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commit: b81e4c632efa6b2d53c8750b84deb2b315c86dd0 |
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Author: Sergei Trofimovich <slyfox <AT> inbox <DOT> ru> |
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AuthorDate: Fri Sep 23 13:16:56 2016 +0000 |
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Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de> |
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CommitDate: Fri Sep 23 13:16:56 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b81e4c63 |
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|
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sci-biology/abyss: tweak for gcc-6, bug #594254 (#681) |
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|
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Build failed as: |
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``` |
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In file included from AssemblyAlgorithms.cpp:4:0: |
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../DataLayer/FastaReader.h: In member function ‘FastaReader::operator void*() const’: |
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../DataLayer/FastaReader.h:49:35: error: cannot convert ‘std::istream {aka std::basic_istream<char>}’ to ‘void*’ ... |
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operator void*() const { return m_in; } |
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^~~~ |
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``` |
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|
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In the following source: |
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|
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```c++ |
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static bool existFile(const char* f) |
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{ |
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ifstream file(f); |
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return file; |
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} |
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|
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``` |
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|
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c++98 provides file->operator void*() |
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c++11 provides file->explicit operator bool() |
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|
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Hence the failure on c++11. |
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|
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The change adds explicit casts around istream. |
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|
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Reported-by: Toralf Förster |
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Bug: https://bugs.gentoo.org/594254 |
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|
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Package-Manager: portage-2.3.0 |
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|
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sci-biology/abyss/abyss-1.9.0.ebuild | 1 + |
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sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch | 34 +++++++++++++++++++++++++ |
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2 files changed, 35 insertions(+) |
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|
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diff --git a/sci-biology/abyss/abyss-1.9.0.ebuild b/sci-biology/abyss/abyss-1.9.0.ebuild |
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index b2de141..c32b477 100644 |
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--- a/sci-biology/abyss/abyss-1.9.0.ebuild |
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+++ b/sci-biology/abyss/abyss-1.9.0.ebuild |
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@@ -33,6 +33,7 @@ DEPEND="${RDEPEND} |
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|
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PATCHES=( |
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"${FILESDIR}"/${P}-ac_prog_ar.patch |
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+ "${FILESDIR}"/${P}-gcc-6.patch |
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) |
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|
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src_prepare() { |
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|
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diff --git a/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch |
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new file mode 100644 |
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index 0000000..49a30f9 |
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--- /dev/null |
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+++ b/sci-biology/abyss/files/abyss-1.9.0-gcc-6.patch |
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@@ -0,0 +1,34 @@ |
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+diff --git a/DataBase/db-csv.cc b/DataBase/db-csv.cc |
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+index 05cac19..48e3b44 100644 |
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+--- a/DataBase/db-csv.cc |
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++++ b/DataBase/db-csv.cc |
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+@@ -18,11 +18,11 @@ static const char TABLE_LIST[] = |
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+ typedef vector<string> vs; |
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+ |
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+ static bool existFile(const char* f) |
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+ { |
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+ ifstream file(f); |
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+- return file; |
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++ return bool(file); |
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+ } |
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+ |
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+ template <typename D> |
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+ static bool existTable( |
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+ D& db, const string& t) |
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+diff --git a/SimpleGraph/SimpleGraph.cpp b/SimpleGraph/SimpleGraph.cpp |
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+index 373ec70..0a9ebd3 100644 |
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+--- a/SimpleGraph/SimpleGraph.cpp |
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++++ b/SimpleGraph/SimpleGraph.cpp |
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+@@ -645,11 +645,11 @@ static void* worker(void* pArg) |
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+ for (;;) { |
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+ /** Lock the input stream. */ |
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+ static pthread_mutex_t inMutex = PTHREAD_MUTEX_INITIALIZER; |
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+ pthread_mutex_lock(&inMutex); |
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+ EstimateRecord er; |
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+- bool good = (*arg.in) >> er; |
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++ bool good = bool((*arg.in) >> er); |
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+ pthread_mutex_unlock(&inMutex); |
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+ if (!good) |
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+ break; |
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+ |
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+ // Flip the anterior distance estimates. |
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