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gentoo-overlay/sci-biology/consed/files/consed-29-fix-c++14.patch

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Fix building with C++14:
* Add 'noexcept(false)' to throwing destructors in C++11 mode
* Properly guard C declarations with extern "C" scopes
* Avoid erroneous overloaded suffix operator errors, due to missing spaces
* Add explicit casts to avoid -Wnarrowing errors
* Add 'this->' for dependent identifiers in derived class templates,
previously required -fpermissive
--- a/bvAlignedReads.cpp
+++ b/bvAlignedReads.cpp
@@ -126,7 +126,11 @@
}
-bvAlignedReads :: ~bvAlignedReads() {
+bvAlignedReads :: ~bvAlignedReads()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
+{
assert( pBamView_->aBVAlignedReads_.remove( this ) );
--- a/bvAlignedReads.h
+++ b/bvAlignedReads.h
@@ -81,7 +81,11 @@
const FileName& filReferenceSequenceFile,
bamView* pBamView );
- ~bvAlignedReads();
+ ~bvAlignedReads()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
+ ;
bool operator==( const bvAlignedReads& myBVAlignedReads ) const {
return( this == &myBVAlignedReads );
--- a/chromatData.h
+++ b/chromatData.h
@@ -58,6 +58,9 @@
#ifndef CHROMATDATA_DEFINED
#define CHROMATDATA_DEFINED
+#ifdef __cplusplus
+extern "C" {
+#endif
#ifndef FLOAT
#define FLOAT double
@@ -131,4 +134,8 @@
int freeChromatData();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/compareContigs.cpp
+++ b/compareContigs.cpp
@@ -126,6 +126,9 @@
compareContigs :: ~compareContigs()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
{
if ( !bCalledFromMakeJoins_ ) {
--- a/compareContigs.h
+++ b/compareContigs.h
@@ -137,7 +137,11 @@
compareContigs( ContigWin* pContigWin, const int nConsPos1);
compareContigs(); // for assemblyView
- ~compareContigs();
+ ~compareContigs()
+#if __cplusplus >= 201103L
+ noexcept(false)
+#endif
+ ;
// this makes RWTPtrOrderedVector in ConsEd happy
bool operator==( const compareContigs& compC ) const {
--- a/filePopupAndGetAceFilename.cpp
+++ b/filePopupAndGetAceFilename.cpp
@@ -317,7 +317,7 @@
struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) );
strftime( szDateTime, nDateTimeSize,
- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y",
+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y",
pTM );
RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile);
@@ -620,7 +620,7 @@
struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) );
strftime( szDateTime, nDateTimeSize,
- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y",
+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y",
pTM );
RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile);
--- a/findTraceExtrema.h
+++ b/findTraceExtrema.h
@@ -44,8 +44,15 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
int findTraceExtrema( ChromatData *chromatData );
+#ifdef __cplusplus
+}
+#endif
#endif
--- a/makeUpper.h
+++ b/makeUpper.h
@@ -42,6 +42,14 @@
#ifndef MAKEUPPER_INCLUDED
#define MAKEUPPER_INCLUDED
+#ifdef __cplusplus
+extern "C" {
+#endif
+
void makeUpper( char* szStringOfMixedCase );
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/nextPhredPipeline.cpp
+++ b/nextPhredPipeline.cpp
@@ -476,7 +476,7 @@
void nextPhredPipeline :: openAndLockControlFile() {
- nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR );
+ nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600);
if ( nFDControlFile_ == -1 ) {
THROW_FILE_ERROR( filControlFile_ );
}
--- a/readABI.h
+++ b/readABI.h
@@ -56,10 +56,18 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
#ifdef ANSI_C
ChromatData *readABI( char *fn, int *status );
#else
ChromatData *readABI();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/readData.h
+++ b/readData.h
@@ -44,6 +44,14 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
ChromatData *readData( char *filename, int* status );
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/readESD.h
+++ b/readESD.h
@@ -53,6 +53,10 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
typedef unsigned int4 DWORD;
typedef unsigned char TCHAR;
typedef char BYTE;
@@ -187,5 +191,7 @@
ChromatData *readESD();
#endif
-
+#ifdef __cplusplus
+}
+#endif
--- a/readSCF.h
+++ b/readSCF.h
@@ -56,6 +56,10 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
/* ---- Constants ---- */
#define SCF_MAGIC (((((int4)'.'<<8)+(int4)'s'<<8)+(int4)'c'<<8)+(int4)'f')
#define scale(V,OLDMAX,NEWMAX) (int2)( (FLOAT) V * (FLOAT) NEWMAX / (FLOAT) OLDMAX )
@@ -144,4 +148,8 @@
int readSCF3();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/readsense_bitmaps.h
+++ b/readsense_bitmaps.h
@@ -56,10 +56,10 @@
static const int forward_bitmap_height = 19;
static char forward_bitmap_bits[] = {
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
- 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00,
- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0xff, 0x3f, 0x00, 0xf8, 0xff, 0xff, 0x07,
- 0xf8, 0xff, 0xff, 0x0f, 0xf8, 0xff, 0xff, 0x07, 0xf8, 0xff, 0x1f, 0x00,
- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00,
+ 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00,
+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, (char)0xff, 0x3f, 0x00, (char)0xf8, (char)0xff, (char)0xff, 0x07,
+ (char)0xf8, (char)0xff, (char)0xff, 0x0f, (char)0xf8, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, 0x1f, 0x00,
+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
@@ -67,10 +67,10 @@
static const int reverse_bitmap_height = 19;
static char reverse_bitmap_bits[] = {
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
- 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, 0xf8, 0x07,
- 0x00, 0xc0, 0xff, 0x07, 0x00, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07,
- 0xfc, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, 0x00, 0xfe, 0xff, 0x07,
- 0x00, 0xc0, 0xff, 0x07, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x00, 0x07,
+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, (char)0xf8, 0x07,
+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07,
+ (char)0xfc, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, 0x00, (char)0xfe, (char)0xff, 0x07,
+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x00, 0x07,
0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
0x00, 0x00, 0x00, 0x00};
--- a/readType.h
+++ b/readType.h
@@ -56,11 +56,19 @@
#include "chromatData.h"
+#ifdef __cplusplus
+extern "C" {
+#endif
+
#ifdef ANSI_C
int readType( char *filename );
#else
int readType();
#endif
+#ifdef __cplusplus
+}
+#endif
+
#endif
--- a/rwtptrsortedvector.h
+++ b/rwtptrsortedvector.h
@@ -57,7 +57,6 @@
#ifdef USE_USING_IN_PUBLIC_TEMPLATE_CLASSES
using RWTPtrOrderedVector<TP>::nCurrentLength_;
using RWTPtrOrderedVector<TP>::isEmpty;
- using RWTPtrOrderedVector<TP>::nCurrentLength_;
using RWTPtrOrderedVector<TP>::length;
using RWTPtrOrderedVector<TP>::ppArray_;
using RWTPtrOrderedVector<TP>::data;
@@ -84,7 +83,7 @@
if ( nInsertBeforeIndex == RW_NPOS )
nInsertBeforeIndex = nCurrentLength_;
- insertAt( nInsertBeforeIndex, pVal );
+ this->insertAt( nInsertBeforeIndex, pVal );
}
// don't copy this. copy mbtValOrderedVectorOfRWCString's method instead
--- a/rwtvalsortedvector.h
+++ b/rwtvalsortedvector.h
@@ -74,7 +74,7 @@
if ( nPos == RW_NPOS )
nPos = nCurrentLength_;
- insertAt( nPos, val );
+ this->insertAt( nPos, val );
}
--- a/rwUtil.h
+++ b/rwUtil.h
@@ -51,6 +51,10 @@
*|***************************************************************************|*
*/
+#ifdef __cplusplus
+extern "C" {
+#endif
+
#ifdef ANSI_C
int2 inSwpSint2( char *ptr );
int4 inSwpSint4( char *ptr );
@@ -97,3 +101,6 @@
int writeUint4();
#endif
+#ifdef __cplusplus
+}
+#endif
--- a/soGetDateTime.cpp
+++ b/soGetDateTime.cpp
@@ -62,13 +62,13 @@
else if ( nFormat == nDotInMiddle ) {
strftime( szDateTime,
nDateTimeSize,
- "%y%m%d."quote(%H)quote(%M)quote(%S),
+ "%y%m%d." quote(%H)quote(%M)quote(%S),
localtime( &timee ) );
}
else {
strftime( szDateTime,
nDateTimeSize,
- "%y%m%d:"quote(%H)quote(%M)quote(%S),
+ "%y%m%d:" quote(%H)quote(%M)quote(%S),
localtime( &timee ) );
}
--- a/szGetTime.h
+++ b/szGetTime.h
@@ -42,9 +42,15 @@
#ifndef szGetTime_included
#define szGetTime_included
-char *szGetTime();
+#ifdef __cplusplus
+extern "C" {
+#endif
+char *szGetTime();
+#ifdef __cplusplus
+}
+#endif
#endif
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