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commit 5ec3b5aface7fea0e2c8fce009d9c426f29c570a Author: Sascha Steinbiss <[email protected]> Date: Fri Aug 19 14:30:23 2016 +0000 fix FTBFS with newer Boost versions --- debian/changelog | 9 +++ debian/control | 4 +- debian/patches/fix-ftbfs-with-new-boost.patch | 90 +++++++++++++++++++++++++++ debian/patches/series | 1 + 4 files changed, 102 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index 3e51f11..a72e214 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,12 @@ +dindel (1.01+dfsg-4) unstable; urgency=medium + + * Team upload. + * Make code compatible with latest Boost version (1.61 and up). + Thanks to Graham Inggs for the patch. + Closes: #833958 + + -- Sascha Steinbiss <[email protected]> Wed, 10 Aug 2016 21:34:19 +0000 + dindel (1.01+dfsg-3) unstable; urgency=medium * Team upload. diff --git a/debian/control b/debian/control index d5e5480..12a689c 100644 --- a/debian/control +++ b/debian/control @@ -8,8 +8,8 @@ Priority: optional Build-Depends: debhelper (>= 9), seqan-dev, libbam-dev, - libboost-program-options1.58-dev, - libboost-math1.58-dev, + libboost-program-options-dev, + libboost-math-dev, zlib1g-dev Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/dindel.git diff --git a/debian/patches/fix-ftbfs-with-new-boost.patch b/debian/patches/fix-ftbfs-with-new-boost.patch new file mode 100644 index 0000000..5594740 --- /dev/null +++ b/debian/patches/fix-ftbfs-with-new-boost.patch @@ -0,0 +1,90 @@ +Description: Use Boost's foreach.hpp instead of embedded copy + This fixes a FTBFS with recent versions of Boost +Bug-Debian: https://bugs.debian.org/833958 +Author: Graham Inggs <[email protected]> +Last-Update: 2016-08-19 +--- a/DInDel.cpp ++++ b/DInDel.cpp +@@ -24,7 +24,7 @@ + #include <boost/math/special_functions/digamma.hpp> + #include <seqan/align.h> + #include <seqan/graph_align.h> +-#include "foreach.hpp" ++#include <boost/foreach.hpp> + #include "bam.h" + #include "DInDel.hpp" + #include "Haplotype.hpp" +--- a/Faster.cpp ++++ b/Faster.cpp +@@ -35,7 +35,7 @@ + #include "Haplotype.hpp" + #include "Faster.hpp" + #include "Utils.hpp" +-#include "foreach.hpp" ++#include <boost/foreach.hpp> + using namespace std; + const int DEBUGS=0; + +--- a/GetCandidates.cpp ++++ b/GetCandidates.cpp +@@ -22,7 +22,7 @@ + #include <fstream> + #include <string> + #include "MyBam.hpp" +-#include "foreach.hpp" ++#include <boost/foreach.hpp> + #include "ObservationModelSeqAn.hpp" + #include "GetCandidates.hpp" + #include "Variant.hpp" +@@ -32,7 +32,6 @@ + #include "Fasta.hpp" + #include "StringHash.hpp" + #include <set> +-#include "foreach.hpp" + using namespace std; + + int GetCandidatesFromCIGAR::getIndelFromCIGARFetchFunc(const bam1_t *b, void *data) +--- a/Haplotype.hpp ++++ b/Haplotype.hpp +@@ -23,7 +23,7 @@ + #include <vector> + #include "Variant.hpp" + #include "MLAlignment.hpp" +-#include "foreach.hpp" ++#include <boost/foreach.hpp> + #include <ext/hash_map> + #include <set> + //#include "Fast.hpp" +--- a/HaplotypeDistribution.hpp ++++ b/HaplotypeDistribution.hpp +@@ -27,7 +27,7 @@ + #include "bam.h" + #include "Haplotype.hpp" + #include "HapBlock.hpp" +-#include "foreach.hpp" ++#include <boost/foreach.hpp> + #include "VariantFile.hpp" + using namespace std; + +--- a/OutputData.hpp ++++ b/OutputData.hpp +@@ -25,7 +25,7 @@ + #include "StringHash.hpp" + #include <string> + #include <iostream> +-#include "foreach.hpp" ++#include <boost/foreach.hpp> + using namespace std; + using namespace boost; + +--- a/StringHash.hpp ++++ b/StringHash.hpp +@@ -25,7 +25,7 @@ + #include <ext/hash_map> + #include <string> + #include <iostream> +-#include "foreach.hpp" ++#include <boost/foreach.hpp> + using namespace std; + using namespace boost; + using __gnu_cxx::hash; diff --git a/debian/patches/series b/debian/patches/series index 8fb20f6..f6ef95f 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ modernize-Makefile.patch compiler_errors.patch fix-ftbfs-with-gcc6.patch +fix-ftbfs-with-new-boost.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/dindel.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
