[med-svn] r17292 - in trunk/packages/gentle/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Jun 25 11:55:28 UTC 2014
Author: tille
Date: 2014-06-25 11:55:27 +0000 (Wed, 25 Jun 2014)
New Revision: 17292
Added:
trunk/packages/gentle/trunk/debian/patches/fix-format-codes.patch
trunk/packages/gentle/trunk/debian/patches/wx3.0-compat.patch
Modified:
trunk/packages/gentle/trunk/debian/README.source
trunk/packages/gentle/trunk/debian/changelog
trunk/packages/gentle/trunk/debian/control
trunk/packages/gentle/trunk/debian/manpages
trunk/packages/gentle/trunk/debian/patches/series
trunk/packages/gentle/trunk/debian/rules
Log:
Apply patch by Olly Betts <olly at survex.com> to enable update to use wxwidgets3.0 (Bug #750906)
Modified: trunk/packages/gentle/trunk/debian/README.source
===================================================================
--- trunk/packages/gentle/trunk/debian/README.source 2014-06-25 06:12:35 UTC (rev 17291)
+++ trunk/packages/gentle/trunk/debian/README.source 2014-06-25 11:55:27 UTC (rev 17292)
@@ -11,3 +11,5 @@
remove_tinyxml.patch - small changes to Makefile.am since tinyurl is now gone
remove_clustalw.patch - small changes to Makefile.am since clustalw is now gone
+
+
Modified: trunk/packages/gentle/trunk/debian/changelog
===================================================================
--- trunk/packages/gentle/trunk/debian/changelog 2014-06-25 06:12:35 UTC (rev 17291)
+++ trunk/packages/gentle/trunk/debian/changelog 2014-06-25 11:55:27 UTC (rev 17292)
@@ -1,3 +1,12 @@
+gentle (1.9+cvs20100605+dfsg1-2.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Update to use wxWidgets 3.0 (new patch wx3.0-compat.patch).
+ * Fix mismatching format codes in printf and scanf (new patch
+ fix-format-codes.patch).
+
+ -- Olly Betts <olly at survex.com> Sun, 08 Jun 2014 18:40:54 +1200
+
gentle (1.9+cvs20100605+dfsg1-2) unstable; urgency=low
* debian/control:
Modified: trunk/packages/gentle/trunk/debian/control
===================================================================
--- trunk/packages/gentle/trunk/debian/control 2014-06-25 06:12:35 UTC (rev 17291)
+++ trunk/packages/gentle/trunk/debian/control 2014-06-25 11:55:27 UTC (rev 17292)
@@ -6,7 +6,7 @@
Priority: optional
Build-Depends: debhelper (>= 9),
autotools-dev,
- libwxgtk2.8-dev,
+ libwxgtk3.0-dev,
libtinyxml-dev,
libmysqlclient-dev,
libsqlite3-dev,
Modified: trunk/packages/gentle/trunk/debian/manpages
===================================================================
--- trunk/packages/gentle/trunk/debian/manpages 2014-06-25 06:12:35 UTC (rev 17291)
+++ trunk/packages/gentle/trunk/debian/manpages 2014-06-25 11:55:27 UTC (rev 17292)
@@ -1 +1 @@
-debian/extra/GENtle.1
+debian/GENtle.1
Added: trunk/packages/gentle/trunk/debian/patches/fix-format-codes.patch
===================================================================
--- trunk/packages/gentle/trunk/debian/patches/fix-format-codes.patch (rev 0)
+++ trunk/packages/gentle/trunk/debian/patches/fix-format-codes.patch 2014-06-25 11:55:27 UTC (rev 17292)
@@ -0,0 +1,159 @@
+Description: Fix printf and scanf format codes to match the types actually passed
+Author: Olly Betts <olly at survex.com>
+Last-Update: 2014-06-08
+
+--- a/ureadseq.c
++++ b/ureadseq.c
+@@ -1344,7 +1344,7 @@
+ for (i=0; i < *skiplines; i++) ReadOneLine(sp);
+ nlines= 0;
+ ReadOneLine(sp);
+- sscanf( sp, "%d%d", &nspp, &nlen);
++ sscanf( sp, "%ld%ld", &nspp, &nlen);
+ ReadOneLine(sp); /* 1st seq line */
+ for (ps= sp+10, ilen=0; *ps!=0; ps++) if (isprint(*ps)) ilen++;
+
+@@ -1590,7 +1590,7 @@
+ seqname[l] = 0;
+
+ sscanf( seqname, "%30s", idword);
+- sprintf(numform, "%d", seqlen);
++ sprintf(numform, "%ld", seqlen);
+ numwidth= strlen(numform)+1;
+ nameform[0]= '\0';
+
+@@ -1619,8 +1619,8 @@
+
+ case kOlsen: /* Olsen seq. editor takes plain nucs OR Genbank */
+ case kGenBank:
+- fprintf(outf,"LOCUS %s %d bp\n", idword, seqlen);
+- fprintf(outf,"DEFINITION %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
++ fprintf(outf,"LOCUS %s %ld bp\n", idword, seqlen);
++ fprintf(outf,"DEFINITION %s, %ld bases, %lX checksum.\n", seqname, seqlen, checksum);
+ /* fprintf(outf,"ACCESSION %s\n", accnum); */
+ fprintf(outf,"ORIGIN \n");
+ spacer = 11;
+@@ -1634,7 +1634,7 @@
+ /* somewhat like genbank... \\\*/
+ /* fprintf(outf,"\\\\\\\n"); << only at top of file, not each entry... */
+ fprintf(outf,"ENTRY %s \n", idword);
+- fprintf(outf,"TITLE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
++ fprintf(outf,"TITLE %s, %ld bases, %lX checksum.\n", seqname, seqlen, checksum);
+ /* fprintf(outf,"ACCESSION %s\n", accnum); */
+ fprintf(outf,"SEQUENCE \n");
+ numwidth = 7;
+@@ -1644,7 +1644,7 @@
+ strcpy(endstr, "\n///");
+ /* run a top number line for PIR */
+ for (j=0; j<numwidth; j++) fputc(' ',outf);
+- for (j= 5; j<=width; j += 5) fprintf(outf,"%10d",j);
++ for (j= 5; j<=width; j += 5) fprintf(outf,"%10ld",j);
+ fputc('\n',outf);
+ linesout += 5;
+ break;
+@@ -1654,7 +1654,7 @@
+ fprintf(outf,">P1;%s\n", idword);
+ else
+ fprintf(outf,">DL;%s\n", idword);
+- fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
++ fprintf(outf,"%s, %ld bases, %lX checksum.\n", seqname, seqlen, checksum);
+ spacer = 11;
+ strcpy(endstr,"*\n");
+ linesout += 3;
+@@ -1663,8 +1663,8 @@
+ case kEMBL:
+ fprintf(outf,"ID %s\n", idword);
+ /* fprintf(outf,"AC %s\n", accnum); */
+- fprintf(outf,"DE %s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
+- fprintf(outf,"SQ %d BP\n", seqlen);
++ fprintf(outf,"DE %s, %ld bases, %lX checksum.\n", seqname, seqlen, checksum);
++ fprintf(outf,"SQ %ld BP\n", seqlen);
+ strcpy(endstr, "\n//"); /* 11Oct90: bug fix*/
+ tab = 4; /** added 31jan91 */
+ spacer = 11; /** added 31jan91 */
+@@ -1675,7 +1675,7 @@
+ case kGCG:
+ fprintf(outf,"%s\n", seqname);
+ /* fprintf(outf,"ACCESSION %s\n", accnum); */
+- fprintf(outf," %s Length: %d (today) Check: %d ..\n", idword, seqlen, checksum);
++ fprintf(outf," %s Length: %ld (today) Check: %lX ..\n", idword, seqlen, checksum);
+ spacer = 11;
+ numleft = true;
+ strcpy(endstr, "\n"); /* this is insurance to help prevent misreads at eof */
+@@ -1684,13 +1684,13 @@
+
+ case kStrider: /* ?? map ?*/
+ fprintf(outf,"; ### from DNA Strider ;-)\n");
+- fprintf(outf,"; DNA sequence %s, %d bases, %X checksum.\n;\n", seqname, seqlen, checksum);
++ fprintf(outf,"; DNA sequence %s, %ld bases, %lX checksum.\n;\n", seqname, seqlen, checksum);
+ strcpy(endstr, "\n//");
+ linesout += 3;
+ break;
+
+ case kFitch:
+- fprintf(outf,"%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
++ fprintf(outf,"%s, %ld bases, %lX checksum.\n", seqname, seqlen, checksum);
+ spacer = 4;
+ width = 60;
+ linesout += 1;
+@@ -1721,7 +1721,7 @@
+ fprintf(outf," id { local id %d },\n", gPretty.atseq);
+ fprintf(outf," descr { title \"%s\" },\n", seqid);
+ fprintf(outf," inst {\n");
+- fprintf(outf," repr raw, mol %s, length %d, topology linear,\n", cp, seqlen);
++ fprintf(outf," repr raw, mol %s, length %ld, topology linear,\n", cp, seqlen);
+ fprintf(outf," seq-data\n");
+ if (seqtype == kAmino)
+ fprintf(outf," iupacaa \"");
+@@ -1743,7 +1743,7 @@
+ tab = 0; /* 1; */
+ /* strcpy(endstr,";\nend;"); << this is end of all seqs.. */
+ /* do a header comment line for paup */
+- fprintf(outf,"[Name: %-16s Len:%6d Check: %8X]\n", idword, seqlen, checksum);
++ fprintf(outf,"[Name: %-16s Len:%6ld Check: %8lX]\n", idword, seqlen, checksum);
+ linesout += 1;
+ break;
+
+@@ -1760,13 +1760,13 @@
+ tab = gPretty.tab;
+ /* also add rtf formatting w/ font, size, style */
+ if (gPretty.nametop) {
+- fprintf(outf,"Name: %-16s Len:%6d Check: %8X\n", idword, seqlen, checksum);
++ fprintf(outf,"Name: %-16s Len:%6ld Check: %8lX\n", idword, seqlen, checksum);
+ linesout++;
+ }
+ break;
+
+ case kMSF:
+- fprintf(outf," Name: %-16s Len:%6d Check: %5d Weight: 1.00\n",
++ fprintf(outf," Name: %-16s Len:%6ld Check: %5ld Weight: 1.00\n",
+ idword, seqlen, checksum);
+ linesout++;
+ nameleft= true;
+@@ -1778,7 +1778,7 @@
+ break;
+
+ case kIG:
+- fprintf(outf,";%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
++ fprintf(outf,";%s, %ld bases, %lX checksum.\n", seqname, seqlen, checksum);
+ fprintf(outf,"%s\n", idword);
+ strcpy(endstr,"1"); /* == linear dna */
+ linesout += 2;
+@@ -1787,7 +1787,7 @@
+ default :
+ case kZuker: /* don't attempt Zuker's ftn format */
+ case kPearson:
+- fprintf(outf,">%s, %d bases, %X checksum.\n", seqname, seqlen, checksum);
++ fprintf(outf,">%s, %ld bases, %lX checksum.\n", seqname, seqlen, checksum);
+ linesout += 1;
+ break;
+ }
+@@ -1828,7 +1828,7 @@
+ s[l++] = ' ';
+ }
+ if (l1 % 10 == 1 || l1 == width) {
+- if (numline==1) fprintf(outf,"%-9d ",i+1);
++ if (numline==1) fprintf(outf,"%-9ld ",i+1);
+ s[l++]= '|'; /* == put a number here */
+ }
+ else s[l++]= ' ';
Modified: trunk/packages/gentle/trunk/debian/patches/series
===================================================================
--- trunk/packages/gentle/trunk/debian/patches/series 2014-06-25 06:12:35 UTC (rev 17291)
+++ trunk/packages/gentle/trunk/debian/patches/series 2014-06-25 11:55:27 UTC (rev 17292)
@@ -1,4 +1,5 @@
forward_slashes.patch
remove_tinyxml.patch
remove_clustalw.patch
-remove_old_sqlite.patch
+wx3.0-compat.patch
+fix-format-codes.patch
Added: trunk/packages/gentle/trunk/debian/patches/wx3.0-compat.patch
===================================================================
--- trunk/packages/gentle/trunk/debian/patches/wx3.0-compat.patch (rev 0)
+++ trunk/packages/gentle/trunk/debian/patches/wx3.0-compat.patch 2014-06-25 11:55:27 UTC (rev 17292)
@@ -0,0 +1,310 @@
+Description: Fix to work with wxWidgets 3.0
+Author: Olly Betts <olly at survex.com>
+Last-Update: 2014-06-08
+
+--- a/TClone.h
++++ b/TClone.h
+@@ -68,7 +68,7 @@
+ void parseLines ( wxArrayString &v , char *t , long l ) ; ///< Breaks text into lines
+ void separateNames ( wxString &s1 , wxString &s2 ) ; ///< ???
+ int cmp ( const wxString &s1 , const wxString &s2 ) ; ///< String comparison
+- int a2i ( wxString &s ) { return atoi ( (char*) s.c_str() ) ; } ///< Converts string to integer
++ int a2i ( wxString &s ) { return atoi ( (const char*) s.c_str() ) ; } ///< Converts string to integer
+
+ wxString filename , name , sequence , description ;
+ int size ; ///< Sequence length
+--- a/TXMLfile.cpp
++++ b/TXMLfile.cpp
+@@ -221,7 +221,7 @@
+ {
+ char u[100] ;
+ sprintf ( u , "short_itemtype%d" , i.getType() ) ;
+- i.name = wxString ( txt(u) , wxConvUTF8 ) ;
++ i.name = txt(u);
+ wxString d2 = i.desc ;
+ int k = d2.find ( _T("\n") ) ;
+ if ( k > -1 ) d2.erase ( k ) ;
+--- a/TVirtualGel.cpp
++++ b/TVirtualGel.cpp
+@@ -8,7 +8,6 @@
+ BEGIN_EVENT_TABLE(TVirtualGel, MyChildBase)
+ EVT_CLOSE(ChildBase::OnClose)
+ EVT_SET_FOCUS(ChildBase::OnFocus)
+- EVT_SIZE(TVirtualGel::OnSize)
+
+ EVT_CHOICE(VG_PERCENT,TVirtualGel::OnPercent)
+ EVT_CHOICE(VG_MARKER,TVirtualGel::OnMarker)
+--- a/MyChild.cpp
++++ b/MyChild.cpp
+@@ -1141,7 +1141,7 @@
+ {
+ MyFrame *f = myapp()->frame ; //(MyFrame*) GetParent() ;
+ TRestrictionEditor ed ( f , _T("") , wxPoint(-1,-1) , wxSize(600,400) ,
+- wxDEFAULT_DIALOG_STYLE|wxCENTRE|wxDIALOG_MODAL);
++ wxDEFAULT_DIALOG_STYLE|wxCENTRE);
+ ed.pre = s ;
+ ed.cocktail = vec->cocktail ;
+ ed.remoteCocktail = &vec->cocktail ;
+--- a/TRestrictionEditor.cpp
++++ b/TRestrictionEditor.cpp
+@@ -376,7 +376,7 @@
+ wxString s = el->GetItemText ( i ) ;
+ TRestrictionEnzyme *e = myapp()->frame->LS->getRestrictionEnzyme ( s ) ;
+ TEnzymeDialog ed ( this , s , wxPoint(-1,-1) , wxSize(600,400) ,
+- wxDEFAULT_DIALOG_STYLE|wxCENTRE|wxDIALOG_MODAL ) ;
++ wxDEFAULT_DIALOG_STYLE|wxCENTRE ) ;
+ ed.initme ( e , true ) ;
+ ed.ShowModal() ;
+ }
+--- a/TVectorEditor.cpp
++++ b/TVectorEditor.cpp
+@@ -400,7 +400,7 @@
+ e->setCut ( 0 ) ;
+ e->setOverlap ( 0 ) ;
+ TEnzymeDialog ed ( this , txt("t_new_protease") , wxPoint(-1,-1) , wxSize(600,400) ,
+- wxDEFAULT_DIALOG_STYLE|wxCENTRE|wxDIALOG_MODAL ) ;
++ wxDEFAULT_DIALOG_STYLE|wxCENTRE ) ;
+ ed.initme ( e ) ;
+ if ( ed.ShowModal() == wxID_OK )
+ {
+--- a/TVectorEditorEnzymes.cpp
++++ b/TVectorEditorEnzymes.cpp
+@@ -116,7 +116,7 @@
+ wxString s = lb->GetString ( vi[k] ) ;
+ TRestrictionEnzyme *e = myapp()->frame->LS->getRestrictionEnzyme ( s ) ;
+ TEnzymeDialog ed ( this , s , wxPoint(-1,-1) , wxSize(600,400) ,
+- wxDEFAULT_DIALOG_STYLE|wxCENTRE|wxDIALOG_MODAL ) ;
++ wxDEFAULT_DIALOG_STYLE|wxCENTRE ) ;
+ ed.initme ( e ) ;
+ if ( ed.ShowModal() == wxID_OK )
+ {
+@@ -149,7 +149,7 @@
+ wxString s = lb->GetString ( vi[0] ) ;
+ TRestrictionEnzyme *e = myapp()->frame->LS->getRestrictionEnzyme ( s ) ;
+ TEnzymeDialog ed ( this , s , wxPoint(-1,-1) , wxSize(600,400) ,
+- wxDEFAULT_DIALOG_STYLE|wxCENTRE|wxDIALOG_MODAL ) ;
++ wxDEFAULT_DIALOG_STYLE|wxCENTRE ) ;
+ ed.initme ( e ) ;
+ ed.ShowModal() ;
+ }
+@@ -335,7 +335,7 @@
+ e->setCut ( 0 ) ;
+ e->setOverlap ( 0 ) ;
+ TEnzymeDialog ed ( this , txt("t_new_enzyme") , wxPoint(-1,-1) , wxSize(600,400) ,
+- wxDEFAULT_DIALOG_STYLE|wxCENTRE|wxDIALOG_MODAL ) ;
++ wxDEFAULT_DIALOG_STYLE|wxCENTRE ) ;
+ ed.initme ( e ) ;
+ if ( ed.ShowModal() == wxID_OK )
+ {
+--- a/AminoAcids.cpp
++++ b/AminoAcids.cpp
+@@ -656,7 +656,7 @@
+ {
+ if ( curDisplay )
+ {
+- h1->Remove ( curDisplay ) ;
++ h1->Detach ( curDisplay ) ;
+ delete curDisplay ;
+ }
+ curDisplay = NULL ;
+--- a/CGview.cpp
++++ b/CGview.cpp
+@@ -111,7 +111,7 @@
+
+ void CGdialog::OnChooseJar ( wxCommandEvent &event )
+ {
+- wxFileDialog d ( this , txt("t_cgview_choose_jar") , cgviewapp->GetLabel() , _T("") , _T("cgview.jar|cgview.jar") , wxOPEN ) ;
++ wxFileDialog d ( this , txt("t_cgview_choose_jar") , cgviewapp->GetLabel() , _T("") , _T("cgview.jar|cgview.jar") , wxFD_OPEN ) ;
+ if ( wxID_OK != d.ShowModal() ) return ;
+ cgviewapp->SetLabel ( d.GetPath() ) ;
+ }
+--- a/ManageDatabase.cpp
++++ b/ManageDatabase.cpp
+@@ -634,7 +634,7 @@
+ void TManageDatabaseDialog::pdOnNew ( wxCommandEvent &ev )
+ {
+ wxString wildcard = _T("GENtle database (*.db)|*.db") ;
+- wxFileDialog d ( this , txt("t_add_new_db") , _T("") , _T("") , wildcard , wxSAVE|wxOVERWRITE_PROMPT ) ;
++ wxFileDialog d ( this , txt("t_add_new_db") , _T("") , _T("") , wildcard , wxFD_SAVE|wxFD_OVERWRITE_PROMPT ) ;
+ int x = d.ShowModal() ;
+ if ( x != wxID_OK ) return ;
+
+@@ -655,7 +655,7 @@
+ void TManageDatabaseDialog::pdOnAdd ( wxCommandEvent &ev )
+ {
+ wxString wildcard = _T("GENtle database (*.db)|*.db") ;
+- wxFileDialog d ( this , txt("t_choose_db") , _T("") , _T("") , wildcard , wxOPEN ) ;
++ wxFileDialog d ( this , txt("t_choose_db") , _T("") , _T("") , wildcard , wxFD_OPEN ) ;
+ int x = d.ShowModal() ;
+ if ( x != wxID_OK ) return ;
+
+@@ -965,7 +965,7 @@
+ TVectorItem i ;
+ i.name = sr[a][sr["di_name"]] ;
+ i.desc = sr[a][sr["di_description"]] ;
+- i.setType ( sr[a][sr["di_type"]].GetChar(0) ) ;
++ i.setType ( (char)sr[a][sr["di_type"]].GetChar(0) ) ;
+ i.from = atoi ( sr[a][sr["di_from"]].mb_str() ) ;
+ i.to = atoi ( sr[a][sr["di_to"]].mb_str() ) ;
+ i.setDirection ( atoi ( sr[a][sr["di_direction"]].mb_str() ) ) ;
+--- a/MyFrame.cpp
++++ b/MyFrame.cpp
+@@ -727,7 +727,7 @@
+ name.Replace ( _T("\\") , _T("_") , TRUE ) ;
+
+ wxString lastdir = LS->getOption ( _T("LAST_IMPORT_DIR") , _T("C:") ) ;
+- wxFileDialog d ( this , txt("t_save_image") , lastdir , name , wildcard , wxSAVE|wxOVERWRITE_PROMPT ) ;
++ wxFileDialog d ( this , txt("t_save_image") , lastdir , name , wildcard , wxFD_SAVE|wxFD_OVERWRITE_PROMPT ) ;
+ if ( d.ShowModal() != wxID_OK ) return ;
+ wxString filename = d.GetPath() ;
+
+@@ -764,7 +764,7 @@
+ _T("|") + wcCM5format ;
+ wxString lastdir = LS->getOption ( _T("LAST_IMPORT_DIR") , _T("C:") ) ;
+ wxFileDialog d ( this , txt("import_file") , lastdir ,
+- _T("") , wildcard , wxOPEN | wxMULTIPLE ) ;
++ _T("") , wildcard , wxFD_OPEN | wxFD_MULTIPLE ) ;
+ int x = d.ShowModal() ;
+ if ( x != wxID_OK ) return ;
+
+@@ -2616,8 +2616,8 @@
+ if ( r == 10 ) { ev.m_keyCode = WXK_LEFT ; msg = _T("LEFT") ; }
+ if ( r == 11 ) { ev.m_keyCode = WXK_UP ; msg = _T("UP") ; }
+ if ( r == 12 ) { ev.m_keyCode = WXK_DOWN ; msg = _T("DOWN") ; }
+- if ( r == 13 ) { ev.m_keyCode = WXK_PRIOR ; msg = _T("PRIOR") ; }
+- if ( r == 14 ) { ev.m_keyCode = WXK_NEXT ; msg = _T("NEXT") ; }
++ if ( r == 13 ) { ev.m_keyCode = WXK_PAGEUP ; msg = _T("PAGEUP") ; }
++ if ( r == 14 ) { ev.m_keyCode = WXK_PAGEDOWN ; msg = _T("PAGEDOWN") ; }
+ mylog ( "Testsuite:Key" , wxString::Format ( "%s" , msg.c_str() ) ) ;
+ if ( ac->def == _T("PrimerDesign") ) ((TPrimerDesign*)ac)->sc->OnCharHook(ev) ;
+ else ac->cSequence->OnCharHook(ev) ;
+--- a/PCR_Troubleshoot.cpp
++++ b/PCR_Troubleshoot.cpp
+@@ -415,13 +415,13 @@
+ if ( ( b - a ) / length > 4 )
+ {
+ add_error ( p , nr , msg ,
+- wxString::Format ( txt("t_pcr_ts_warning_runs_text") , (char*)s.Mid(a,length).c_str() ) ) ;
++ wxString::Format ( txt("t_pcr_ts_warning_runs_text") , (const char*)s.Mid(a,length).c_str() ) ) ;
+ a = b - length ;
+ }
+ else if ( ( b - a ) / length == 4 )
+ {
+ add_warning ( p , nr , msg ,
+- wxString::Format ( txt("t_pcr_ts_warning_runs_text2") , (char*)s.Mid(a,length).c_str() ) ) ;
++ wxString::Format ( txt("t_pcr_ts_warning_runs_text2") , (const char*)s.Mid(a,length).c_str() ) ) ;
+ a = b - length ;
+ }
+ }
+@@ -489,7 +489,7 @@
+ int a ;
+ for ( a = 0 ; a < s.length() ; a++ )
+ {
+- switch ( s.GetChar ( a ) )
++ switch ( (char)s.GetChar ( a ) )
+ {
+ case 'A' : s.SetChar ( a , 'T' ) ; break ;
+ case 'C' : s.SetChar ( a , 'G' ) ; break ;
+--- a/SequenceCanvas.cpp
++++ b/SequenceCanvas.cpp
+@@ -394,13 +394,13 @@
+ {
+ mark ( id , the_sequence->length() , the_sequence->length() , 2 ) ;
+ }
+- else if ( k == WXK_PRIOR )
++ else if ( k == WXK_PAGEUP )
+ {
+ from -= page ;
+ if ( from < 1 ) from = 1 ;
+ mark ( id , from , from , 2 ) ;
+ }
+- else if ( k == WXK_NEXT )
++ else if ( k == WXK_PAGEDOWN )
+ {
+ from += page ;
+ if ( from > the_sequence->length() ) from = the_sequence->length() ;
+--- a/SequenceTypeAAstructure.cpp
++++ b/SequenceTypeAAstructure.cpp
+@@ -400,7 +400,7 @@
+ dc.SetPen ( *pen_C ) ;
+ for ( a = 0 ; a < atom_pos.size() ; a++ )
+ {
+- switch ( atom_type.GetChar ( a ) )
++ switch ( (char)atom_type.GetChar ( a ) )
+ {
+ case 'C' : if ( can->isPrinting() ) dc.SetPen ( *pen_C ) ; dc.SetBrush ( *brush_C ) ; break ;
+ case 'S' : if ( can->isPrinting() ) dc.SetPen ( *pen_S ) ; dc.SetBrush ( *brush_S ) ; break ;
+--- a/SequenceTypePlot.cpp
++++ b/SequenceTypePlot.cpp
+@@ -538,7 +538,7 @@
+ mylog ( "SeqPlot::useNcoils" , wxString::Format ( _T("BEGIN ncoils_function (%d): ") , b ) + s ) ;
+ x = ncoils_function ( (const char*) s.mb_str() , b ) . c_str() ;
+ mylog ( "SeqPlot::useNcoils" , "END ncoils_function" ) ;
+- wxString t ( (char*) x.c_str() , wxConvUTF8 ) ;
++ wxString t ( (const char*) x.c_str() , wxConvUTF8 ) ;
+ wxArrayString ta ;
+ explode ( _T("\n") , t , ta ) ;
+ for ( b = 0 ; b < s.length() ; b++ )
+--- a/TImageDisplay.cpp
++++ b/TImageDisplay.cpp
+@@ -310,7 +310,7 @@
+
+ if ( invert )
+ {
+- int lf = pdc.GetLogicalFunction() ;
++ wxRasterOperationMode lf = pdc.GetLogicalFunction() ;
+ pdc.SetLogicalFunction ( wxINVERT ) ;
+ pdc.SetBrush ( *wxWHITE_BRUSH ) ;
+ pdc.SetPen ( *wxWHITE_PEN ) ;
+--- a/TPhyloTree.cpp
++++ b/TPhyloTree.cpp
+@@ -3,7 +3,6 @@
+ BEGIN_EVENT_TABLE(TPhyloTree, MyChildBase)
+ EVT_CLOSE(ChildBase::OnClose)
+ EVT_SET_FOCUS(ChildBase::OnFocus)
+- EVT_SIZE(ChildBase::OnSize)
+ EVT_CHECKBOX(PHYLIP_DIRECT_LINES,TPhyloTree::OnDirectLines)
+ EVT_LISTBOX(PHYLIP_TREE_LIST,TPhyloTree::OnTreeList)
+ EVT_MENU(MDI_FILE_SAVE,TPhyloTree::OnFileSave)
+--- a/TStorage.cpp
++++ b/TStorage.cpp
+@@ -272,7 +272,7 @@
+ } while ( rc == SQLITE_BUSY ) ;
+
+ ierror = e ? 1 : 0 ;
+- if ( e ) error = wxString ( _T("An error has occurred when executing query ") + query , wxConvUTF8 ) ;
++ if ( e ) error = _T("An error has occurred when executing query ") + query;
+ else error = _T("Alles OK") ;
+
+ sqlite3_close ( db ) ;
+@@ -531,7 +531,7 @@
+ s1 = s2 = _T("") ;
+ for ( b = 0 ; b < f.GetCount() ; b++ )
+ {
+- int id = r[(char*)f[b].c_str()] ;
++ int id = r[(const char*)f[b].c_str()] ;
+ if ( id > -1 ) sqlAdd ( s1 , s2 , f[b] , r[a][id] ) ;
+ else sqlAdd ( s1 , s2 , f[b] , _T("") ) ;
+ }
+--- a/main.cpp
++++ b/main.cpp
+@@ -253,7 +253,7 @@
+ if ( wxGetEnv ( _T("COILSDIR") , NULL ) ) wxUnsetEnv ( _T("COILSDIR") ) ;
+ wxSetEnv ( _T("COILSDIR") , homedir ) ;
+ #else
+- putenv ( (char*) ncoilsdir.c_str() ) ;
++ setenv ( "COILSDIR" , homedir.c_str() , 1 ) ;
+ #endif
+
+
+--- a/ChildBase.cpp
++++ b/ChildBase.cpp
+@@ -223,7 +223,7 @@
+
+ wxString wildcard = getExportFilters () ;
+ wxString lastdir = myapp()->frame->LS->getOption ( _T("LAST_IMPORT_DIR") , _T("C:") ) ;
+- wxFileDialog d ( this , txt("export_file") , lastdir , _T("") , wildcard , wxSAVE|wxOVERWRITE_PROMPT ) ;
++ wxFileDialog d ( this , txt("export_file") , lastdir , _T("") , wildcard , wxFD_SAVE|wxFD_OVERWRITE_PROMPT ) ;
+ d.SetFilterIndex ( myapp()->frame->LS->getOption ( _T("LAST_EXPORT_FILTER") , 0 ) ) ;
+ int x = d.ShowModal() ;
+ if ( x != wxID_OK ) return ;
Modified: trunk/packages/gentle/trunk/debian/rules
===================================================================
--- trunk/packages/gentle/trunk/debian/rules 2014-06-25 06:12:35 UTC (rev 17291)
+++ trunk/packages/gentle/trunk/debian/rules 2014-06-25 11:55:27 UTC (rev 17292)
@@ -13,7 +13,7 @@
CXXFLAGS=$(CXXFLAGS) dh_auto_configure
override_dh_auto_build:
- $(MAKE) CXXFLAGS=$(CXXFLAGS)
+ $(MAKE) -k CXXFLAGS=$(CXXFLAGS)
override_dh_install:
dh_install
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