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
_______________________________________________ Reproducible-builds mailing list Reproducible-builds@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/reproducible-builds