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Gentoo's Bugzilla – Attachment 659144 Details for
Bug 741184
sci-biology/eugene-4.1d fails to compile: markov.cc:793:9: error: cannot initialize a variable of type 'char *' with
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build.log
build.log (text/plain), 28.09 KB, created by
Agostino Sarubbo
on 2020-09-08 13:09:53 UTC
(
hide
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Description:
build.log
Filename:
MIME Type:
Creator:
Agostino Sarubbo
Created:
2020-09-08 13:09:53 UTC
Size:
28.09 KB
patch
obsolete
> * Package: sci-biology/eugene-4.1d > * Repository: gentoo > * Maintainer: sci-biology@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox > > >@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ >This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; >This ebuild was merged at the following commit: >https://github.com/gentoo-mirror/gentoo/commit/8ee8c827d24103fff75a89608576ea8214b94cb1 (Tue Sep 8 10:05:30 UTC 2020) >@@@@@ END @@@@@ > > > >emerge --info: >Portage 3.0.6 (python 3.8.5-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r1, 5.4.0-1021-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1021-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.2.5 >KiB Mem: 64359960 total, 28134588 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Tue, 08 Sep 2020 10:05:30 +0000 >sh bash 5.0_p18 >ld GNU ld (Gentoo 2.34 p6) 2.34.0 >app-shells/bash: 5.0_p18::gentoo >dev-lang/perl: 5.30.3-r1::gentoo >dev-lang/python: 2.7.18-r1::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo >dev-util/cmake: 3.18.2::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.20::gentoo >sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo >sys-devel/automake: 1.16.2::gentoo >sys-devel/binutils: 2.34-r2::gentoo >sys-devel/gcc: 10.2.0-r1::gentoo >sys-devel/gcc-config: 2.3.2::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers) >sys-libs/glibc: 2.32-r1::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-extra-opts: > sync-rsync-verify-jobs: 1 > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-max-age: 24 > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="* Artistic" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-clang" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >CHOST="x86_64-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXX="x86_64-pc-linux-gnu-clang++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >DISTDIR="/var/tmp/portage/sci-biology/eugene-4.1d/distdir" >EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -b -k" >ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld" >MAKEOPTS="-j16 V=1" >PKGDIR="/root/.packages" >PORTAGE_CONFIGROOT="/" >PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" >PORTAGE_TMPDIR="/var/tmp" >USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd test unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" USERLAND="GNU" >Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS > > > >>>> Unpacking source... >>>> Unpacking eugene-4.1d.tar.gz to /var/tmp/portage/sci-biology/eugene-4.1d/work >>>> Source unpacked in /var/tmp/portage/sci-biology/eugene-4.1d/work >>>> Preparing source in /var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d ... > * Applying eugene-3.6-overflow.patch ... > [ ok ] > * Applying eugene-3.6-plugins.patch ... > [ ok ] > * Applying eugene-4.1-format-security.patch ... > [ ok ] > * Applying eugene-4.1d-fix-c++14.patch ... > [ ok ] > * Applying eugene-4.1d-Wformat.patch ... > [ ok ] > * Running eautoreconf in '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' ... > * Running aclocal ... > [ ok ] > * Running autoconf --force ... > [ ok ] > * Running autoheader ... > [ ok ] > * Running automake --add-missing --copy --force-missing ... > [ ok ] > * Running elibtoolize in: eugene-4.1d/ >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d ... >./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/eugene-4.1d --htmldir=/usr/share/doc/eugene-4.1d/html --libdir=/usr/lib64 >checking for a BSD-compatible install... /usr/lib/portage/python3.8/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 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-clang++ accepts -g... yes >checking whether make supports the include directive... yes (GNU style) >checking dependency style of x86_64-pc-linux-gnu-clang++... none >checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-clang >checking whether we are using the GNU C compiler... yes >checking whether x86_64-pc-linux-gnu-clang accepts -g... yes >checking for x86_64-pc-linux-gnu-clang option to accept ISO C89... none needed >checking whether x86_64-pc-linux-gnu-clang understands -c and -o together... yes >checking dependency style of x86_64-pc-linux-gnu-clang... none >checking for gawk... (cached) gawk >checking whether ln -s works... yes >checking for x86_64-pc-linux-gnu-ranlib... llvm-ranlib >checking for main in -lc... yes >checking for main in -ldl... yes >checking for main in -lgcc... yes >checking for main in -lgd... yes >checking for main in -lm... yes >checking for main in -lpng... yes >checking for main in -lz... yes >checking how to run the C preprocessor... x86_64-pc-linux-gnu-clang -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 netdb.h usability... yes >checking netdb.h presence... yes >checking for netdb.h... yes >checking for stdlib.h... (cached) yes >checking for string.h... (cached) yes >checking for strings.h... (cached) yes >checking for unistd.h... (cached) yes >checking values.h usability... yes >checking values.h presence... yes >checking for values.h... yes >checking getopt.h usability... yes >checking getopt.h presence... yes >checking for getopt.h... yes >checking for an ANSI C-conforming const... yes >checking for inline... inline >checking whether struct tm is in sys/time.h or time.h... time.h >checking for size_t... yes >checking for stdlib.h... (cached) yes >checking for GNU libc compatible malloc... yes >checking whether lstat correctly handles trailing slash... yes >checking whether stat accepts an empty string... no >checking for floor... yes >checking for pow... yes >checking for sqrt... yes >checking for strchr... yes >checking for strspn... yes >checking for uname... yes >checking for getopt... yes >checking that generated files are newer than configure... done >configure: creating ./config.status >config.status: creating Makefile >config.status: creating README >config.status: creating src/Makefile >config.status: creating src/GDIF/Makefile >config.status: creating src/Parametrization/Makefile >config.status: creating src/SensorPlugins/Makefile >config.status: creating src/SensorPlugins/0_SensorTk/Makefile >config.status: creating src/SensorPlugins/0_SensorTk/GetData/Makefile >config.status: creating src/SensorPlugins/AnnotaStruct/Makefile >config.status: creating src/SensorPlugins/BlastX/Makefile >config.status: creating src/SensorPlugins/Est/Makefile >config.status: creating src/SensorPlugins/EuStop/Makefile >config.status: creating src/SensorPlugins/FrameShift/Makefile >config.status: creating src/SensorPlugins/GCPlot/Makefile >config.status: creating src/SensorPlugins/GFF/Makefile >config.status: creating src/SensorPlugins/GSplicer/Makefile >config.status: creating src/SensorPlugins/Homology/Makefile >config.status: creating src/SensorPlugins/IfElse/Makefile >config.status: creating src/SensorPlugins/MarkovConst/Makefile >config.status: creating src/SensorPlugins/MarkovIMM/Makefile >config.status: creating src/SensorPlugins/MarkovIMM/GetData/Makefile >config.status: creating src/SensorPlugins/MarkovProt/Makefile >config.status: creating src/SensorPlugins/MarkovProt/GetData/Makefile >config.status: creating src/SensorPlugins/NcRNA/Makefile >config.status: creating src/SensorPlugins/NG2/Makefile >config.status: creating src/SensorPlugins/NStart/Makefile >config.status: creating src/SensorPlugins/NStretch/Makefile >config.status: creating src/SensorPlugins/PatConst/Makefile >config.status: creating src/SensorPlugins/PepSignal/Makefile >config.status: creating src/SensorPlugins/ProStart/Makefile >config.status: creating src/SensorPlugins/Plotter/Makefile >config.status: creating src/SensorPlugins/QualData/Makefile >config.status: creating src/SensorPlugins/Repeat/Makefile >config.status: creating src/SensorPlugins/RibosomalFrameShift/Makefile >config.status: creating src/SensorPlugins/Riken/Makefile >config.status: creating src/SensorPlugins/SMachine/Makefile >config.status: creating src/SensorPlugins/SPred/Makefile >config.status: creating src/SensorPlugins/SpliceWAM/Makefile >config.status: creating src/SensorPlugins/StartWAM/Makefile >config.status: creating src/SensorPlugins/Tester/Makefile >config.status: creating src/SensorPlugins/Transcript/Makefile >config.status: creating plugins/Makefile >config.status: creating doc/Makefile >config.status: creating config.h >config.status: executing depfiles commands >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d ... >make -j16 V=1 >(CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/config/missing autoheader) >rm -f stamp-h1 >touch config.h.in >cd . && /bin/sh ./config.status config.h >config.status: creating config.h >config.status: config.h is unchanged >make all-recursive >make[1]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' >Making all in src >make[2]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' >Making all in Parametrization >make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/Parametrization' >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o ParaOptimization.o ParaOptimization.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o OptiAlgorithm.o OptiAlgorithm.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Random.o Random.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o LineSearch.o LineSearch.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Genetic.o Genetic.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o CrossingOver.o CrossingOver.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Mutating.o Mutating.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Scaling.o Scaling.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Selecting.o Selecting.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Sharing.o Sharing.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o SimulatedAnnealing.o SimulatedAnnealing.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../.. -rdynamic -fPIC -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Chromosome.o Chromosome.cc >clang-10clang-10clang-10clang-10: : : : warningwarningwarningwarning: : : : argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] > >argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] > >clang-10clang-10: : warningwarning: : argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] > >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warningclang-10: : argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]warning >: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >rm -f libParametrization.a >ar cru libParametrization.a ParaOptimization.o OptiAlgorithm.o Random.o LineSearch.o Genetic.o CrossingOver.o Mutating.o Scaling.o Selecting.o Sharing.o SimulatedAnnealing.o Chromosome.o >llvm-ranlib libParametrization.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/Parametrization' >Making all in GDIF >make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/GDIF' >x86_64-pc-linux-gnu-clang -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o gdIF.o gdIF.c >rm -f libGDIF.a >ar cru libGDIF.a gdIF.o >llvm-ranlib libGDIF.a >make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/GDIF' >Making all in . >make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o AltEst.o AltEst.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Attributes.o Attributes.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o BackP.o BackP.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o DAG.o DAG.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o DNASeq.o DNASeq.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Dll.o Dll.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o EuGene.o EuGene.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Gap.o Gap.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o GeneFeature.o GeneFeature.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o GeneFeatureSet.o GeneFeatureSet.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Gff3Line.o Gff3Line.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Hits.o Hits.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Locus.o Locus.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o MSensor.o MSensor.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Param.o Param.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o PenaltyDist.o PenaltyDist.cc >clang-10clang-10clang-10clang-10clang-10clang-10: : : : : : warningwarning: warningwarning: warningwarning: : : : argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument]argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10 > > >: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Prediction.o Prediction.cc >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Range.o Range.cc >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >AltEst.cc:317:13: warning: add explicit braces to avoid dangling else > [-Wdangling-else] > else return false; > ^ >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Sensor.o Sensor.cc >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o State.o State.cc >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >DAG.cc:1309:17: warning: equality comparison with extraneous parentheses > [-Wparentheses-equality] > if ((FrameF == k)) > ~~~~~~~^~~~ >DAG.cc:1309:17: note: remove extraneous parentheses around the comparison to > silence this warning > if ((FrameF == k)) > ~ ^ ~ >DAG.cc:1309:17: note: use '=' to turn this equality comparison into an > assignment > if ((FrameF == k)) > ^~ > = >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o SoTerms.o SoTerms.cc >DAG.cc:1511:17: warning: equality comparison with extraneous parentheses > [-Wparentheses-equality] > if ((FrameR == k)) > ~~~~~~~^~~~ >DAG.cc:1511:17: note: remove extraneous parentheses around the comparison to > silence this warning > if ((FrameR == k)) > ~ ^ ~ >DAG.cc:1511:17: note: use '=' to turn this equality comparison into an > assignment > if ((FrameR == k)) > ^~ > = >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o System.o System.cc >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I.. -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o Target.o Target.cc >clang-10: warning: argument unused during compilation: '-rdynamic' [-Wunused-command-line-argument] >Prediction.cc:2459:12: warning: data argument not used by format string > [-Wformat-extra-args] > PAR.getC ( "EuGene.version" ), PAR.getC ( "EuGene.orga... > ^ >State.cc:399:1: warning: non-void function does not return a value in all > control paths [-Wreturn-type] >} >^ >State.cc:418:1: warning: non-void function does not return a value in all > control paths [-Wreturn-type] >} >^ >1 warning generated. >2 warnings generated. >2 warnings generated. >1 warning generated. >x86_64-pc-linux-gnu-clang++ -rdynamic -fPIC -DDEFAULT_EUGENE_DIR=\"/usr/share/eugene\" -DLIB_DIR=\"/usr/lib64\" -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld -o eugene AltEst.o Attributes.o BackP.o DAG.o DNASeq.o Dll.o EuGene.o Gap.o GeneFeature.o GeneFeatureSet.o Gff3Line.o Hits.o Locus.o MSensor.o Param.o PenaltyDist.o Prediction.o Range.o Sensor.o State.o SoTerms.o System.o Target.o Parametrization/libParametrization.a GDIF/libGDIF.a -ldl -lz -lpng -lm -lgd -lgcc -ldl -lc >make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' >Making all in SensorPlugins >make[3]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/SensorPlugins' >Making all in 0_SensorTk >make[4]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/SensorPlugins/0_SensorTk' >Making all in GetData >make[5]: Entering directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/SensorPlugins/0_SensorTk/GetData' >x86_64-pc-linux-gnu-clang++ -DHAVE_CONFIG_H -I. -I../../../.. -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c -o WAMbuilder.o WAMbuilder.cc >In file included from WAMbuilder.cc:31: >./../markov.cc:793:9: error: cannot initialize a variable of type 'char *' with > an lvalue of type 'const char *' > char* codegenetique=CODEGENETIQUE; > ^ ~~~~~~~~~~~~~ >1 error generated. >make[5]: *** [Makefile:381: WAMbuilder.o] Error 1 >make[5]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/SensorPlugins/0_SensorTk/GetData' >make[4]: *** [Makefile:424: all-recursive] Error 1 >make[4]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/SensorPlugins/0_SensorTk' >make[3]: *** [Makefile:336: all-recursive] Error 1 >make[3]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src/SensorPlugins' >make[2]: *** [Makefile:499: all-recursive] Error 1 >make[2]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d/src' >make[1]: *** [Makefile:462: all-recursive] Error 1 >make[1]: Leaving directory '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' >make: *** [Makefile:401: all] Error 2 > * ERROR: sci-biology/eugene-4.1d::gentoo failed (compile phase): > * emake failed > * > * If you need support, post the output of `emerge --info '=sci-biology/eugene-4.1d::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-biology/eugene-4.1d::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-biology/eugene-4.1d:20200908-113647.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/eugene-4.1d/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-biology/eugene-4.1d/temp/environment'. > * Working directory: '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d' > * S: '/var/tmp/portage/sci-biology/eugene-4.1d/work/eugene-4.1d'
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bug 741184
: 659144