[med-svn] [Git][med-team/proftmb][master] 4 commits: Add gcc-11.patch; fix ftbfs
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Nov 15 21:34:12 GMT 2021
Étienne Mollier pushed to branch master at Debian Med / proftmb
Commits:
bf153faa by Étienne Mollier at 2021-11-15T22:28:17+01:00
Add gcc-11.patch; fix ftbfs
Closes: #984301
Fix several problems of conformance with ISO C++17.
- - - - -
155168cc by Étienne Mollier at 2021-11-15T22:30:02+01:00
update changelog
- - - - -
008dc230 by Étienne Mollier at 2021-11-15T22:30:21+01:00
routine-update: Standards-Version: 4.6.0
- - - - -
843d13c1 by Étienne Mollier at 2021-11-15T22:33:07+01:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc-11.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+proftmb (1.1.12-10) unstable; urgency=medium
+
+ * Team upload.
+ * Add gcc-11.patch; fix ftbfs (Closes: #984301)
+ * Standards-Version: 4.6.0 (routine-update)
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 15 Nov 2021 22:30:45 +0100
+
proftmb (1.1.12-9) unstable; urgency=medium
* Standards-Version: 4.5.1 (routine-update)
=====================================
debian/control
=====================================
@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 13),
help2man,
libgsl-dev,
opt
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/proftmb
Vcs-Git: https://salsa.debian.org/med-team/proftmb.git
Homepage: https://rostlab.org/
=====================================
debian/patches/gcc-11.patch
=====================================
@@ -0,0 +1,205 @@
+Description: fix ftbfs with gcc-11
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=984301
+Forwarded: no
+Last-Update: 2021-11-15
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- proftmb.orig/src/Par.h
++++ proftmb/src/Par.h
+@@ -31,13 +31,13 @@
+ static void InitAbet(const char*);
+ static void InitConst(double,double,double, int, int, double);
+ static void InitMaps(char*,char*,char*,char*);
+- static void LoadL2L(char*) throw (string&);
+- static void LoadL2A(char*) throw (string&);
+- static void LoadA2E(char*) throw (string&);
+- static void LoadConnect(char*) throw (string&);
++ static void LoadL2L(char*);
++ static void LoadL2A(char*);
++ static void LoadA2E(char*);
++ static void LoadConnect(char*);
+ static void LoadRedux(char *,vector<string>&,
+ map<string, unsigned int>&,
+- vector<unsigned int>&) throw (string&);
++ vector<unsigned int>&);
+ static void UpdateA(vector<vector<double> >&,uint,uint);
+ static void UpdateA2(vector<vector<double> >&,uint,uint);
+
+@@ -117,8 +117,8 @@
+ static void InitDirichlet(char*);
+ static void InitZCalibration(char*);
+ static void PrintZCurve(vector<pair<double,double> >&,char *);
+- static void ReadZCurve(char *) throw (string &);
+- static void ReadNullFreq(char *) throw (string &);
++ static void ReadZCurve(char *);
++ static void ReadNullFreq(char *);
+ static double CalcDelta(pair<double, double>&, pair<double, double>&);
+ static void LoadStrandStates(char *);
+ };
+--- proftmb.orig/src/Seq.h
++++ proftmb/src/Seq.h
+@@ -82,7 +82,7 @@
+ //void IncrAtom(double (*) (unsigned int,unsigned int));
+ void InitProfile(set<pair<string,string> >&,unsigned int);
+ void InitProfile(const char*);
+- bool InitLabels(set<pair<string,string> >&) throw (string&);
++ bool InitLabels(set<pair<string,string> >&);
+
+ //from Posterior.cpp
+ void CountPredStrands();
+@@ -191,7 +191,7 @@
+ double ReturnP(unsigned int,unsigned int,Par&);
+
+ static void InitSeq();
+- static map<string,set<pair<string,string> > > Read(char*) throw (string&);
++ static map<string,set<pair<string,string> > > Read(char*);
+ static pair<string,set<pair<string,string> > > ReadOne(ifstream&);
+ };
+
+--- proftmb.orig/src/Eval.h
++++ proftmb/src/Eval.h
+@@ -45,4 +45,4 @@
+ vector<pair<string,vector<double> > >AccCov(vector<evaldat>&,string &, bool dQ=false);
+ pair<double, double> CalcAccCovFromZ(double&);
+ map<string,map<int,int> >CoverageTable(vector<pair<double,string> >&);
+-float RelativeEntropy(vector<float>& A, vector<float>& B) throw (char *);
++float RelativeEntropy(vector<float>& A, vector<float>& B);
+--- proftmb.orig/src/Zscore.h
++++ proftmb/src/Zscore.h
+@@ -6,7 +6,7 @@
+ using namespace std;
+
+ vector<pair<double,double> >
+-Z_Calibrate(set<pair<int,double> >&,int,double) throw (string&);
++Z_Calibrate(set<pair<int,double> >&,int,double);
+
+
+ set<pair<double,pair<double,double> > >
+--- proftmb.orig/src/proftmb.cpp
++++ proftmb/src/proftmb.cpp
+@@ -65,7 +65,7 @@
+
+
+ void ProcessOneFile(const char *, ofstream&, ofstream&,
+- const char *, double, Par&, const char*, bool) throw (string &);
++ const char *, double, Par&, const char*, bool);
+
+
+ int Run(int argc,char** argv)
+@@ -270,7 +270,7 @@
+
+
+ void ProcessOneFile(const char *qfile, ofstream& ts, ofstream& tstab,
+- const char *datfile, double cut, Par& m, const char *name, bool multiQ) throw (string &) {
++ const char *datfile, double cut, Par& m, const char *name, bool multiQ){
+
+ ostringstream errs;
+ Seq seq;
+--- proftmb.orig/src/Eval.cpp
++++ proftmb/src/Eval.cpp
+@@ -651,7 +651,7 @@
+ }
+
+
+-float RelativeEntropy(vector<float>& A, vector<float>& B) throw (char *){
++float RelativeEntropy(vector<float>& A, vector<float>& B){
+ //compute the mutual information between vectors A and B
+ unsigned int e;
+ float re = 0.0,sum;
+--- proftmb.orig/src/Par.cpp
++++ proftmb/src/Par.cpp
+@@ -260,7 +260,7 @@
+ }
+
+
+-void Par::LoadConnect(char* cf) throw (string&){
++void Par::LoadConnect(char* cf){
+ //Loads the architecture file, (option -r)
+ //The format is a sparse matrix representation
+ //of the nodes of the HMM, e.g.
+@@ -345,7 +345,7 @@
+ }
+
+
+-void Par::LoadL2L(char* l2lfile) throw (string&){
++void Par::LoadL2L(char* l2lfile){
+ //static function
+ //loads SLNmap and SLNrev
+ //parses Label2Label file (option -l), e.g.
+@@ -412,7 +412,7 @@
+ }
+
+
+-void Par::LoadL2A(char* l2afile) throw (string&){
++void Par::LoadL2A(char* l2afile){
+ //this is a static function
+
+ // parses l2afile, format:
+@@ -551,7 +551,7 @@
+ }
+
+
+-void Par::LoadA2E(char* a2efile) throw (string&){
++void Par::LoadA2E(char* a2efile){
+ // static function, parses A2Efile, producing:
+ // A2Efile format:
+ // sen san san san san
+@@ -649,7 +649,7 @@
+ void Par::LoadRedux(char *file,
+ vector<string>& srcmap,
+ map<string, unsigned int>& tarmap,
+- vector<unsigned int>& redux) throw (string&){
++ vector<unsigned int>& redux){
+
+ //load mapping in file, translating first string on each line
+ //('source') into an integer, storing it in srcmap
+@@ -739,7 +739,7 @@
+ }
+
+
+-void Par::ReadZCurve(char *ifile) throw (string&){
++void Par::ReadZCurve(char *ifile){
+ //assume we are reading a file created by PrintZCurve
+ //which contains tab-separated lines (mean,sd)
+ ifstream is(ifile);
+@@ -760,7 +760,7 @@
+ }
+
+
+-void Par::ReadNullFreq(char *ifile) throw (string&){
++void Par::ReadNullFreq(char *ifile){
+ //Load NULL Frequency file
+
+ char aa;
+--- proftmb.orig/src/Seq.cpp
++++ proftmb/src/Seq.cpp
+@@ -96,7 +96,7 @@
+
+
+
+-bool Seq::InitLabels(SS& sdat) throw (string&){
++bool Seq::InitLabels(SS& sdat){
+
+ SS::iterator sit;
+ bool foundQ = false;
+@@ -310,7 +310,7 @@
+ }
+
+
+-map<string,SS > Seq::Read(char* file) throw (string&){
++map<string,SS > Seq::Read(char* file){
+
+ //load data into dat
+
+--- proftmb.orig/src/Zscore.cpp
++++ proftmb/src/Zscore.cpp
+@@ -33,7 +33,7 @@
+ extern int quiet;
+
+ vector<pair<double,double> > Z_Calibrate(set<pair<int,double> >& Raw,
+- int windowsize,double zmax) throw (string&){
++ int windowsize,double zmax){
+
+ ostringstream errs;
+
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
avoid-dnl-in-makefiles.diff
gcc-6.patch
+gcc-11.patch
View it on GitLab: https://salsa.debian.org/med-team/proftmb/-/compare/0d9d9dc8e4970a5c19ea470771a9ac57491ba8ed...843d13c1673fa0da821bce14eb16f098e0521908
--
View it on GitLab: https://salsa.debian.org/med-team/proftmb/-/compare/0d9d9dc8e4970a5c19ea470771a9ac57491ba8ed...843d13c1673fa0da821bce14eb16f098e0521908
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