Source: salmon
Version: 0.4.2+ds1-1
Severity: wishlist
Tags: patch
User: reproducible-builds@lists.alioth.debian.org
Usertags: environment
X-Debbugs-Cc: reproducible-builds@lists.alioth.debian.org
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
`. `'` la...@debian.org / 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
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