* Package: sci-biology/clustal-omega-1.2.2-r1 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking clustal-omega-1.2.2.tar.gz to /var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2 ... * Running eautoreconf in '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2' ... * Running libtoolize --install --copy --force --automake ... [ ok ] * Running aclocal -I m4 ... [ ok ] * Running autoconf --force ... [ ok ] * Running autoheader ... [ ok ] * Running automake --add-missing --copy --force-missing ... [ ok ] * Running elibtoolize in: clustal-omega-1.2.2/ * Applying portage/1.2.0 patch ... * Applying sed/1.5.6 patch ... * Applying as-needed/2.4.3 patch ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2 ... * econf: updating clustal-omega-1.2.2/config.sub with /usr/share/gnuconfig/config.sub * econf: updating clustal-omega-1.2.2/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/clustal-omega-1.2.2-r1 --htmldir=/usr/share/doc/clustal-omega-1.2.2-r1/html --libdir=/usr/lib64 configure: Welcome to Clustal Omega - version 1.2.2 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 checking for a BSD-compatible install... /usr/lib/portage/python2.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for style of include used by make... 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(cached) none checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++ checking whether we are using the GNU C++ compiler... yes checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes checking dependency style of x86_64-pc-linux-gnu-g++... none checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64 checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... 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(cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... yes checking for fseeko64... yes checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 16 checking if malloc debugging is wanted... no checking whether to build with debug information... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2 ... make -j1 Making all in src make[1]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2/src' make all-recursive make[2]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2/src' Making all in hhalign make[3]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2/src/hhalign' /bin/sh ../../libtool --tag=CXX --mode=compile x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -march=native -O2 -pipe -c -o hhalign.lo hhalign.cpp libtool: compile: x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I../../src -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -march=native -O2 -pipe -c hhalign.cpp -fPIC -DPIC -o .libs/hhalign.o In file included from hhalign.cpp:56:0: util-C.h: In function ‘float log2(float)’: util-C.h:54:26: 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/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: previous declaration ‘constexpr float std::log2(float)’ log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h: In function ‘float log10(float)’: util-C.h:55:27: 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/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:380:3: note: previous declaration ‘constexpr float std::log10(float)’ log10(float __x) ^~~~~ In file included from hhalign.cpp:56:0: util-C.h: In function ‘char* sprintg(float, int)’: util-C.h:246:35: error: call of overloaded ‘log10(float)’ is ambiguous float log10val = log10(fabs(val)); ^ In file included from /usr/include/features.h:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:112:1: note: candidate: double log10(double) __MATHCALL (log10,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:384:3: note: candidate: constexpr long double std::log10(long double) log10(long double __x) ^~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:380:3: note: candidate: constexpr float std::log10(float) log10(float __x) ^~~~~ In file included from hhalign.cpp:56:0: util-C.h:55:14: note: candidate: float log10(float) inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));} ^~~~~ In file included from hhalign.cpp:62:0: hhutil-C.h: In function ‘void ReadDefaultsFile(int&, char**)’: hhutil-C.h:516:53: 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.h:521:56: 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 hhalign.cpp:63:0: hhmatrices-C.h: In function ‘void SetSubstitutionMatrix()’: hhmatrices-C.h:433:35: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h:443:56: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h:447:37: error: call of overloaded ‘log2(float&)’ is ambiguous entropy-=P[a][b]*log2(R[a][b]); ^ In file included from /usr/include/features.h:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h: In function ‘void SetRnaSubstitutionMatrix()’: hhmatrices-C.h:541:35: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h:551:56: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h:555:37: error: call of overloaded ‘log2(float&)’ is ambiguous entropy-=P[a][b]*log2(R[a][b]); ^ In file included from /usr/include/features.h:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h: In function ‘void SetDnaSubstitutionMatrix()’: hhmatrices-C.h:649:35: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h:659:56: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h:663:37: error: call of overloaded ‘log2(float&)’ is ambiguous entropy-=P[a][b]*log2(R[a][b]); ^ In file included from /usr/include/features.h:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h: In function ‘void SetSecStrucSubstitutionMatrix()’: hhmatrices-C.h:742:38: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:63:0: hhmatrices-C.h:753:36: error: call of overloaded ‘log2(float&)’ is ambiguous S33[B][cf][BB][ccf] = log2(sum); ^ In file included from /usr/include/features.h:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:70:0: hhhmm-C.h: In member function ‘HMM& HMM::operator=(HMM&)’: hhhmm-C.h:189:44: 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.h:194:40: 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.h: In member function ‘int HMM::Read(FILE*, char*)’: hhhmm-C.h:330:48: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in ^ hhhmm-C.h:361:43: 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.h:368:43: 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.h:464:40: 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.h: In member function ‘int HMM::ReadHMMer(FILE*, char*)’: hhhmm-C.h:736:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:757:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:778:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:860:55: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1036:46: 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.h:1038:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h:1041:29: 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.h:1059:44: 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.h:1063:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h: In member function ‘int HMM::ReadHMMer3(FILE*, char*)’: hhhmm-C.h:1238:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1259:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1280:77: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1336:74: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:70:0: hhhmm-C.h:1350:69: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1474:82: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:70:0: hhhmm-C.h:1530:49: 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.h:1532:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h:1535:32: 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.h:1553:47: 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.h:1555:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h: In member function ‘void HMM::InsertCalibration(char*)’: hhhmm-C.h:2110:39: 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.h:2139:44: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ In file included from hhalign.cpp:71:0: hhalignment-C.h: In constructor ‘Alignment::Alignment(int, int)’: hhalignment-C.h:85:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:86:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:87:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] l = new(int[maxres]); ^ hhalignment-C.h:88:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:89:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] I = new(short unsigned int*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:90:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] keep = new(char[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:91:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] display = new(char[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:92:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wg = new(float[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:93:28: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] nseqs = new(int[maxres+2]); /* MR1 */ ^ hhalignment-C.h: In member function ‘void Alignment::Read(FILE*, char*, char*)’: hhalignment-C.h:146:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char *cur_seq=new(char[par.maxColCnt]); ^ hhalignment-C.h:188:61: 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.h:190:59: 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.h:192:73: 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 hhalign.cpp:71:0: hhalignment-C.h:241:58: 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.h:356:45: 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.h:358:43: 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.h:360:57: 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.h: In member function ‘void Alignment::Compress(const char*)’: hhalignment-C.h:428:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */ ^ hhalignment-C.h:560:52: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] percent_gaps = new(float[par.maxColCnt]); ^ hhalignment-C.h:566:47: 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.h:804:50: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] match_state = new(char[par.maxColCnt]); ^ hhalignment-C.h: In member function ‘int Alignment::FilterForDisplay(int, int, int, float, int)’: hhalignment-C.h:966:35: 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.h: In member function ‘int Alignment::Filter2(char*, int, int, float, int, int, int)’: hhalignment-C.h:1029:30: 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.h:1030:32: 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.h:1031:27: 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 /* MR1, used to be called idmax*/ ^ hhalignment-C.h:1032:31: 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.h:1033:36: 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.h:1034:24: 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.h:1062:32: 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.h:1063:32: 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.h:1078:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] nres=new(int[N_in]); ^ hhalignment-C.h:1092:32: 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.h: In member function ‘int Alignment::HomologyFilter(int, float, float)’: hhalignment-C.h:1358:33: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query) ^ hhalignment-C.h: In member function ‘int Alignment::FilterWithCoreHMM(char*, float, HMM&)’: hhalignment-C.h:1409:36: 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.h:1418:32: 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.h:1419:32: 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.h:1432:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] nres=new(int[N_in]); ^ hhalignment-C.h: In member function ‘void Alignment::FrequenciesAndTransitions(HMM&, char*)’: hhalignment-C.h:1715:49: 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.h:1722:64: 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.h:1726:50: 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.h:1784:61: 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.h:1787:57: 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.h: In member function ‘void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)’: hhalignment-C.h:1874:41: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:1881:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wi = new(float[N_in+2]); ^ hhalignment-C.h:1891:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h:2050:41: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:71:0: hhalignment-C.h:2051:41: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:71:0: hhalignment-C.h:2052:41: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:71:0: hhalignment-C.h: In member function ‘void Alignment::Transitions_from_I_state(HMM&, char*)’: hhalignment-C.h:2166:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:2174:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wi = new(float[N_in+2]); ^ hhalignment-C.h:2185:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h:2312:47: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:71:0: hhalignment-C.h:2313:47: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:71:0: hhalignment-C.h: In member function ‘void Alignment::Transitions_from_D_state(HMM&, char*)’: hhalignment-C.h:2368:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:2377:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] wi = new(float[N_in+2]); /* FIXME: FS */ ^ hhalignment-C.h:2388:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h:2571:43: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:71:0: hhalignment-C.h:2572:43: 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:368:0, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/os_defines.h:39, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/x86_64-pc-linux-gnu/bits/c++config.h:495, from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/iostream:38, from hhalign.cpp:34: /usr/include/bits/mathcalls.h:144:1: note: candidate: double log2(double) __MATHCALL (log2,, (_Mdouble_ __x)); ^ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/math.h:36:0, from hhalign.cpp:39: /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1546:3: note: candidate: constexpr long double std::log2(long double) log2(long double __x) ^~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/6.2.0/include/g++-v6/cmath:1542:3: note: candidate: constexpr float std::log2(float) log2(float __x) ^~~~ In file included from hhalign.cpp:56:0: util-C.h:54:14: note: candidate: float log2(float) inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));} ^~~~ In file included from hhalign.cpp:71:0: hhalignment-C.h: In member function ‘void Alignment::MergeMasterSlave(Hit&, char*)’: hhalignment-C.h:2699:31: 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.h:2831:34: 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.h:2844:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment-C.h:2847:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X[N_in]=new(char[h]); ^ hhalignment-C.h:2849:35: 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.h:2851:47: 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.h: In member function ‘void Alignment::AddSequence(char*, int*)’: hhalignment-C.h:2882:23: 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.h: In member function ‘void Alignment::GetPositionSpecificWeights(float**)’: hhalignment-C.h:2932:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function ‘void Alignment::Transfer(char**, int)’: hhalignment-C.h:3049:59: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]); ^ hhalignment-C.h:3050:45: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] X[k] = new(char[iLen+2+GOOD_MEASURE]); ^ hhalignment-C.h:3051:47: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq[k] = new(char[iLen+2+GOOD_MEASURE]); ^ In file included from hhalign.cpp:72:0: hhhit-C.h: In member function ‘void Hit::AllocateBacktraceMatrix(int, int)’: hhhit-C.h:180:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMM=new(char*[Nq]); ^ hhhit-C.h:181:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMI=new(char*[Nq]); ^ hhhit-C.h:182:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bIM=new(char*[Nq]); ^ hhhit-C.h:183:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bDG=new(char*[Nq]); ^ hhhit-C.h:184:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bGD=new(char*[Nq]); ^ hhhit-C.h:185:25: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] cell_off=new(char*[Nq]); ^ hhhit-C.h:188:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMM[i]=new(char[Nt]); ^ hhhit-C.h:189:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bMI[i]=new(char[Nt]); ^ hhhit-C.h:190:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bIM[i]=new(char[Nt]); ^ hhhit-C.h:191:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bGD[i]=new(char[Nt]); ^ hhhit-C.h:192:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] bDG[i]=new(char[Nt]); ^ hhhit-C.h:193:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] cell_off[i]=new(char[Nt]); ^ hhhit-C.h: In member function ‘void Hit::AllocateForwardMatrix(int, int)’: hhhit-C.h:240:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MM=new(double*[Nq]); ^ hhhit-C.h:241:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MI=new(double*[Nq]); ^ hhhit-C.h:242:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_DG=new(double*[Nq]); ^ hhhit-C.h:243:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_IM=new(double*[Nq]); ^ hhhit-C.h:244:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_GD=new(double*[Nq]); ^ hhhit-C.h:245:25: 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.h:248:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MM[i] = new(double[Nt]); ^ hhhit-C.h:249:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_MI[i] = new(double[Nt]); ^ hhhit-C.h:250:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_DG[i] = new(double[Nt]); ^ hhhit-C.h:251:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_IM[i] = new(double[Nt]); ^ hhhit-C.h:252:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] F_GD[i] = new(double[Nt]); ^ hhhit-C.h: In member function ‘void Hit::AllocateBackwardMatrix(int, int)’: hhhit-C.h:297:23: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] B_MM=new(double*[Nq]); ^ hhhit-C.h:304:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] B_MM[i] = new(double[Nt]); ^ hhhit-C.h: In member function ‘void Hit::Viterbi(HMM&, HMM&, float**)’: hhhit-C.h:377:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sMM = new(float[par.maxResLen]); // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match) ^ hhhit-C.h:378:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sGD = new(float[par.maxResLen]); // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete) ^ hhhit-C.h:379:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sDG = new(float[par.maxResLen]); // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap) ^ hhhit-C.h:380:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sIM = new(float[par.maxResLen]); // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match) ^ hhhit-C.h:381:42: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] float *sMI = new(float[par.maxResLen]); // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins) ^ hhhit-C.h: In member function ‘void Hit::Backtrace(HMM&, HMM&)’: hhhit-C.h:1127:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1128:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1129:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h: In member function ‘void Hit::StochasticBacktrace(HMM&, HMM&, char)’: hhhit-C.h:1229:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double* scale_cum = new(double[q.L+2]); ^ hhhit-C.h:1248:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double* sumF=new(double[q.L+t.L]); ^ hhhit-C.h:1372:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1373:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1374:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h: In member function ‘void Hit::BacktraceMAC(HMM&, HMM&)’: hhhit-C.h:1476:40: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1477:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1478:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h:1479:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] P_posterior = new( float[nsteps+1]); ^ hhhit-C.h: In member function ‘void Hit::InitializeBacktrace(HMM&, HMM&)’: hhhit-C.h:1684:54: 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.h:1685:50: 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.h:1686:50: 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.h:1697:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] sname=new(char*[t.n_display])(); // Call Compare only once with irep=1 ^ hhhit-C.h:1698:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] seq =new(char*[t.n_display])(); // Call Compare only once with irep=1 ^ hhhit-C.h:1731:34: 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.h:1732:34: 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.h:1733:35: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] states = new( char[i2+j2+2])(); ^ In file included from hhalign.cpp:73:0: hhhalfalignment-C.h: In constructor ‘HalfAlignment::HalfAlignment(int)’: hhhalfalignment-C.h:67:25: 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.h:68:27: 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.h:69:26: 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.h:70:26: 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 hhalign.cpp:74:0: hhfullalignment-C.h: In member function ‘void FullAlignment::PrintHHR(FILE*, Hit&)’: hhfullalignment-C.h:360:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] lq = new(short unsigned int[qa->n+2]); ^ hhfullalignment-C.h:361:39: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] lt = new(short unsigned int[ta->n+2]); ^ In file included from hhalign.cpp:75:0: hhhitlist-C.h: In member function ‘void HitList::TransitiveScoring()’: hhhitlist-C.h:1286:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Z = new(float*[N]); ^ hhhitlist-C.h:1289:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Z[k] = new(float[N]); ^ hhhitlist-C.h:1294:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] C = new(float*[N]); ^ hhhitlist-C.h:1297:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] C[k] = new(float[N]); ^ hhhitlist-C.h:1304:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Zq = new(float[N]); ^ hhhitlist-C.h:1305:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Ztq = new(float[N]); ^ hhhitlist-C.h:1306:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Zrq = new(float[N]); ^ hhhitlist-C.h:1307:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] fold = new(char*[N]); ^ hhhitlist-C.h:1308:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] fam = new(char*[N]); ^ hhhitlist-C.h:1309:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Prob = new(float[N]); ^ hhhitlist-C.h:1310:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] ll = new(int[N]); ^ hhhitlist-C.h:1311:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] w = new(float[N]); ^ hhhitlist-C.h:1374:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Csub = new(double*[M]); ^ hhhitlist-C.h:1375:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Cinv = new(double*[M]); ^ hhhitlist-C.h:1378:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Csub[m] = new(double[M]); ^ hhhitlist-C.h:1379:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Cinv[m] = new(double[M]); ^ hhhitlist-C.h:1454:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Csub = new(double*[M]); ^ hhhitlist-C.h:1457:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] Csub[m] = new(double[M]); ^ hhhitlist-C.h:1471:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] double** Cinv = new(double*[M]); ^ hhhitlist-C.h:1472:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] for (m=0; m