* Package: sci-biology/clustalw-1.83-r4 * 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/6fbccbc21e17d8e828124b17f58f2aeca5d3871f (Tue Sep 8 09:35:32 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, 29087388 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Tue, 08 Sep 2020 09:35:32 +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-verify-metamanifest: yes sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* clustalw" 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/clustalw-1.83-r4/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 clustalw1.83.UNIX.tar.gz to /var/tmp/portage/sci-biology/clustalw-1.83-r4/work >>> Source unpacked in /var/tmp/portage/sci-biology/clustalw-1.83-r4/work >>> Preparing source in /var/tmp/portage/sci-biology/clustalw-1.83-r4/work/clustalw1.83 ... * Applying 1.83-as-needed.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/clustalw-1.83-r4/work/clustalw1.83 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/clustalw-1.83-r4/work/clustalw1.83 ... make -j16 V=1 x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c interface.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c sequence.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c showpair.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c malign.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c util.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c trees.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c gcgcheck.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c prfalign.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c pairalign.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c calcgapcoeff.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c calcprf1.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c calcprf2.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c calctree.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c readmat.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c alnscore.c x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c random.c util.c:177:2: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(outstr); ^ util.c:188:3: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(line); ^interface.c :213:20: error: non-void function 'check_param' should return a value [-Wreturn-type] if(args[0]==NULL) return; ^ util.c:213:3:x86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c amenu.c warning: implicit declaration of functionx86_64-pc-linux-gnu-clang -O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color -c clustalw.c interface.c:522: 7'gets': iswarning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:546:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:570:7: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ invalid in C99 [-Wimplicit-function-declaration] gets(line); ^ interface.c:861:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:881:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:911:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:931:4: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:1510:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:1518:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:1534:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:1542:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:1550:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:1567:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:1584:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if(profile_type == SEQUENCE) { ^ interface.c:1605:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if(profile_type == SEQUENCE) { ^ interface.c:1625:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if(profile_type == SEQUENCE) { ^ interface.c:1646:3: warning: add explicit braces to avoid dangling else [-Wdangling-else] else if(profile_type == SEQUENCE) { ^ interface.c:2179:4: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(temp); ^ interface.c:2187:3: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(temp); ^ interface.c:2388:17: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(temp); ^ interface.c:2620:18: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(temp); ^ interface.c:2722:17: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(temp); ^ interface.c:2748:17: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(temp); ^ interface.c:3403:6: warning: expression result unused [-Wunused-value] *s++; ^~~~ interface.c:3869:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else { ^ interface.c:3888:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:3898:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:3908:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:3918:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:3928:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:3940:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ interface.c:4206:5: warning: implicit declaration of function 'gets' is invalid in C99 [-Wimplicit-function-declaration] gets(temp); ^ amenu.c:1060:59: warning: format specifies type 'double' but the argument has type 'int' [-Wformat] interface.c:4286:5: warning: add ...Weight Currently: %1.2f\n",(pint)transition_weight);explicit ~~~~~ ^~~~~~~~~~~~~~~~~~~~~~~ braces %1.2d to avoid dangling else [-Wdangling-else] else fprintf(parout,"-case=upper \\\n"); ^ 33 warnings and 1 error generated. make: *** [makefile:21: interface.o] Error 1 make: *** Waiting for unfinished jobs.... 3 warnings generated. 1 warning generated. * ERROR: sci-biology/clustalw-1.83-r4::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/clustalw-1.83-r4::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/clustalw-1.83-r4::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-biology/clustalw-1.83-r4:20200908-104033.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/clustalw-1.83-r4/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/clustalw-1.83-r4/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/clustalw-1.83-r4/work/clustalw1.83' * S: '/var/tmp/portage/sci-biology/clustalw-1.83-r4/work/clustalw1.83'