path: root/sci-biology/consed/files/consed-29-fix-c++14.patch

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