Source: hhsuite Version: 2.0.16-6 Severity: serious Tags: stretch sid User: debian...@lists.debian.org 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.
