Your message dated Sun, 07 Feb 2016 12:22:41 +0000
with message-id <[email protected]>
and subject line Bug#813994: fixed in salmon 0.4.2+ds1-2
has caused the Debian Bug report #813994,
regarding salmon: please make the build 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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--
813994: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813994
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: salmon
Version: 0.4.2+ds1-1
Severity: wishlist
Tags: patch
User: [email protected]
Usertags: environment
X-Debbugs-Cc: [email protected]
Hi,
Whilst working on the "reproducible builds" effort [0], we noticed that salmon
could not be built reproducibly.
Patch attached.
[0] https://wiki.debian.org/ReproducibleBuilds
Regards,
--
,''`.
: :' : Chris Lamb
`. `'` [email protected] / chris-lamb.co.uk
`-
--- a/debian/patches/reproducible-build 1970-01-01 01:00:00.000000000 +0100
--- b/debian/patches/reproducible-build 2016-02-07 12:00:50.428831600 +0100
@@ -0,0 +1,19 @@
+--- salmon-0.4.2+ds1.orig/src/BuildSalmonIndex.cpp
++++ salmon-0.4.2+ds1/src/BuildSalmonIndex.cpp
+@@ -151,7 +151,6 @@ int salmonIndex(int argc, char* argv[])
+ bool useStreamingParser = true;
+
+ uint32_t saSampInterval = 1;
+- uint32_t maxThreads = std::thread::hardware_concurrency();
+ uint32_t numThreads;
+
+ po::options_description generic("Command Line Options");
+@@ -160,7 +159,7 @@ int salmonIndex(int argc, char* argv[])
+ ("help,h", "produce help message")
+ ("transcripts,t", po::value<string>()->required(), "Transcript fasta
file.")
+ ("index,i", po::value<string>()->required(), "Salmon index.")
+- ("threads,p",
po::value<uint32_t>(&numThreads)->default_value(maxThreads)->required(),
++ ("threads,p",
po::value<uint32_t>(&numThreads)->default_value(2)->required(),
+ "Number of threads to use (only used for
computing bias features)")
+ ("sasamp,s",
po::value<uint32_t>(&saSampInterval)->default_value(1)->required(),
+ "The interval at which the suffix array should be
sampled. "
--- a/debian/patches/series 2016-02-07 11:52:00.283637299 +0100
--- b/debian/patches/series 2016-02-07 12:00:47.460802047 +0100
@@ -8,3 +8,4 @@
0007-Remove-unnecessarily-linked-libraries.patch
0008-Remove-salmon_core-lib.patch
0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
+reproducible-build
--- End Message ---
--- Begin Message ---
Source: salmon
Source-Version: 0.4.2+ds1-2
We believe that the bug you reported is fixed in the latest version of
salmon, 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.
Michael R. Crusoe <[email protected]> (supplier of updated salmon 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: SHA256
Format: 1.8
Date: Sun, 07 Feb 2016 03:58:27 -0800
Source: salmon
Binary: salmon
Architecture: source
Version: 0.4.2+ds1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Description:
salmon - wicked-fast transcript quantification from RNA-seq data
Closes: 813994
Changes:
salmon (0.4.2+ds1-2) unstable; urgency=medium
.
* Make build reproducible.
Closes: #813994
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