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