Go to:
Gentoo Home
Documentation
Forums
Lists
Bugs
Planet
Store
Wiki
Get Gentoo!
Gentoo's Bugzilla – Attachment 447182 Details for
Bug 594692
sci-biology/clustal-omega-1.2.2-r1 : util-C.h:54:26: error: ‘float log2(float)’ conflicts with a previous declaration
Home
|
New
–
[Ex]
|
Browse
|
Search
|
Privacy Policy
|
[?]
|
Reports
|
Requests
|
Help
|
New Account
|
Log In
[x]
|
Forgot Password
Login:
[x]
sci-biology:clustal-omega-1.2.2-r1:20160921-115536.log
sci-biology:clustal-omega-1.2.2-r1:20160921-115536.log (text/plain), 92.72 KB, created by
Toralf Förster
on 2016-09-21 17:05:54 UTC
(
hide
)
Description:
sci-biology:clustal-omega-1.2.2-r1:20160921-115536.log
Filename:
MIME Type:
Creator:
Toralf Förster
Created:
2016-09-21 17:05:54 UTC
Size:
92.72 KB
patch
obsolete
> * 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... GNU >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc >checking whether the C compiler works... yes >checking for C compiler default output file name... a.out >checking for suffix of executables... >checking whether we are cross compiling... no >checking for suffix of object files... o >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes >checking dependency style of x86_64-pc-linux-gnu-gcc... none >checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E >checking for grep that handles long lines and -e... /bin/grep >checking for egrep... /bin/grep -E >checking for ANSI C header files... yes >checking for sys/types.h... yes >checking for sys/stat.h... yes >checking for stdlib.h... yes >checking for string.h... yes >checking for memory.h... yes >checking for strings.h... yes >checking for inttypes.h... yes >checking for stdint.h... yes >checking for unistd.h... yes >checking minix/config.h usability... no >checking minix/config.h presence... no >checking for minix/config.h... no >checking whether it is safe to define __EXTENSIONS__... yes >checking build system type... x86_64-pc-linux-gnu >checking host system type... x86_64-pc-linux-gnu >checking whether make sets $(MAKE)... (cached) yes >checking how to print strings... printf >checking for a sed that does not truncate output... /bin/sed >checking for fgrep... /bin/grep -F >checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld >checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes >checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B >checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm >checking whether ln -s works... yes >checking the maximum length of command line arguments... 1572864 >checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop >checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop >checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r >checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump >checking how to recognize dependent libraries... pass_all >checking for x86_64-pc-linux-gnu-dlltool... no >checking for dlltool... no >checking how to associate runtime and link libraries... printf %s\n >checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar >checking for archiver @FILE support... @ >checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip >checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib >checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok >checking for sysroot... no >checking for a working dd... /bin/dd >checking how to truncate binary pipes... /bin/dd bs=4096 count=1 >checking for x86_64-pc-linux-gnu-mt... no >checking for mt... mt >checking if mt is a manifest tool... no >checking for dlfcn.h... yes >checking for objdir... .libs >checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no >checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC >checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes >checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes >checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes >checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes >checking whether -lc should be explicitly linked in... no >checking dynamic linker characteristics... GNU/Linux ld.so >checking how to hardcode library paths into programs... immediate >checking whether stripping libraries is possible... yes >checking if libtool supports shared libraries... yes >checking whether to build shared libraries... yes >checking whether to build static libraries... yes >checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc >checking whether we are using the GNU C compiler... (cached) yes >checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes >checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... (cached) none needed >checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... (cached) yes >checking dependency style of x86_64-pc-linux-gnu-gcc... (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... (cached) yes >checking stdarg.h usability... yes >checking stdarg.h presence... yes >checking for stdarg.h... yes >checking stdio.h usability... yes >checking stdio.h presence... yes >checking for stdio.h... yes >checking for stdlib.h... (cached) yes >checking for string.h... (cached) yes >checking time.h usability... yes >checking time.h presence... yes >checking for time.h... yes >checking for unistd.h... (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 âfloat log2(float)â: >util-C.h:54:26: error: âfloat log2(float)â 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 âconstexpr float std::log2(float)â > log2(float __x) > ^~~~ >In file included from hhalign.cpp:56:0: >util-C.h: In function âfloat log10(float)â: >util-C.h:55:27: error: âfloat log10(float)â 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 âconstexpr float std::log10(float)â > log10(float __x) > ^~~~~ >In file included from hhalign.cpp:56:0: >util-C.h: In function âchar* sprintg(float, int)â: >util-C.h:246:35: error: call of overloaded âlog10(float)â 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 âvoid ReadDefaultsFile(int&, char**)â: >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 âvoid SetSubstitutionMatrix()â: >hhmatrices-C.h:433:35: error: call of overloaded âlog2(float)â 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 âlog2(float&)â 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 âlog2(float&)â 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 âvoid SetRnaSubstitutionMatrix()â: >hhmatrices-C.h:541:35: error: call of overloaded âlog2(float)â 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 âlog2(float&)â 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 âlog2(float&)â 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 âvoid SetDnaSubstitutionMatrix()â: >hhmatrices-C.h:649:35: error: call of overloaded âlog2(float)â 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 âlog2(float&)â 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 âlog2(float&)â 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 âvoid SetSecStrucSubstitutionMatrix()â: >hhmatrices-C.h:742:38: error: call of overloaded âlog2(float&)â 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 âlog2(float&)â 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 âHMM& HMM::operator=(HMM&)â: >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 âint HMM::Read(FILE*, char*)â: >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 âint HMM::ReadHMMer(FILE*, char*)â: >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 âint HMM::ReadHMMer3(FILE*, char*)â: >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 âlog2(float)â 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 âlog2(float)â 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 âvoid HMM::InsertCalibration(char*)â: >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 âAlignment::Alignment(int, int)â: >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 âvoid Alignment::Read(FILE*, char*, char*)â: >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 âvoid Alignment::Compress(const char*)â: >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 âint Alignment::FilterForDisplay(int, int, int, float, int)â: >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 âint Alignment::Filter2(char*, int, int, float, int, int, int)â: >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 âint Alignment::HomologyFilter(int, float, float)â: >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 âint Alignment::FilterWithCoreHMM(char*, float, HMM&)â: >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 âvoid Alignment::FrequenciesAndTransitions(HMM&, char*)â: >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 âvoid Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)â: >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 âlog2(float)â 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 âlog2(float)â 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 âlog2(float)â 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 âvoid Alignment::Transitions_from_I_state(HMM&, char*)â: >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 âlog2(float)â 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 âlog2(float)â 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 âvoid Alignment::Transitions_from_D_state(HMM&, char*)â: >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 âlog2(float)â 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 âlog2(float)â 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 âvoid Alignment::MergeMasterSlave(Hit&, char*)â: >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 âvoid Alignment::AddSequence(char*, int*)â: >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 âvoid Alignment::GetPositionSpecificWeights(float**)â: >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 âvoid Alignment::Transfer(char**, int)â: >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 âvoid Hit::AllocateBacktraceMatrix(int, int)â: >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 âvoid Hit::AllocateForwardMatrix(int, int)â: >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 âvoid Hit::AllocateBackwardMatrix(int, int)â: >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 âvoid Hit::Viterbi(HMM&, HMM&, float**)â: >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 âvoid Hit::Backtrace(HMM&, HMM&)â: >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 âvoid Hit::StochasticBacktrace(HMM&, HMM&, char)â: >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 âvoid Hit::BacktraceMAC(HMM&, HMM&)â: >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 âvoid Hit::InitializeBacktrace(HMM&, HMM&)â: >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 âHalfAlignment::HalfAlignment(int)â: >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 âvoid FullAlignment::PrintHHR(FILE*, Hit&)â: >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 âvoid HitList::TransitiveScoring()â: >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<M; m++) Cinv[m] = new(double[M]); > ^ >hhhitlist-C.h: In member function âvoid HitList::TransitiveScoring2()â: >hhhitlist-C.h:1651:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Z = new(float*[N]); > ^ >hhhitlist-C.h:1654:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Z[k] = new(float[N]); > ^ >hhhitlist-C.h:1659:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > C = new(float*[N]); > ^ >hhhitlist-C.h:1662:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > C[k] = new(float[N]); > ^ >hhhitlist-C.h:1669:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Zq = new(float[N]); > ^ >hhhitlist-C.h:1670:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Ztq = new(float[N]); > ^ >hhhitlist-C.h:1671:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Zrq = new(float[N]); > ^ >hhhitlist-C.h:1672:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > fold = new(char*[N]); > ^ >hhhitlist-C.h:1673:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > fam = new(char*[N]); > ^ >hhhitlist-C.h:1674:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Prob = new(float[N]); > ^ >hhhitlist-C.h:1675:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > ll = new(int[N]); > ^ >hhhitlist-C.h:1676:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > w = new(float[N]); > ^ >hhhitlist-C.h:1740:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Csub = new(double*[M]); > ^ >hhhitlist-C.h:1741:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Cinv = new(double*[M]); > ^ >hhhitlist-C.h:1744:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Csub[m] = new(double[M]); > ^ >hhhitlist-C.h:1745:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Cinv[m] = new(double[M]); > ^ >hhhitlist-C.h:1822:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Csub = new(double*[M]); > ^ >hhhitlist-C.h:1825:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Csub[m] = new(double[M]); > ^ >hhhitlist-C.h:1839:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Cinv = new(double*[M]); > ^ >hhhitlist-C.h:1840:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > for (m=0; m<M; m++) Cinv[m] = new(double[M]); > ^ >hhhitlist-C.h: In member function âvoid HitList::TransitiveScoring3()â: >hhhitlist-C.h:2021:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Z = new(float*[N]); > ^ >hhhitlist-C.h:2024:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Z[k] = new(float[N]); > ^ >hhhitlist-C.h:2029:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > C = new(float*[N]); > ^ >hhhitlist-C.h:2032:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > C[k] = new(float[N]); > ^ >hhhitlist-C.h:2039:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Zq = new(float[N]); > ^ >hhhitlist-C.h:2040:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Ztq = new(float[N]); > ^ >hhhitlist-C.h:2041:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Zrq = new(float[N]); > ^ >hhhitlist-C.h:2042:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > fold = new(char*[N]); > ^ >hhhitlist-C.h:2043:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > fam = new(char*[N]); > ^ >hhhitlist-C.h:2044:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Prob = new(float[N]); > ^ >hhhitlist-C.h:2045:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > ll = new(int[N]); > ^ >hhhitlist-C.h:2046:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > w = new(float[N]); > ^ >hhhitlist-C.h:2115:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Csub = new(double*[M]); > ^ >hhhitlist-C.h:2116:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Cinv = new(double*[M]); > ^ >hhhitlist-C.h:2119:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Csub[m] = new(double[M]); > ^ >hhhitlist-C.h:2120:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Cinv[m] = new(double[M]); > ^ >hhhitlist-C.h:2187:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Csub = new(double*[M]); > ^ >hhhitlist-C.h:2190:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Csub[m] = new(double[M]); > ^ >hhhitlist-C.h:2204:38: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Cinv = new(double*[M]); > ^ >hhhitlist-C.h:2205:51: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > for (m=0; m<M; m++) Cinv[m] = new(double[M]); > ^ >hhhitlist-C.h: In member function âvoid HitList::TransitiveScoring4()â: >hhhitlist-C.h:2386:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Z = new(float*[N]); > ^ >hhhitlist-C.h:2389:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Z[k] = new(float[N]); > ^ >hhhitlist-C.h:2394:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > C = new(float*[N]); > ^ >hhhitlist-C.h:2397:26: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > C[k] = new(float[N]); > ^ >hhhitlist-C.h:2404:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Zq = new(float[N]); > ^ >hhhitlist-C.h:2405:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Ztq = new(float[N]); > ^ >hhhitlist-C.h:2406:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Zrq = new(float[N]); > ^ >hhhitlist-C.h:2407:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > fold = new(char*[N]); > ^ >hhhitlist-C.h:2408:21: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > fam = new(char*[N]); > ^ >hhhitlist-C.h:2409:22: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Prob = new(float[N]); > ^ >hhhitlist-C.h:2410:18: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > ll = new(int[N]); > ^ >hhhitlist-C.h:2411:19: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > w = new(float[N]); > ^ >hhhitlist-C.h:2473:37: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Csub = new(double*[M]); > ^ >hhhitlist-C.h:2476:27: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Csub[m] = new(double[M]); > ^ >hhhitlist-C.h:2539:34: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** Csub = new(double*[M]); > ^ >hhhitlist-C.h:2542:31: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > Csub[m] = new(double[M]); > ^ >hhhitlist-C.h: In member function âvoid HitList::InvertMatrix(double**, double**, int)â: >hhhitlist-C.h:2841:30: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double** V = new(double*[N]); > ^ >hhhitlist-C.h:2842:29: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > double* s = new(double[N]); > ^ >hhhitlist-C.h:2843:43: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > for (k=0; k<N; k++) V[k] = new(double[N]); > ^ >hhhitlist-C.h: In member function âvoid HitList::SVD(double**, int, double*, double**)â: >hhhitlist-C.h:2926:20: warning: non-constant array new length must be specified without parentheses around the type-id [-Wvla] > rv1=new(double[n]); > ^ >make[3]: *** [Makefile:447: hhalign.lo] Error 1 >make[3]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2/src/hhalign' >make[2]: *** [Makefile:652: all-recursive] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2/src' >make[1]: *** [Makefile:426: all] Error 2 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2/src' >make: *** [Makefile:478: all-recursive] Error 1 > * ERROR: sci-biology/clustal-omega-1.2.2-r1::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/clustal-omega-1.2.2-r1::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/clustal-omega-1.2.2-r1::gentoo'`. > * The complete build log is located at '/var/log/portage/sci-biology:clustal-omega-1.2.2-r1:20160921-115536.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2' > * S: '/var/tmp/portage/sci-biology/clustal-omega-1.2.2-r1/work/clustal-omega-1.2.2'
<b>You cannot view the attachment while viewing its details because your browser does not support IFRAMEs. <a href="attachment.cgi?id=447182">View the attachment on a separate page</a>.</b>
View Attachment As Raw
Actions:
View
Attachments on
bug 594692
:
447178
|
447180
| 447182
