sci-biology:clustal-omega-1.2.4-r1:20231204-110826.log

sci-biology:clustal-omega-1.2.4-r1:20231204-110826.log (text/plain), 14.69 KB, created by Toralf Förster on 2023-12-04 17:37:59 UTC

 * Package:    sci-biology/clustal-omega-1.2.4-r1:0
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox

>>> Unpacking source...
>>> Unpacking clustal-omega-1.2.4.tar.gz to /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work
>>> Source unpacked in /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work
>>> Preparing source in /var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4 ...
 * Running eautoreconf in '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4' ...
 * Running 'libtoolize --install --copy --force --automake' ...
 [ ok ]
 * Running 'aclocal -I m4 --system-acdir=/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/temp/aclocal' ...
 [ ok ]
 * Running 'autoconf --force' ...
 [ ok ]
 * Running 'autoheader' ...
 [ ok ]
 * Running 'automake --add-missing --copy --force-missing' ...
 [ ok ]
 * Running elibtoolize in: clustal-omega-1.2.4/
 *   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-1.2.4-r1/work/clustal-omega-1.2.4 ...
 * econf: updating clustal-omega-1.2.4/config.guess with /usr/share/gnuconfig/config.guess
 * econf: updating clustal-omega-1.2.4/config.sub with /usr/share/gnuconfig/config.sub
./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 --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --disable-static --docdir=/usr/share/doc/clustal-omega-1.2.4-r1 --htmldir=/usr/share/doc/clustal-omega-1.2.4-r1/html --with-sysroot=/ --libdir=/usr/lib64
configure:

    Welcome to Clustal Omega - version 1.2.4 (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/python3.11/ebuild-helpers/xattr/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports the include directive... yes (GNU style)
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 the compiler supports GNU C... yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... 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 for stdio.h... yes
checking for stdlib.h... yes
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checking whether it is safe to define __EXTENSIONS__... yes
checking whether _XOPEN_SOURCE should be defined... no
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
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checking for grep that handles long lines and -e... /bin/grep
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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-file... no
checking for file... file
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... x86_64-pc-linux-gnu-dlltool
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... /
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... no
checking if : 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... no
checking for x86_64-pc-linux-gnu-gcc... (cached) x86_64-pc-linux-gnu-gcc
checking whether the compiler supports GNU C... (cached) yes
checking whether x86_64-pc-linux-gnu-gcc accepts -g... (cached) yes
checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... (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 the compiler supports GNU C++... yes
checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
checking for x86_64-pc-linux-gnu-g++ option to enable C++11 features... none needed
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 egrep... (cached) /bin/grep -E
checking for assert.h... yes
checking for ctype.h... yes
checking for float.h... yes
checking for limits.h... yes
checking for math.h... yes
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checking for stdarg.h... yes
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checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
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checking for inline... inline
checking for log in -lm... yes
checking for log2 in -lm... 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
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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
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checking for ftello... yes
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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-1.2.4-r1/work/clustal-omega-1.2.4 ...
make -j4 
Making all in src
make[1]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src'
make  all-recursive
make[2]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src'
Making all in hhalign
make[3]: Entering directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/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    -O3 -pipe -march=native -fno-diagnostics-color -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 -O3 -pipe -march=native -fno-diagnostics-color -c hhalign.cpp  -fPIC -DPIC -o .libs/hhalign.o
In file included from hhalign.cpp:70:
hhhmm-C.h: In member function 'void HMM::UseSecStrucDependentGapPenalties()':
hhhmm-C.h:1748:16: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=]
 1748 |   iis[0]=iis[L]=0;
      |          ~~~~~~^~
hhhmm-C.h:1734:17: note: at offset [-2147483648, -1] into destination object 'iis' of size [0, 2147483647]
 1734 |   unsigned char iis[par.maxResLen]; // inside-integer array
      |                 ^~~
during GIMPLE pass: ch_vect
In file included from hhalign.cpp:75:
hhhitlist-C.h: In member function 'void HitList::SVD(double**, int, double*, double**)':
hhhitlist-C.h:2919:1: internal compiler error: in check_loop_closed_ssa_def, at tree-ssa-loop-manip.cc:647
 2919 | HitList::SVD(double **A, int n, double w[], double **V)
      | ^~~~~~~
0x5633810ca20d internal_error(char const*, ...)
	???:0
0x56337f081c60 fancy_abort(char const*, int, char const*)
	???:0
0x56337fd540a6 verify_loop_closed_ssa(bool, loop*)
	???:0
Please submit a full bug report, with preprocessed source (by using -freport-bug).
Please include the complete backtrace with any bug report.
See <https://bugs.gentoo.org/> for instructions.
make[3]: *** [Makefile:457: hhalign.lo] Error 1
make[3]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src/hhalign'
make[2]: *** [Makefile:663: all-recursive] Error 1
make[2]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src'
make[1]: *** [Makefile:431: all] Error 2
make[1]: Leaving directory '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4/src'
make: *** [Makefile:482: all-recursive] Error 1
 * ERROR: sci-biology/clustal-omega-1.2.4-r1::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/clustal-omega-1.2.4-r1::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/clustal-omega-1.2.4-r1::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:clustal-omega-1.2.4-r1:20231204-110826.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4'
 * S: '/var/tmp/portage/sci-biology/clustal-omega-1.2.4-r1/work/clustal-omega-1.2.4'