build.log

build.log (text/plain), 13.29 KB, created by Agostino Sarubbo on 2020-09-08 13:09:42 UTC

 * Package:    sci-biology/clustalw-1.83-r4
 * Repository: gentoo
 * Maintainer: [e-mail]
 * 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'