--- Begin Message ---
Source: hhsuite
Version: 2.0.16-6
Severity: serious
Tags: stretch sid
User: [email protected]
Usertags: qa-ftbfs-20160713 qa-ftbfs
Justification: FTBFS with GCC 6 on amd64
Hi,
During a rebuild of all packages in sid using the gcc-defaults package
available in experimental to make GCC default to version 6, your package failed
to build on amd64. For more information about GCC 6 and Stretch, see:
- https://wiki.debian.org/GCC6
- https://lists.debian.org/debian-devel-announce/2016/06/msg00007.html
Relevant part (hopefully):
> g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat
> -Werror=format-security -O3 -Wall -Wno-deprecated -Wno-char-subscripts
> -fno-strict-aliasing -Ics -fopenmp -DHH_SSE3 -msse3 -Wl,-z,relro hhblits.C
> -o hhblits cs/blosum_matrix.o cs/log.o cs/application.o cs/getopt_pp.o
> cs/assert_helpers.o cs/aa.o cs/as.o -lpthread -fopenmp -lrt -lffindex
> In file included from cs/count_profile-inl.h:8:0,
> from cs/context_profile.h:7,
> from cs/context_library.h:8,
> from hhblits.C:123:
> cs/alignment-inl.h: In function 'Vector<double>
> cs::PositionSpecificWeightsAndDiversity(const cs::Alignment<Abc>&,
> Matrix<double>&)':
> cs/alignment-inl.h:823:16: warning: suggest explicit braces to avoid
> ambiguous 'else' [-Wparentheses]
> if (ncoli < kMinCols) // number of columns in subalignment
> insufficient?
> ^
> In file included from hhblits.C:128:0:
> util.C: In function 'float log2(float)':
> util.C:58:26: error: 'float log2(float)' conflicts with a previous declaration
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1542:3: note: previous declaration 'constexpr float
> std::log2(float)'
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C: In function 'float log10(float)':
> util.C:59:27: error: 'float log10(float)' conflicts with a previous
> declaration
> inline float log10(float x) {return (x<=0?
> (float)(-100000):0.434294481*log(x));}
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:380:3: note: previous declaration 'constexpr float
> std::log10(float)'
> log10(float __x)
> ^~~~~
> In file included from hhblits.C:128:0:
> util.C: In function 'char* sprintg(float, int)':
> util.C:379:35: error: call of overloaded 'log10(float)' is ambiguous
> float log10val = log10(fabs(val));
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:112:1: note: candidate: double
> log10(double)
> __MATHCALL (log10,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:384:3: note: candidate: constexpr long double
> std::log10(long double)
> log10(long double __x)
> ^~~~~
> /usr/include/c++/6/cmath:380:3: note: candidate: constexpr float
> std::log10(float)
> log10(float __x)
> ^~~~~
> In file included from hhblits.C:128:0:
> util.C:59:14: note: candidate: float log10(float)
> inline float log10(float x) {return (x<=0?
> (float)(-100000):0.434294481*log(x));}
> ^~~~~
> In file included from hhblits.C:132:0:
> hhutil.C: In function 'void ReadDefaultsFile(int&, char**, char*)':
> hhutil.C:478:67: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
> ^
> hhutil.C:483:63: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
> ^
> In file included from hhblits.C:133:0:
> hhmatrices.C: In function 'void SetSubstitutionMatrix()':
> hhmatrices.C:380:35: error: call of overloaded 'log2(float)' is ambiguous
> S[a][b] = log2(R[a][b]/pb[a]); // S[a][b] = log2(P(a,b)/P(a)/P(b))
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:133:0:
> hhmatrices.C:390:56: error: call of overloaded 'log2(float&)' is ambiguous
> for (a=0; a<20; ++a) entropy_pb-=pb[a]*log2(pb[a]);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:133:0:
> hhmatrices.C:394:37: error: call of overloaded 'log2(float&)' is ambiguous
> entropy-=P[a][b]*log2(R[a][b]);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:133:0:
> hhmatrices.C: In function 'void SetSecStrucSubstitutionMatrix()':
> hhmatrices.C:473:38: error: call of overloaded 'log2(float&)' is ambiguous
> S73[A][B][cf] = log2(P73[A][B][cf]);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:133:0:
> hhmatrices.C:484:36: error: call of overloaded 'log2(float&)' is ambiguous
> S33[B][cf][BB][ccf] = log2(sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:142:0:
> hhhmm.C: In member function 'HMM& HMM::operator=(HMM&)':
> hhhmm.C:169:44: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname[k]=new(char[strlen(q.sname[k])+1]);
> ^
> hhhmm.C:174:40: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k]=new(char[strlen(q.seq[k])+1]);
> ^
> hhhmm.C: In member function 'int HMM::Read(FILE*, char*)':
> hhhmm.C:360:57: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k-1]=new(char[strlen(cur_seq)+1]);
> ^
> hhhmm.C:367:57: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname[k] = new (char[strlen(line+1)+1]); //+1 for
> terminating '\0'
> ^
> hhhmm.C:468:47: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k]=new(char[strlen(cur_seq)+1]);
> ^
> hhhmm.C: In member function 'int HMM::ReadHMMer(FILE*, char*)':
> hhhmm.C:719:53: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nsa_dssp] = new(char[par.maxres+2]);
> ^
> hhhmm.C:740:53: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_pred] = new(char[par.maxres+2]);
> ^
> hhhmm.C:761:53: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_conf] = new(char[par.maxres+2]);
> ^
> hhhmm.C:835:49: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_dssp] = new(char[par.maxres+2]);
> ^
> hhhmm.C:1009:46: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname[k+1]=new(char[strlen(longname)+1]);
> ^
> hhhmm.C:1011:27: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k]=new(char[L+2]);
> ^
> hhhmm.C:1014:29: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k+1]=new(char[L+2]);
> ^
> hhhmm.C:1032:44: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname[k]=new(char[strlen(longname)+1]);
> ^
> hhhmm.C:1034:27: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k]=new(char[L+2]);
> ^
> hhhmm.C: In member function 'int HMM::ReadHMMer3(FILE*, char*)':
> hhhmm.C:1182:53: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nsa_dssp] = new(char[par.maxres+2]);
> ^
> hhhmm.C:1203:53: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_pred] = new(char[par.maxres+2]);
> ^
> hhhmm.C:1224:53: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_conf] = new(char[par.maxres+2]);
> ^
> hhhmm.C:1281:58: error: call of overloaded 'log2(float)' is ambiguous
> tr[0][a] = log2((float) exp(-1.0*strflta(ptr,99999))); //store
> transition probabilites as log2 values
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:142:0:
> hhhmm.C:1295:49: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_dssp] = new(char[par.maxres+2]);
> ^
> hhhmm.C:1415:69: error: call of overloaded 'log2(float)' is ambiguous
> tr[i][a] = log2((float) exp(-1.0*strflta(ptr,99999)));
> //store transition prob's as log2-values
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:142:0:
> hhhmm.C:1471:46: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname[k+1]=new(char[strlen(longname)+1]);
> ^
> hhhmm.C:1473:27: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k]=new(char[L+2]);
> ^
> hhhmm.C:1476:29: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k+1]=new(char[L+2]);
> ^
> hhhmm.C:1494:44: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname[k]=new(char[strlen(longname)+1]);
> ^
> hhhmm.C:1496:27: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k]=new(char[L+2]);
> ^
> hhhmm.C: In member function 'void HMM::InsertCalibration(char*)':
> hhhmm.C:2177:39: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> char** lines = new(char*[3*L+100000]);
> ^
> hhhmm.C:2205:44: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> lines[nline]=new(char[strlen(line)+1]);
> ^
> hhhmm.C: In member function 'void HMM::AddSSPrediction(char*, char*)':
> hhhmm.C:2329:34: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_pred]=new(char[L+2]);
> ^
> hhhmm.C:2336:34: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[nss_conf]=new(char[L+2]);
> ^
> In file included from hhblits.C:143:0:
> hhalignment.C: In constructor 'Alignment::Alignment(int, int)':
> hhalignment.C:47:30: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname = new(char*[maxseq+2]);
> ^
> hhalignment.C:48:28: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq = new(char*[maxseq+2]);
> ^
> hhalignment.C:49:22: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> l = new(int[maxres]);
> ^
> hhalignment.C:50:26: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> X = new(char*[maxseq+2]);
> ^
> hhalignment.C:51:40: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> I = new(short unsigned int*[maxseq+2]);
> ^
> hhalignment.C:52:28: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> keep = new(char[maxseq+2]);
> ^
> hhalignment.C:53:31: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> display = new(char[maxseq+2]);
> ^
> hhalignment.C:54:27: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> wg = new(float[maxseq+2]);
> ^
> hhalignment.C:55:28: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> nseqs = new(int[maxres+2]);
> ^
> hhalignment.C: In member function 'Alignment&
> Alignment::operator=(Alignment&)':
> hhalignment.C:144:25: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> nres=new(int[N_in]);
> ^
> hhalignment.C:150:48: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> sname[k]=new(char[strlen(ali.sname[k])+1]);
> ^
> hhalignment.C:156:44: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> seq[k]=new(char[strlen(ali.seq[k])+1]);
> ^
> hhalignment.C:162:42: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[k]=new(char[strlen(ali.seq[k])+2]);
> ^
> hhalignment.C:167:56: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> I[k]=new(short unsigned int[strlen(ali.seq[k])+2]);
> ^
> hhalignment.C: In member function 'void Alignment::Read(FILE*, char*, char*)':
> hhalignment.C:252:49: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> seq[k]=new(char[strlen(cur_seq)+2]);
> ^
> hhalignment.C:254:47: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[k]=new(char[strlen(cur_seq)+2]);
> ^
> hhalignment.C:256:61: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> I[k]=new(short unsigned int[strlen(cur_seq)+2]);
> ^
> In file included from hhblits.C:143:0:
> hhalignment.C:315:50: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> sname[k] = new(char[strlen(cur_name)+1]);
> ^
> hhalignment.C:431:41: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> seq[k]=new(char[strlen(cur_seq)+2]);
> ^
> hhalignment.C:433:39: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[k]=new(char[strlen(cur_seq)+2]);
> ^
> hhalignment.C:435:53: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> I[k]=new(short unsigned int[strlen(cur_seq)+2]);
> ^
> hhalignment.C: In member function 'void Alignment::Compress(const char*)':
> hhalignment.C:649:36: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> if (nres==NULL) nres=new(int[N_in]);
> ^
> hhalignment.C: In member function 'void Alignment::GetSeqsFromHMM(HMM*)':
> hhalignment.C:923:44: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> seq[k]=new(char[strlen(q->seq[qk])+1]);
> ^
> hhalignment.C:926:42: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[k]=new(char[strlen(q->seq[qk])+1]);
> ^
> hhalignment.C:928:56: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> I[k]=new(short unsigned int[strlen(q->seq[qk])+1]);
> ^
> hhalignment.C:949:50: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> sname[k] = new(char[strlen(q->sname[qk])+1]);
> ^
> hhalignment.C: In member function 'int Alignment::FilterForDisplay(int, int,
> int, float, int)':
> hhalignment.C:972:33: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> char *dummy = new(char[N_in+1]);
> ^
> hhalignment.C: In member function 'int Alignment::Filter2(char*, int, int,
> float, int, int, int)':
> hhalignment.C:1031:28: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted;
> in[k]=0: seq k has not yet been accepted at current seqid
> ^
> hhalignment.C:1032:30: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0;
> ^
> hhalignment.C:1033:25: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> int* Nmax=new(int[L+2]); // position-dependent
> maximum-sequence-identity threshold for filtering? (variable used in former
> version was idmax)
> ^
> hhalignment.C:1034:29: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL]
> ^
> hhalignment.C:1035:34: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold
> used in previous round of filtering (with lower seqid)
> ^
> hhalignment.C:1036:22: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> int* N=new(int[L+2]); // N[i] number of already accepted
> sequences at position i
> ^
> hhalignment.C:1064:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> first=new(int[N_in]);// first non-gap position in sequence k
> ^
> hhalignment.C:1065:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> last =new(int[N_in]);// last non-gap position in sequence k
> ^
> hhalignment.C:1079:25: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> nres=new(int[N_in]);
> ^
> hhalignment.C:1095:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> ksort=new(int[N_in]); // never reuse alignment object for new
> alignment with more sequences
> ^
> hhalignment.C: In member function 'int Alignment::FilterWithCoreHMM(char*,
> float, HMM*)':
> hhalignment.C:1303:34: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore
> ^
> hhalignment.C:1312:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> first=new(int[N_in]);// first non-gap position in sequence k
> ^
> hhalignment.C:1313:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> last =new(int[N_in]);// last non-gap position in sequence k
> ^
> hhalignment.C:1326:25: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> nres=new(int[N_in]);
> ^
> hhalignment.C: In member function 'void
> Alignment::FrequenciesAndTransitions(HMM*, char*, bool)':
> hhalignment.C:1598:41: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> q->seq[q->ncons]=new(char[L+2]);
> ^
> hhalignment.C:1605:56: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> q->sname[q->nfirst]=new(char[strlen(name)+11]);
> ^
> hhalignment.C:1609:42: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> q->seq[q->nfirst]=new(char[L+2]);
> ^
> hhalignment.C:1661:52: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> q->sname[nn]=new(char[strlen(sname[k])+1]);
> ^
> hhalignment.C:1664:48: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> q->seq[nn]=new(char[strlen(seq[k])+1]);
> ^
> hhalignment.C: In member function 'void
> Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM*, char*)':
> hhalignment.C:1764:20: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> n = new(int*[L+2]);
> ^
> hhalignment.C:1823:18: warning: suggest explicit braces to avoid ambiguous
> 'else' [-Wparentheses]
> if (ncol<NCOLMIN)
> ^
> hhalignment.C:1876:43: error: call of overloaded 'log2(float)' is ambiguous
> q->tr[i][M2M]=log2(q->tr[i][M2M]/sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:143:0:
> hhalignment.C:1877:43: error: call of overloaded 'log2(float)' is ambiguous
> q->tr[i][M2I]=log2(q->tr[i][M2I]/sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:143:0:
> hhalignment.C:1878:43: error: call of overloaded 'log2(float)' is ambiguous
> q->tr[i][M2D]=log2(q->tr[i][M2D]/sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:143:0:
> hhalignment.C: In member function 'void
> Alignment::Transitions_from_I_state(HMM*, char*)':
> hhalignment.C:1980:20: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> n = new(int*[L+2]);
> ^
> hhalignment.C:2044:18: warning: suggest explicit braces to avoid ambiguous
> 'else' [-Wparentheses]
> if (ncol>=NCOLMIN)
> ^
> hhalignment.C:2108:43: error: call of overloaded 'log2(float)' is ambiguous
> q->tr[i][I2M]=log2(q->tr[i][I2M]/sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:143:0:
> hhalignment.C:2109:43: error: call of overloaded 'log2(float)' is ambiguous
> q->tr[i][I2I]=log2(q->tr[i][I2I]/sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:143:0:
> hhalignment.C: In member function 'void
> Alignment::Transitions_from_D_state(HMM*, char*)':
> hhalignment.C:2173:20: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> n = new(int*[L+2]);
> ^
> hhalignment.C:2240:18: warning: suggest explicit braces to avoid ambiguous
> 'else' [-Wparentheses]
> if (ncol<NCOLMIN)
> ^
> hhalignment.C:2314:43: error: call of overloaded 'log2(float)' is ambiguous
> q->tr[i][D2M]=log2(q->tr[i][D2M]/sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:143:0:
> hhalignment.C:2315:43: error: call of overloaded 'log2(float)' is ambiguous
> q->tr[i][D2D]=log2(q->tr[i][D2D]/sum);
> ^
> In file included from /usr/include/features.h:364:0,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/os_defines.h:39,
> from
> /usr/include/x86_64-linux-gnu/c++/6/bits/c++config.h:495,
> from /usr/include/c++/6/iostream:38,
> from hhblits.C:62:
> /usr/include/x86_64-linux-gnu/bits/mathcalls.h:144:1: note: candidate: double
> log2(double)
> __MATHCALL (log2,, (_Mdouble_ __x));
> ^
> In file included from /usr/include/c++/6/math.h:36:0,
> from hhblits.C:70:
> /usr/include/c++/6/cmath:1546:3: note: candidate: constexpr long double
> std::log2(long double)
> log2(long double __x)
> ^~~~
> /usr/include/c++/6/cmath:1542:3: note: candidate: constexpr float
> std::log2(float)
> log2(float __x)
> ^~~~
> In file included from hhblits.C:128:0:
> util.C:58:14: note: candidate: float log2(float)
> inline float log2(float x) {return (x<=0?
> (float)(-100000):1.442695041*log(x));}
> ^~~~
> In file included from hhblits.C:143:0:
> hhalignment.C: In member function 'void Alignment::MergeMasterSlave(Hit&,
> Alignment&, char*)':
> hhalignment.C:2430:39: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> char* cur_seq = new(char[par.maxcol]); // Sequence currently read in
> ^
> hhalignment.C:2442:32: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> int* imatch=new(int[hit.j2+1]);
> ^
> hhalignment.C:2574:47: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> char* new_seq=new(char[2*maxcol]);
> ^
> hhalignment.C:2587:28: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> seq[N_in]=new(char[h]);
> ^
> hhalignment.C:2590:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[N_in]=new(char[h]);
> ^
> hhalignment.C:2592:40: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> I[N_in]=new(short unsigned int[h]);
> ^
> hhalignment.C:2594:52: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> sname[N_in]=new(char[strlen(Tali.sname[k])+1]);
> ^
> hhalignment.C: In member function 'void Alignment::AddSequence(char*, int*)':
> hhalignment.C:2625:24: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[N_in]=new(char[L+2]);
> ^
> hhalignment.C: In member function 'void Alignment::AddSSPrediction(char*,
> char*)':
> hhalignment.C:2663:30: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> seq[N_in]=new(char[L+2]);
> ^
> hhalignment.C:2665:28: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[N_in]=new(char[L+2]);
> ^
> hhalignment.C:2667:42: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> I[N_in]=new(short unsigned int[L+2]);
> ^
> hhalignment.C:2686:30: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> seq[N_in]=new(char[L+2]);
> ^
> hhalignment.C:2688:28: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> X[N_in]=new(char[L+2]);
> ^
> hhalignment.C:2690:42: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> I[N_in]=new(short unsigned int[L+2]);
> ^
> hhalignment.C: In member function 'void
> Alignment::GetPositionSpecificWeights(float**)':
> hhalignment.C:2743:24: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> n = new(int*[L+2]);
> ^
> In file included from hhblits.C:144:0:
> hhhit.C: In member function 'void Hit::Delete()':
> hhhit.C:122:5: warning: this 'for' clause does not guard...
> [-Wmisleading-indentation]
> for (int k=0; k<n_display; ++k) delete[] sname[k]; delete[] sname;
> ^~~
> hhhit.C:122:56: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the 'for'
> for (int k=0; k<n_display; ++k) delete[] sname[k]; delete[] sname;
> ^~~~~~
> hhhit.C:125:5: warning: this 'for' clause does not guard...
> [-Wmisleading-indentation]
> for (int k=0; k<n_display; ++k) delete[] seq[k]; delete[] seq;
> ^~~
> hhhit.C:125:54: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the 'for'
> for (int k=0; k<n_display; ++k) delete[] seq[k]; delete[] seq;
> ^~~~~~
> hhhit.C: In member function 'void Hit::AllocateBacktraceMatrix(int, int)':
> hhhit.C:141:20: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bMM=new(char*[Nq]);
> ^
> hhhit.C:142:20: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bMI=new(char*[Nq]);
> ^
> hhhit.C:143:20: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bIM=new(char*[Nq]);
> ^
> hhhit.C:144:20: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bDG=new(char*[Nq]);
> ^
> hhhit.C:145:20: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bGD=new(char*[Nq]);
> ^
> hhhit.C:146:25: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> cell_off=new(char*[Nq]);
> ^
> hhhit.C:149:26: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bMM[i]=new(char[Nt]);
> ^
> hhhit.C:150:26: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bMI[i]=new(char[Nt]);
> ^
> hhhit.C:151:26: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bIM[i]=new(char[Nt]);
> ^
> hhhit.C:152:26: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bGD[i]=new(char[Nt]);
> ^
> hhhit.C:153:26: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> bDG[i]=new(char[Nt]);
> ^
> hhhit.C:154:31: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> cell_off[i]=new(char[Nt]);
> ^
> hhhit.C: In member function 'void Hit::AllocateForwardMatrix(int, int)':
> hhhit.C:192:23: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> F_MM=new(double*[Nq]);
> ^
> hhhit.C:199:25: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> scale=new(double[Nq+1]); // need Nq+3?
> ^
> hhhit.C:202:31: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> F_MM[i] = new(double[Nt]);
> ^
> hhhit.C: In member function 'void Hit::AllocateBackwardMatrix(int, int)':
> hhhit.C:252:23: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> B_MM=new(double*[Nq]);
> ^
> hhhit.C:261:31: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> B_MM[i] = new(double[Nt]);
> ^
> hhhit.C: In member function 'void Hit::AllocateIndices(int)':
> hhhit.C:291:19: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> i = new(int[len]);
> ^
> hhhit.C:292:19: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> j = new(int[len]);
> ^
> hhhit.C: In member function 'void Hit::Backtrace(HMM*, HMM*)':
> hhhit.C:1147:30: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> S = new( float[nsteps+1]);
> ^
> hhhit.C:1148:30: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> S_ss = new( float[nsteps+1]);
> ^
> hhhit.C: In member function 'void Hit::BacktraceMAC(HMM*, HMM*)':
> hhhit.C:1487:30: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> S = new( float[nsteps+1]);
> ^
> hhhit.C:1488:30: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> S_ss = new( float[nsteps+1]);
> ^
> hhhit.C:1489:37: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> P_posterior = new( float[nsteps+1]);
> ^
> hhhit.C: In member function 'void Hit::InitializeBacktrace(HMM*, HMM*)':
> hhhit.C:1795:43: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> longname=new(char[strlen(t->longname)+1]);
> ^
> hhhit.C:1796:39: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> name =new(char[strlen(t->name)+1]);
> ^
> hhhit.C:1797:39: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> file =new(char[strlen(t->file)+1]);
> ^
> hhhit.C:1808:30: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> this->i = new( int[i2+j2+2]);
> ^
> hhhit.C:1809:30: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> this->j = new( int[i2+j2+2]);
> ^
> hhhit.C:1810:31: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> states = new( char[i2+j2+2]);
> ^
> hhhit.C:1813:32: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname=new(char*[t->n_display]);
> ^
> hhhit.C:1814:32: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq =new(char*[t->n_display]);
> ^
> hhhit.C:1833:46: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> sname[k] = new(char[strlen(t->sname[k])+1]);
> ^
> hhhit.C:1834:44: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> seq[k] = new(char[strlen(t->seq[k])+1]);
> ^
> hhhit.C:1840:34: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> dbfile = new(char[strlen(ptr)+1]);
> ^
> In file included from hhblits.C:145:0:
> hhhalfalignment.C: In constructor 'HalfAlignment::HalfAlignment(int)':
> hhhalfalignment.C:46:25: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> h = new(int[maxseqdis]); //h[k] = next position of sequence k to be
> written
> ^
> hhhalfalignment.C:47:27: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k
> of output alignment
> ^
> hhhalfalignment.C:48:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of
> last residue AT OR BEFORE match state i in seq k
> ^
> hhhalfalignment.C:49:26: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> m = new(int*[maxseqdis]); //counts positions: m[k][i] = position
> of match state i in string seq[k]
> ^
> In file included from hhblits.C:262:0:
> hhprefilter.C: In function 'void init_no_prefiltering()':
> hhprefilter.C:794:52: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]);
> ^
> hhprefilter.C: In function 'void init_prefilter()':
> hhprefilter.C:846:45: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> dbnames[num_dbs]=new(char[strlen(word)+1]);
> ^
> hhprefilter.C: In function 'void prefilter_db()':
> hhprefilter.C:1045:42: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> __m128i** workspace = new(__m128i*[cpu]);
> ^
> hhprefilter.C:1144:56: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> dbfiles_old[ndb_old]=new(char[strlen(db_name)+1]);
> ^
> hhprefilter.C:1150:56: warning: non-constant array new length must be
> specified without parentheses around the type-id [-Wvla]
> dbfiles_new[ndb_new]=new(char[strlen(db_name)+1]);
> ^
> hhblits.C: In function 'void ReadQueryA3MFile()':
> hhblits.C:781:54: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> Qali.longname = new(char[strlen(q->longname)+1]);
> ^
> hhblits.C: In function 'void DoViterbiSearch(char**, int, bool)':
> hhblits.C:914:55: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]);
> ^
> hhblits.C: In function 'void RescoreWithViterbiKeepAlignment(int)':
> hhblits.C:1120:51: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> dbfiles[ndb]=new(char[strlen(hit_cur.dbfile)+1]);
> ^
> hhblits.C: In function 'void perform_realign(char**, int)':
> hhblits.C:1406:57: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> hit[bin]->dbfile = new(char[strlen(hit_cur.dbfile)+1]);
> ^
> hhblits.C:1716:59: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> hit[bin]->dbfile = new(char[strlen(dbfiles[idb])+1]);
> ^
> hhblits.C: In function 'int main(int, char**)':
> hhblits.C:2140:25: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> format = new(int[bins]);
> ^
> hhblits.C:2190:5: warning: this 'if' clause does not guard...
> [-Wmisleading-indentation]
> if (par.prefilter)
> ^~
> hhblits.C:2192:7: note: ...this statement, but the latter is misleadingly
> indented as if it is guarded by the 'if'
> prefilter_db(); // in hhprefilter.C
> ^~~~~~~~~~~~
> hhblits.C:2240:58: warning: non-constant array new length must be specified
> without parentheses around the type-id [-Wvla]
> dbfiles_new[ndb_new]=new(char[strlen(dbfiles_old[a])+1]);
> ^
> make[3]: *** [hhblits] Error 1
The full build log is available from:
http://people.debian.org/~lucas/logs/2016/07/13/hhsuite_2.0.16-6_unstable_gcc6.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
