[med-svn] [Git][med-team/gentle][master] Added my PRs from GitHub as patches to address bugs
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Fri Jul 28 13:11:16 BST 2023
Steffen Möller pushed to branch master at Debian Med / gentle
Commits:
97db7e59 by Steffen Moeller at 2023-07-28T13:19:27+02:00
Added my PRs from GitHub as patches to address bugs
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/AdjustDeleteForArrays.patch
- + debian/patches/OperatorPrecedence.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+gentle (1.9+cvs20100605+dfsg1-11) unstable; urgency=medium
+
+ * clang pointed to mismatch between dynamic allocations of arrays
+ with new and omitted []s in corresponding delete
+ (forwarded as PR#3)
+ * Fixed prior unnoticed issues with operator precedence
+ (forwarded as PR#4)
+ * Standards-Version: 4.6.2
+
+ -- Steffen Moeller <moeller at debian.org>
+
gentle (1.9+cvs20100605+dfsg1-10) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -9,7 +9,7 @@ Build-Depends: debhelper-compat (= 13),
libsqlite3-dev,
libtinyxml-dev,
libwxgtk3.2-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/gentle
Vcs-Git: https://salsa.debian.org/med-team/gentle.git
Homepage: http://gentle.magnusmanske.de
=====================================
debian/patches/AdjustDeleteForArrays.patch
=====================================
@@ -0,0 +1,119 @@
+Description: PR#3 Match dynamic arrays with new [] to delete with []
+Author: Steffen Moeller <moeller at debian.org>
+Last-Update: 2023-07-28
+Forwarded: yes
+
+diff --git a/ABItype.cpp b/ABItype.cpp
+index 146994c..3ba447f 100755
+--- a/ABItype.cpp
++++ b/ABItype.cpp
+@@ -14,7 +14,7 @@ ABItype::ABItype ()
+ ABItype::~ABItype ()
+ {
+ for ( unsigned int a = 0 ; a < vf.size() ; a++ )
+- if ( vf[a].data ) delete vf[a].data ;
++ if ( vf[a].data ) delete [] vf[a].data ;
+ vf.clear () ;
+ }
+
+@@ -90,7 +90,7 @@ void ABItype::parse ( wxString filename )
+ nrecords-- ;
+ }
+
+- delete t ;
++ delete [] t ;
+ }
+
+ /** \brief Deterimnes the position of the "ABIF" key
+diff --git a/CloneManager.cpp b/CloneManager.cpp
+index 2e6cfda..bc9a781 100644
+--- a/CloneManager.cpp
++++ b/CloneManager.cpp
+@@ -62,7 +62,7 @@ void TCloneManager::load ( wxString file )
+
+ if ( t[0] != 26 || t[1] != 'S' || t[2] != 'E' || t[3] != 'S' )
+ {
+- delete t ;
++ delete [] t ;
+ return ;
+ }
+
+@@ -104,7 +104,7 @@ void TCloneManager::load ( wxString file )
+
+ _v.push_back ( v ) ;
+ _success = true ;
+- delete t ;
++ delete [] t ;
+ }
+
+ int TCloneManager::countVectors ()
+diff --git a/GenBank.cpp b/GenBank.cpp
+index 88c71c0..ab31359 100755
+--- a/GenBank.cpp
++++ b/GenBank.cpp
+@@ -61,7 +61,7 @@ void TGenBank::load ( wxString s )
+ d = c+1 ;
+ }
+ }
+- delete t ;
++ delete [] t ;
+ mylog ( "-GenBank import" , "file added" ) ;
+
+ parseLines () ; // Calling parser
+diff --git a/SendHTTP.cpp b/SendHTTP.cpp
+index 9f41c2d..d70c1c4 100644
+--- a/SendHTTP.cpp
++++ b/SendHTTP.cpp
+@@ -133,7 +133,7 @@ wxString myExternal::getTextLocal ( wxString url )
+ in.Read ( c , l ) ;
+ in.Close() ;
+ wxString ret = wxString ( c , wxConvUTF8 ) ;
+- delete c ;
++ delete [] c ;
+ return ret ;
+ }
+
+diff --git a/TClone.cpp b/TClone.cpp
+index 7cc048a..4c1a812 100755
+--- a/TClone.cpp
++++ b/TClone.cpp
+@@ -55,7 +55,7 @@ void TClone::loadEnzymeList ( TStorage *st , wxString filename )
+
+ vr.push_back ( r ) ;
+ }
+- delete t ;
++ delete [] t ;
+
+ for ( i = 0 ; i < vr.size() ; i++ )
+ {
+@@ -171,7 +171,7 @@ void TClone::separateNames ( wxString &s1 , wxString &s2 )
+ s2 = wxString ( t , *wxConvCurrent ) ;
+ }
+
+- delete t ;
++ delete [] t ;
+ }
+
+ void TClone::load ( wxString s )
+@@ -184,7 +184,7 @@ void TClone::load ( wxString s )
+
+ wxArrayString v ;
+ parseLines ( v , t , l ) ;
+- delete t ;
++ delete [] t ;
+
+ success = true ;
+ if ( v.GetCount() < 3 || v[0].IsEmpty() || v[0].length() > 50 )
+diff --git a/TPhylip.cpp b/TPhylip.cpp
+index 79f5b2c..ede93d6 100644
+--- a/TPhylip.cpp
++++ b/TPhylip.cpp
+@@ -307,7 +307,7 @@ wxString TPhylip::runapp ( wxString app , const wxString s )
+ outtree.Close () ;
+ n[l] = 0 ;
+ wxString result ( n , wxConvUTF8 ) ;
+- delete n ;
++ delete [] n ;
+
+ // result = "(3:0.23647,(4:0.12270,2:0.00296):0.29673,1:0.65529);(4:0.12270,2:0.00296);" ; // Test
+
=====================================
debian/patches/OperatorPrecedence.patch
=====================================
@@ -0,0 +1,52 @@
+Description: PR#4 Operator precedings cause warnings+problems
+Author: Steffen Moeller <moeller at debian.org>
+Last-Update: 2023-07-28
+Forwarded: yes
+
+Index: gentle/MiscDialogs.cpp
+===================================================================
+--- gentle.orig/MiscDialogs.cpp
++++ gentle/MiscDialogs.cpp
+@@ -835,14 +835,14 @@ TMyMultipleChoiceDialog::TMyMultipleChoi
+ wxSizer *v0 = new wxBoxSizer ( wxVERTICAL ) ;
+ wxSizer *h0 = new wxBoxSizer ( wxHORIZONTAL ) ;
+
+- if ( options & wxCANCEL > 0 )
++ if ( options & wxCANCEL )
+ {
+ wxButton *b = new wxButton ( this , wxID_CANCEL , txt("b_cancel") ) ;
+ h0->Add ( b , wxEXPAND|wxALL , 2 ) ;
+ }
+ else h0->Add ( new wxStaticText ( this , -1 , _T("") ) , wxEXPAND|wxALL , 2 ) ;
+
+- if ( options & wxOK > 0 )
++ if ( options & wxOK )
+ {
+ wxButton *b = new wxButton ( this , MCD_OK , txt("b_ok") ) ;
+ h0->Add ( b , wxEXPAND|wxALL , 2 ) ;
+@@ -865,7 +865,7 @@ TMyMultipleChoiceDialog::TMyMultipleChoi
+ SetSizer ( v0 ) ;
+ v0->Layout () ;
+
+- if ( options & wxCENTRE > 0 ) Center () ;
++ if ( options & wxCENTRE ) Center () ;
+ }
+
+ TMyMultipleChoiceDialog::~TMyMultipleChoiceDialog ()
+Index: gentle/SequenceCanvas.cpp
+===================================================================
+--- gentle.orig/SequenceCanvas.cpp
++++ gentle/SequenceCanvas.cpp
+@@ -2712,9 +2712,9 @@ SequenceCharMarkup::SequenceCharMarkup()
+
+ void SequenceCharMarkup::draw ( wxDC &dc , const wxRect &rect , wxString s , int mode , int lastx )
+ {
+- bool mark = ( mode & SEQUENCECHARMARKUP_MARK ) > 0 ;
+- bool mono = ( mode & SEQUENCECHARMARKUP_MONO ) > 0 ;
+- bool bold = ( mode & SEQUENCECHARMARKUP_BOLD ) > 0 | this->bold ;
++ bool mark = ( mode & SEQUENCECHARMARKUP_MARK ) > 0 ;
++ bool mono = ( mode & SEQUENCECHARMARKUP_MONO ) > 0 ;
++ bool bold = (( mode & SEQUENCECHARMARKUP_BOLD ) > 0) | this->bold ;
+ bool invert = ( mode & SEQUENCECHARMARKUP_INVERT ) > 0 ;
+
+ wxColour bg ;
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,5 @@
+OperatorPrecedence.patch
+AdjustDeleteForArrays.patch
forward_slashes.patch
remove_tinyxml.patch
remove_clustalw.patch
View it on GitLab: https://salsa.debian.org/med-team/gentle/-/commit/97db7e596e60e77e283b2d71827b7a0cc642e9f5
--
View it on GitLab: https://salsa.debian.org/med-team/gentle/-/commit/97db7e596e60e77e283b2d71827b7a0cc642e9f5
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