[normaliz] 03/03: Debian patch 3.1.0+ds-1
Jerome Benoit
calculus-guest at moszumanska.debian.org
Thu Feb 18 05:28:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
calculus-guest pushed a commit to branch master
in repository normaliz.
commit b9c2f6b12eee9ffa22a375d2fd918386893d4538
Author: Jerome Benoit <calculus at rezozer.net>
Date: Thu Feb 18 06:25:41 2016 +0100
Debian patch 3.1.0+ds-1
---
debian/changelog | 8 +-
debian/control | 4 +-
debian/patches/series | 2 -
.../patches/upstream-fix-gmp-ambiguous_call.patch | 70 -----
debian/patches/upstream-fix-std_exception.patch | 350 ---------------------
5 files changed, 7 insertions(+), 427 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 1fbf30d..a7a4cf6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-normaliz (3.1.0+ds-1) UNRELEASED; urgency=medium
+normaliz (3.1.0+ds-1) unstable; urgency=medium
* New upstream version.
* Debianization:
@@ -8,9 +8,11 @@ normaliz (3.1.0+ds-1) UNRELEASED; urgency=medium
- copyright, refresh;
- debian/control:
- Homepage field, update;
- - debian/watch, update.
+ - Vcs-*, secure;
+ - debian/watch, update;
+ - debian/patches, drop off upstream patches which were integrated.
- -- Jerome Benoit <calculus at rezozer.net> Thu, 18 Feb 2016 04:20:02 +0000
+ -- Jerome Benoit <calculus at rezozer.net> Thu, 18 Feb 2016 05:24:37 +0000
normaliz (3.0.0+ds-3) unstable; urgency=medium
diff --git a/debian/control b/debian/control
index ce782af..f4978b7 100644
--- a/debian/control
+++ b/debian/control
@@ -12,8 +12,8 @@ Build-Depends-Indep:
texlive-fonts-recommended, texlive-fonts-extra
Standards-Version: 3.9.6
Homepage: https://www.normaliz.uni-osnabrueck.de/
-Vcs-Git: git://anonscm.debian.org/debian-science/packages/normaliz.git
-Vcs-Browser: http://anonscm.debian.org/cgit/debian-science/packages/normaliz.git
+Vcs-Git: https://anonscm.debian.org/git/debian-science/packages/normaliz.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-science/packages/normaliz.git
Package: normaliz
Architecture: any
diff --git a/debian/patches/series b/debian/patches/series
index ed1f043..acb4d6a 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
-upstream-fix-std_exception.patch
-upstream-fix-gmp-ambiguous_call.patch
debianization.patch
debianization-documentation.patch
diff --git a/debian/patches/upstream-fix-gmp-ambiguous_call.patch b/debian/patches/upstream-fix-gmp-ambiguous_call.patch
deleted file mode 100644
index 9c36f4e..0000000
--- a/debian/patches/upstream-fix-gmp-ambiguous_call.patch
+++ /dev/null
@@ -1,70 +0,0 @@
-Description: gmp: ambiguity fix
- Fix gmp ambiguities revealed by gmp 6.1.0
- Patch extracted and adapted from uptream commits 14b874f
- by Jerome Benoit <calculus at rezozer.net>.
-Origin: upstream team
-Author: Christof Soeger <csoeger at uos.de>
-Last-Update: 2015-11-19
-
---- a/source/libnormaliz/HilbertSeries.cpp
-+++ b/source/libnormaliz/HilbertSeries.cpp
-@@ -399,7 +399,7 @@
- //divide by gcd //TODO operate directly on vector
- Matrix<mpz_class> QP(quasi_poly);
- mpz_class g = QP.matrix_gcd();
-- g = gcd(g,quasi_denom);
-+ g = libnormaliz::gcd(g,quasi_denom);
- quasi_denom /= g;
- QP.scalar_division(g);
- //we use a normed shift, so that the cylcic shift % period always yields a non-negative integer
---- a/source/libnormaliz/matrix.cpp
-+++ b/source/libnormaliz/matrix.cpp
-@@ -735,7 +735,7 @@
- Integer g=0,h;
- for (size_t i = 0; i <nr; i++) {
- h = v_gcd(elem[i]);
-- g = gcd<Integer>(g, h);
-+ g = libnormaliz::gcd<Integer>(g, h);
- if (g==1) return g;
- }
- return g;
-@@ -1766,7 +1766,7 @@
- return vector<Integer>();
- }
- }
-- Integer total_gcd =gcd(denom,v_gcd(Linear_Form)); // extract the gcd of denom and solution
-+ Integer total_gcd = libnormaliz::gcd(denom,v_gcd(Linear_Form)); // extract the gcd of denom and solution
- denom/=total_gcd;
- v_scalar_division(Linear_Form,total_gcd);
- return Linear_Form;
---- a/source/libnormaliz/sublattice_representation.cpp
-+++ b/source/libnormaliz/sublattice_representation.cpp
-@@ -213,7 +213,7 @@
-
- //check if a factor can be extraced from B //TODO necessary?
- Integer g = B.matrix_gcd();
-- g = gcd(g,c); //TODO necessary??
-+ g = libnormaliz::gcd(g,c); //TODO necessary??
- if (g > 1) {
- c /= g;
- B.scalar_division(g);
---- a/source/libnormaliz/vector_operations.cpp
-+++ b/source/libnormaliz/vector_operations.cpp
-@@ -240,7 +240,7 @@
- size_t i, size=v.size();
- Integer g=0;
- for (i = 0; i < size; i++) {
-- g=gcd(g,v[i]);
-+ g = libnormaliz::gcd(g,v[i]);
- if (g==1) {
- return 1;
- }
-@@ -255,7 +255,7 @@
- size_t i,size=v.size();
- Integer g=1;
- for (i = 0; i < size; i++) {
-- g=lcm(g,v[i]);
-+ g = libnormaliz::lcm(g,v[i]);
- if (g==0) {
- return 0;
- }
diff --git a/debian/patches/upstream-fix-std_exception.patch b/debian/patches/upstream-fix-std_exception.patch
deleted file mode 100644
index ffd14fb..0000000
--- a/debian/patches/upstream-fix-std_exception.patch
+++ /dev/null
@@ -1,350 +0,0 @@
-Description: exception_ptr: neutralize whenever not supported
- Fix non support for std::exception_ptr revealed on a armel machine (#804742).
- Patch extracted from uptream commits a11c07d and f340b56, and tested on a
- armel Debian porter by Jerome Benoit <calculus at rezozer.net>.
-Origin: upstream team
-Author: Christof Soeger <csoeger at uos.de>
-Last-Update: 2015-11-19
-
---- a/source/libnormaliz/bottom.cpp
-+++ b/source/libnormaliz/bottom.cpp
-@@ -158,7 +158,9 @@
- q_gens.push_back(gens);
- int level = 0;
-
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- // list for the simplices that could not be decomposed
- vector< Matrix<Integer> > big_simplices;
-@@ -238,7 +240,9 @@
- }
- #endif
- } // end parallel
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- // if we still have big_simplices we approx again
-
---- a/source/libnormaliz/cone_dual_mode.cpp
-+++ b/source/libnormaliz/cone_dual_mode.cpp
-@@ -284,7 +284,9 @@
- }
- }
-
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- #pragma omp parallel num_threads(3)
- {
-@@ -325,7 +327,9 @@
- Neutral_Irred.last_hyp=hyp_counter;
- }
- }
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- CandidateList<Integer> New_Positive_Irred(true),New_Negative_Irred(true),New_Neutral_Irred(true);
- New_Positive_Irred.verbose=New_Negative_Irred.verbose=New_Neutral_Irred.verbose=verbose;
-@@ -568,7 +572,9 @@
-
- } //END PARALLEL
-
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- } // steps
-
---- a/source/libnormaliz/full_cone.cpp
-+++ b/source/libnormaliz/full_cone.cpp
-@@ -333,7 +333,9 @@
- // parallel from here
-
- bool skip_remaining = false;
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- #pragma omp parallel private(jj)
- {
-@@ -660,7 +662,9 @@
- } // end !skip_remaining
- } //END parallel
-
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
- //=====================================================================
- // parallel until here
-
-@@ -709,7 +713,9 @@
- // listsize = visible.size(); // now acczmulated above
- // cout << "Pyr Level " << pyr_level << " Visible " << listsize << " Triang " << TriangulationSize << endl;
-
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- typename list< SHORTSIMPLEX<Integer> >::iterator oldTriBack = --Triangulation.end();
- #pragma omp parallel private(i)
-@@ -824,7 +830,9 @@
-
- } // parallel
-
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- // GensInCone.push_back(new_generator); // now in extend_cone
- TriSectionFirst.push_back(++oldTriBack);
-@@ -984,7 +992,9 @@
-
- deque<bool> done(old_nr_supp_hyps,false);
- bool skip_remaining;
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
- typename list< FACETDATA >::iterator hyp;
- size_t nr_done=0;
-
-@@ -1059,7 +1069,9 @@
- #endif
- } // end parallel loop over hyperplanes
-
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- if (!omp_in_parallel())
- try_offload(0);
-@@ -1109,7 +1121,9 @@
- }
- if (height != 0 && (do_triangulation || do_partial_triangulation)) {
- if(multithreaded_pyramid) {
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
- #pragma omp critical(TRIANG)
- {
- #ifndef NCATCH
-@@ -1123,7 +1137,9 @@
- }
- #endif
- } // end critical
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
- } else {
- store_key(Pyramid_key,height,0,Triangulation);
- nrTotalComparisons+=dim*dim/2;
-@@ -1503,7 +1519,9 @@
- collect_pos_supphyps(PosHyps,Zero_P,nr_pos);
-
- nrTotalComparisons+=nr_pos*nrLargeRecPyrs;
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- #pragma omp parallel
- {
-@@ -1525,7 +1543,9 @@
- #endif
- }
- } // parallel
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- LargeRecPyrs.clear();
- }
-@@ -1606,7 +1626,9 @@
- typename list<vector<key_t> >::iterator p;
- size_t ppos;
- bool skip_remaining;
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- while (nrPyramids[level] > eval_down_to) {
-
-@@ -1649,7 +1671,9 @@
- }
- #endif
- } //end parallel for
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- // remove done pyramids
- p = Pyramids[level].begin();
-@@ -1761,7 +1785,9 @@
-
- long long nr_pos=0; long long nr_neg=0;
- vector<Integer> L;
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- size_t lpos=0;
- #pragma omp parallel for private(L,scalar_product) firstprivate(lpos,l) reduction(+: nr_pos, nr_neg)
-@@ -1788,7 +1814,9 @@
- }
- #endif
- } //end parallel for
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- if(!is_new_generator)
- continue;
-@@ -2240,7 +2268,9 @@
-
- deque<bool> done(TriangulationSize,false);
- bool skip_remaining;
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- do{ // allows multiple run of loop below in case of interruption for the update of reducers
-
-@@ -2294,7 +2324,9 @@
- }
- Results[tn].transfer_candidates();
- } // end parallel
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- if (verbose)
- verboseOutput() << endl;
---- a/source/libnormaliz/simplex.cpp
-+++ b/source/libnormaliz/simplex.cpp
-@@ -735,7 +735,9 @@
- progess_report=1;
-
- bool skip_remaining;
-+#ifndef NCATCH
- std::exception_ptr tmp_exception;
-+#endif
-
- deque<bool> done(actual_nr_blocks,false);
-
-@@ -777,7 +779,9 @@
-
- } // parallel
-
-+#ifndef NCATCH
- if (!(tmp_exception == 0)) std::rethrow_exception(tmp_exception);
-+#endif
-
- if(skip_remaining){
-
---- a/source/CMakeLists.txt
-+++ b/source/CMakeLists.txt
-@@ -79,26 +79,6 @@
- SET (CXX_WARNING_FLAGS "-Wall -pedantic")
- SET (CXX_OPTIMIZATION_FLAGS "-O3")
- ENDIF ()
--SET (NMZ_OPENMP "YES" CACHE BOOL "use openmp")
--IF (NMZ_OPENMP)
-- FIND_PACKAGE(OpenMP)
-- IF (OPENMP_FOUND)
-- SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-- SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-- SET (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
-- ELSE (OPENMP_FOUND)
-- MESSAGE(STATUS "Not using OpenMP, compiler does not support it")
-- SET (NMZ_OPENMP "NO" CACHE BOOL "use openmp" FORCE)
-- ENDIF(OPENMP_FOUND)
--ENDIF (NMZ_OPENMP)
--IF (NOT NMZ_OPENMP)
-- SET (CXX_WARNING_FLAGS "${CXX_WARNING_FLAGS} -Wno-unknown-pragmas")
--ENDIF (NOT NMZ_OPENMP)
--
--# add compiler flags
--SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_WARNING_FLAGS} ${CXX_OPTIMIZATION_FLAGS}")
--
--INCLUDE_DIRECTORIES(.)
-
- IF (NOT MSVC)
- include(CheckCXXCompilerFlag)
-@@ -119,6 +99,36 @@
- ENDIF ()
- ENDIF()
-
-+
-+SET (NMZ_OPENMP "YES" CACHE BOOL "use openmp")
-+IF (NMZ_OPENMP)
-+ FIND_PACKAGE(OpenMP)
-+ IF (NOT OPENMP_FOUND)
-+ MESSAGE(STATUS "Not using OpenMP, compiler does not support it")
-+ SET (NMZ_OPENMP "NO" CACHE BOOL "use openmp" FORCE)
-+ ENDIF(NOT OPENMP_FOUND)
-+ENDIF (NMZ_OPENMP)
-+IF (NMZ_OPENMP)
-+ include("${CMAKE_SOURCE_DIR}/cmake/detect_features.cmake")
-+ NMZ_CHECK_FOR_EXCEPTION_PTR()
-+ IF (NOT HAVE_EXCEPTION_PTR)
-+ MESSAGE(STATUS "Not using OpenMP, compiler does not support std::exception_ptr and std::rethrow")
-+ SET (NMZ_OPENMP "NO" CACHE BOOL "use openmp" FORCE)
-+ ENDIF (NOT HAVE_EXCEPTION_PTR)
-+ENDIF (NMZ_OPENMP)
-+IF (NMZ_OPENMP)
-+ SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-+ SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-+ SET (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
-+ELSE (NMZ_OPENMP)
-+ SET (CXX_WARNING_FLAGS "${CXX_WARNING_FLAGS} -Wno-unknown-pragmas")
-+ENDIF (NMZ_OPENMP)
-+
-+# add compiler flags
-+SET (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX_WARNING_FLAGS} ${CXX_OPTIMIZATION_FLAGS}")
-+
-+INCLUDE_DIRECTORIES(.)
-+
- # handle static compilation
- SET (NMZ_BUILD_STATIC "NO" CACHE BOOL "build normaliz statically")
- IF (NMZ_BUILD_STATIC)
---- /dev/null
-+++ b/source/cmake/detect_features.cmake
-@@ -0,0 +1,35 @@
-+###############################################################################
-+# Check for the presence of std::exception_ptr and std::rethrow
-+macro(NMZ_CHECK_FOR_EXCEPTION_PTR)
-+
-+ # We need to check whether the compiler supports the rethrowing mechanism
-+ include(CheckCXXSourceRuns)
-+ # at least the c++11 flag needs to be set
-+ set(CMAKE_REQUIRED_FLAGS "${CMAKE_CXX_FLAGS}")
-+ check_cxx_source_runs("
-+ #include <iostream>
-+ #include <exception>
-+ #include <stdexcept>
-+
-+ int main () {
-+ std::exception_ptr tmp_exception;
-+ try {
-+ throw std::overflow_error(\"some overflow exception\");
-+ } catch(const std::exception& e) {
-+ tmp_exception = std::current_exception();
-+ std::cout << \"exception caught, but continuing...\" << std::endl;
-+ }
-+
-+ std::cout << \"(after exception)\" << std::endl;
-+
-+ try {
-+ if (tmp_exception != std::exception_ptr()) std::rethrow_exception(tmp_exception);
-+ } catch (const std::exception& e) {
-+ std::cout << \"exception caught again \" << e.what() << std::endl;
-+ }
-+ return 0;
-+ }
-+"
-+ HAVE_EXCEPTION_PTR)
-+
-+endmacro(NMZ_CHECK_FOR_EXCEPTION_PTR)
--
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