: Re: [Debian-med-packaging] Bug#863015: Patch for reproducible builds breaks build time test

Date: Sun, 27 Aug 2017 22:00:09 +0100

Hi Andreas,

  7 --- a/include/jellyfish/generic_file_header.hpp
  8 +++ b/include/jellyfish/generic_file_header.hpp
  9 @@ -180,6 +180,8 @@ public:
 10 
 11  protected:
 12    std::string get_hostname() const {
 13 +    if(std::getenv("SOURCE_DATE_EPOCH"))
 14 +      return "";
                  ^^

Just change this to "hostname".

The test was checking whether it was not the empty string. Thinking about
it, returning an empty string is probably not a good idea anyway.

Enjoy :)


Best wishes,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      lamby@debian.org / chris-lamb.co.uk
       `-

Message #25 received at 863015-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 863015-close@bugs.debian.org

Subject: Bug#863015: fixed in jellyfish 2.2.6-4

Date: Mon, 28 Aug 2017 13:35:23 +0000

Source: jellyfish
Source-Version: 2.2.6-4

We believe that the bug you reported is fixed in the latest version of
jellyfish, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 863015@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated jellyfish package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Mon, 28 Aug 2017 14:40:40 +0200
Source: jellyfish
Binary: jellyfish libjellyfish-2.0-2 libjellyfish-2.0-dev python3-dna-jellyfish libjellyfish-perl jellyfish-examples
Architecture: source
Version: 2.2.6-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 jellyfish  - count k-mers in DNA sequences
 jellyfish-examples - count k-mers in DNA sequences (examples for testing)
 libjellyfish-2.0-2 - count k-mers in DNA sequences (dynamic library of jellyfish)
 libjellyfish-2.0-dev - count k-mers in DNA sequences (development files of jellyfish)
 libjellyfish-perl - count k-mers in DNA sequences (Perl bindings of jellyfish)
 python3-dna-jellyfish - count k-mers in DNA sequences (Python bindings of jellyfish)
Closes: 863015
Changes:
 jellyfish (2.2.6-4) unstable; urgency=medium
 .
   * Make sure reproducible patch will not break test suite (Thanks to
     Chris Lamb <lamby@debian.org> for the fix)
     Closes: #863015
   * Autoreconf not needed with debhelper 10
   * Do not parse debian/changelog
   * Fix whatis entry in manpage
   * Fix spelling in manpage
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