Your message dated Mon, 28 Aug 2017 13:35:23 +0000
with message-id <[email protected]>
and subject line Bug#863015: fixed in jellyfish 2.2.6-4
has caused the Debian Bug report #863015,
regarding jellyfish: please make the output reproducible
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
863015: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=863015
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: jellyfish
Version: 2.2.6-1
Severity: wishlist
Tags: patch
User: [email protected]
Usertags: timestamps toolchain buildpath
X-Debbugs-Cc: [email protected]
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
`. `'` [email protected] / chris-lamb.co.uk
`-
diff --git a/include/jellyfish/generic_file_header.hpp
b/include/jellyfish/generic_file_header.hpp
index a8ddf82..99f80b2 100644
--- a/include/jellyfish/generic_file_header.hpp
+++ b/include/jellyfish/generic_file_header.hpp
@@ -180,6 +180,8 @@ public:
protected:
std::string get_hostname() const {
+ if(std::getenv("SOURCE_DATE_EPOCH"))
+ return "";
struct utsname buf;
if(uname(&buf) == -1)
return "";
@@ -187,6 +189,8 @@ protected:
}
std::string get_pwd() const {
+ if(std::getenv("SOURCE_DATE_EPOCH"))
+ return ".";
#ifdef PATH_MAX
size_t len = PATH_MAX;
#else
@@ -202,6 +206,16 @@ protected:
std::string get_localtime() const {
time_t t = time(0);
std::string res(ctime(&t));
+ char *source_date_epoch = std::getenv("SOURCE_DATE_EPOCH");
+ if(source_date_epoch) {
+ std::istringstream iss(source_date_epoch);
+ iss >> t;
+ if(iss.fail() || !iss.eof()) {
+ std::cerr << "Error: Cannot parse SOURCE_DATE_EPOCH as integer\n";
+ exit(27);
+ }
+ res = asctime(gmtime(&t));
+ }
chomp(res);
return res;
}
--- End Message ---
--- Begin Message ---
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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (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 [email protected])
-----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
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
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 <[email protected]> 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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