* Package: sci-biology/wise-2.4.0_alpha-r1:0 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox 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/420c9bb0270a709952c98e97127230a35560955b (Thu Dec 15 05:46:51 UTC 2022) @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.41 (python 3.10.9-final-0, default/linux/amd64/17.1, gcc-12, glibc-2.36-r6, 5.15.77-gentoo-dist x86_64) ================================================================= System uname: Linux-5.15.77-gentoo-dist-x86_64-AMD_EPYC_7513_32-Core_Processor-with-glibc2.36 KiB Mem: 263533016 total, 3053964 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 15 Dec 2022 05:46:51 +0000 sh bash 5.2_p15 ld GNU ld (Gentoo 2.39 p5) 2.39.0 app-misc/pax-utils: 1.3.5::gentoo app-shells/bash: 5.2_p15::gentoo dev-lang/perl: 5.36.0-r1::gentoo dev-lang/python: 3.8.16::gentoo, 3.9.16::gentoo, 3.10.9::gentoo, 3.11.1::gentoo dev-util/cmake: 3.25.1::gentoo dev-util/meson: 0.64.1::gentoo sys-apps/baselayout: 2.9::gentoo sys-apps/openrc: 0.45.2-r2::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.71-r5::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.39-r4::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 15.0.6::gentoo sys-devel/gcc: 12.2.1_p20221210::gentoo sys-devel/gcc-config: 2.8::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/llvm: 15.0.6::gentoo sys-devel/make: 4.4::gentoo sys-kernel/linux-headers: 6.0::gentoo (virtual/os-headers) sys-libs/glibc: 2.36-r6::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-extra-opts: sync-rsync-verify-max-age: 24 sync-rsync-verify-jobs: 1 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* BSD" CBUILD="x86_64-pc-linux-gnu" CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" 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/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXX="clang++" CXXFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" DISTDIR="/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" 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 XDG_STATE_HOME" FCFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live 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 unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" GENTOO_MIRRORS="http://mirror.leaseweb.com/gentoo/ http://ftp.snt.utwente.nl/pub/os/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/ http://distfiles.gentoo.org" LANG="C.UTF8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" LEX="flex" MAKEOPTS="-j16" PKGDIR="/root/tbci/binpkg" 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" SHELL="/bin/bash" USE="acl amd64 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 test-rust unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" USERLAND="GNU" Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ############################## # emerge history (qlop -mv): # ############################## 2022-12-15T07:37:02 >>> sci-biology/hmmer-2.3.2-r5 2022-12-15T07:37:03 >>> dev-libs/icu-72.1 2022-12-15T07:37:05 >>> media-libs/libjpeg-turbo-2.1.4 2022-12-15T07:37:06 >>> dev-libs/zziplib-0.13.72-r2 2022-12-15T07:37:08 >>> app-text/libpaper-2.0.4 2022-12-15T07:37:09 >>> app-text/dvipsk-2021.1_p20210325-r1 2022-12-15T07:37:11 >>> sys-apps/ed-1.18 2022-12-15T07:37:12 >>> virtual/jpeg-100-r1 2022-12-15T07:37:13 >>> x11-misc/xdg-user-dirs-0.18 2022-12-15T07:37:16 >>> app-shells/tcsh-6.24.01-r1 2022-12-15T07:37:15 >>> media-libs/libwebp-1.2.4 2022-12-15T07:37:17 >>> app-text/docbook-xml-dtd-4.3-r2 2022-12-15T07:37:18 >>> dev-libs/kpathsea-6.3.3_p20210325-r1 2022-12-15T07:37:21 >>> dev-perl/MRO-Compat-0.130.0-r1 2022-12-15T07:37:22 >>> dev-perl/XString-0.5.0 2022-12-15T07:37:23 >>> dev-perl/PadWalker-2.500.0 2022-12-15T07:37:20 >>> virtual/perl-Test-Simple-1.302.190 2022-12-15T07:37:24 >>> dev-perl/Class-Data-Inheritable-0.90.0 2022-12-15T07:37:25 >>> dev-lang/nasm-2.15.05 2022-12-15T07:37:29 >>> dev-perl/Sub-Install-0.928.0-r1 2022-12-15T07:37:27 >>> virtual/perl-Storable-3.260.0 2022-12-15T07:37:28 >>> virtual/perl-Sys-Syslog-0.360.0-r2 2022-12-15T07:37:30 >>> dev-perl/Devel-StackTrace-2.40.0 2022-12-15T07:37:31 >>> dev-perl/Sub-Identify-0.140.0-r1 2022-12-15T07:37:32 >>> dev-perl/Package-Stash-XS-0.290.0 2022-12-15T07:37:33 >>> dev-perl/Variable-Magic-0.620.0-r1 2022-12-15T07:37:34 >>> dev-perl/PerlIO-utf8_strict-0.8.0 2022-12-15T07:37:35 >>> dev-perl/Role-Tiny-2.2.4 2022-12-15T07:37:36 >>> dev-perl/Perl-Tidy-20211029.0.0 2022-12-15T07:37:37 >>> dev-perl/Ref-Util-XS-0.117.0 2022-12-15T07:37:39 >>> dev-perl/File-Which-1.270.0 2022-12-15T07:37:40 >>> dev-perl/CPAN-Meta-Check-0.14.0-r1 2022-12-15T07:37:41 >>> dev-perl/ExtUtils-HasCompiler-0.23.0 2022-12-15T07:37:42 >>> dev-perl/Capture-Tiny-0.480.0-r1 2022-12-15T07:37:44 >>> dev-perl/Module-Runtime-0.16.0-r1 2022-12-15T07:37:43 >>> dev-perl/Sub-Quote-2.6.6-r1 2022-12-15T07:37:45 >>> media-libs/harfbuzz-5.3.1-r1 2022-12-15T07:37:54 >>> dev-libs/ptexenc-1.3.9_p20210325-r1 2022-12-15T07:37:56 >>> dev-tex/bibtexu-3.71_p20210325 2022-12-15T07:37:55 >>> app-text/ps2pkm-1.8_p20210325-r1 2022-12-15T07:38:02 >>> dev-perl/Devel-Caller-2.60.0-r2 2022-12-15T07:38:05 >>> dev-perl/Test-Fatal-0.16.0 2022-12-15T07:38:10 >>> media-libs/gd-2.3.3-r1 2022-12-15T07:38:15 >>> dev-perl/Exception-Class-1.450.0 2022-12-15T07:38:22 >>> dev-perl/File-Slurper-0.12.0 2022-12-15T07:38:26 >>> dev-perl/Ref-Util-0.204.0 2022-12-15T07:38:28 >>> dev-perl/File-HomeDir-1.6.0 2022-12-15T07:38:34 >>> dev-perl/Dist-CheckConflicts-0.110.0-r1 2022-12-15T07:38:35 >>> dev-perl/Module-Implementation-0.90.0-r1 2022-12-15T07:38:45 >>> dev-perl/Devel-LexAlias-0.50.0-r1 2022-12-15T07:38:53 >>> dev-perl/Config-AutoConf-0.320.0 2022-12-15T07:39:00 >>> dev-perl/Package-Stash-0.390.0 2022-12-15T07:39:03 >>> dev-perl/Eval-Closure-0.140.0-r1 2022-12-15T07:39:06 >>> dev-perl/Params-Util-1.102.0 2022-12-15T07:39:10 >>> dev-perl/Params-ValidationCompiler-0.300.0 2022-12-15T07:39:11 >>> dev-perl/Specio-0.480.0 2022-12-15T07:39:12 >>> dev-perl/Data-OptList-0.112.0 2022-12-15T07:39:18 >>> dev-perl/Sub-Exporter-0.988.0 2022-12-15T07:39:21 >>> dev-perl/Sub-Exporter-Progressive-0.1.13-r1 2022-12-15T07:39:24 >>> dev-perl/B-Hooks-EndOfScope-0.240.0-r1 2022-12-15T07:39:25 >>> dev-perl/Devel-GlobalDestruction-0.140.0-r1 2022-12-15T07:39:28 >>> dev-perl/namespace-clean-0.270.0-r1 2022-12-15T07:39:31 >>> dev-perl/namespace-autoclean-0.290.0 2022-12-15T07:39:34 >>> dev-perl/Log-Dispatch-2.700.0 2022-12-15T07:39:37 >>> app-text/texlive-core-2021-r5 2022-12-15T07:39:41 >>> dev-texlive/texlive-basic-2021 2022-12-15T07:39:47 >>> dev-texlive/texlive-fontutils-2021 2022-12-15T07:39:48 >>> dev-texlive/texlive-fontsrecommended-2021 2022-12-15T07:39:49 >>> dev-texlive/texlive-latex-2021 2022-12-15T07:40:02 >>> dev-texlive/texlive-latexrecommended-2021 2022-12-15T07:40:06 >>> virtual/latex-base-1.0 ####################################### # installed packages (qlist -ICvUSS): # ####################################### acct-group/audio-0-r1:0 acct-group/cdrom-0-r1:0 acct-group/dialout-0-r1:0 acct-group/disk-0-r1:0 acct-group/input-0-r1:0 acct-group/kmem-0-r1:0 acct-group/kvm-0-r1:0 acct-group/lp-0-r1:0 acct-group/man-0-r1:0 acct-group/messagebus-0-r1:0 acct-group/polkitd-0-r1:0 acct-group/portage-0:0 acct-group/render-0-r1:0 acct-group/sgx-0:0 acct-group/sshd-0-r1:0 acct-group/tape-0-r1:0 acct-group/tty-0-r1:0 acct-group/video-0-r1:0 acct-user/man-1-r1:0 acct-user/messagebus-0-r1:0 acct-user/polkitd-0-r1:0 acct-user/portage-0:0 acct-user/sshd-0-r1:0 app-admin/eselect-1.4.20:0 -doc -emacs -vim-syntax app-admin/perl-cleaner-2.30:0 app-alternatives/awk-3:0 -busybox gawk -mawk -nawk split-usr app-alternatives/bc-0:0 -gh gnu app-alternatives/bzip2-1:0 -lbzip2 -pbzip2 reference split-usr app-alternatives/gzip-0:0 -pigz reference split-usr app-alternatives/lex-0-r1:0 flex -reflex app-alternatives/tar-0:0 gnu -libarchive split-usr app-alternatives/yacc-1-r2:0 bison -byacc -reference app-arch/bzip2-1.0.8-r4:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 split-usr -static -static-libs -verify-sig app-arch/gzip-1.12-r3:0 -pic -static -verify-sig app-arch/libarchive-3.6.1-r1:0/13 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 acl -blake2 bzip2 e2fsprogs -expat iconv -lz4 lzma -lzo -nettle -static-libs -verify-sig xattr -zstd app-arch/tar-1.34-r2:0 acl -minimal nls -selinux -verify-sig xattr app-arch/unzip-6.0_p27-r1:0 bzip2 -natspec unicode app-arch/xz-utils-5.4.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 extra-filters nls split-usr -static-libs -verify-sig app-arch/zstd-1.5.2-r3:0/1 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -lz4 split-usr -static-libs app-crypt/gnupg-2.3.8:0 bzip2 -doc -ldap nls readline -selinux smartcard ssl -test tofu -tools -tpm -usb -user-socket -verify-sig -wks-server app-crypt/gpgme-1.18.0-r2:1/11.6.15.1 -common-lisp cxx -python python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -qt5 -static-libs -test -verify-sig app-crypt/libb2-0.98.1-r3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -native-cflags openmp -static-libs app-crypt/pinentry-1.2.1-r1:0 -caps -efl -emacs -gnome-keyring -gtk ncurses -qt5 -verify-sig app-crypt/rhash-1.4.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug nls ssl -static-libs app-editors/nano-7.1:0 -debug -justify -magic -minimal ncurses nls spell -static unicode app-eselect/eselect-fontconfig-20220403:0 app-eselect/eselect-iptables-20220320:0 app-eselect/eselect-lib-bin-symlink-0.1.1-r1:0 app-eselect/eselect-pinentry-0.7.2:0 app-i18n/man-pages-ja-20180315-r1:0 app-i18n/man-pages-l10n-4.14.0-r1:0 l10n_cs l10n_da l10n_de l10n_el l10n_es l10n_fi l10n_fr l10n_hu l10n_id l10n_it l10n_mk l10n_nb l10n_nl l10n_pl l10n_pt-BR l10n_ro l10n_sr l10n_sv l10n_uk l10n_vi app-i18n/man-pages-ru-5.03.2390.2390.20191017-r1:0 app-i18n/man-pages-zh_CN-1.6.3.6:0 app-misc/c_rehash-1.7-r1:0 app-misc/ca-certificates-20211016.3.86:0 -cacert app-misc/editor-wrapper-4-r1:0 app-misc/mime-types-2.1.53:0 -nginx app-misc/pax-utils-1.3.5:0 -caps man -python python_single_target_python3_10 -python_single_target_python3_11 -python_single_target_python3_8 -python_single_target_python3_9 seccomp -test app-misc/tmux-3.3a-r1:0 -debug -selinux -systemd -utempter -vim-syntax app-portage/eix-0.36.5:0 -debug -doc nls -sqlite app-portage/elt-patches-20221210:0 app-portage/gemato-17.0:0 gpg -pretty-log python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test -tools app-portage/gentoolkit-0.6.1-r3:0 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test app-portage/portage-utils-0.94.4:0 openmp qmanifest qtegrity -static app-shells/bash-5.2_p15:0 -afs -bashlogger -examples -mem-scramble net nls -pgo -plugins readline -verify-sig app-shells/bash-completion-2.11:0 eselect -test app-shells/gentoo-bashcomp-20190211-r1:0 app-shells/push-3.4:0 app-shells/quoter-4.2:0 app-shells/tcsh-6.24.01-r1:0 -doc nls app-text/ansifilter-2.18:0 -qt5 app-text/build-docbook-catalog-2.3-r1:0 app-text/docbook-xml-dtd-4.5-r2:4.5 app-text/docbook-xml-dtd-4.4-r3:4.4 app-text/docbook-xml-dtd-4.3-r2:4.3 app-text/docbook-xml-dtd-4.2-r3:4.2 app-text/docbook-xml-dtd-4.1.2-r7:4.1.2 app-text/docbook-xsl-stylesheets-1.79.1-r3:0 -ruby app-text/dvipsk-2021.1_p20210325-r1:0 doc -source app-text/libpaper-2.0.4:0/2 app-text/manpager-1:0 app-text/opensp-1.5.2-r9:0 -doc nls -static-libs -test app-text/po4a-0.68:0 -test -test app-text/ps2pkm-1.8_p20210325-r1:0 app-text/sgml-common-0.6.3-r7:0 app-text/texlive-core-2021-r5:0 -X -cjk -doc luajittex -source -tk -xetex -xindy app-text/xmlto-0.0.28-r10:0 -latex text dev-db/sqlite-3.40.0:3 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug -doc -icu readline -secure-delete -static-libs -tcl -test -tools dev-lang/duktape-2.7.0-r3:0/2.7.0 dev-lang/nasm-2.15.05:0 -doc dev-lang/perl-5.36.0-r1:0/5.36 -berkdb -debug -doc gdbm ithreads -minimal -quadmath dev-lang/python-3.11.1:3.11 -bluetooth -build ensurepip -examples gdbm -hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig dev-lang/python-3.10.9:3.10 -bluetooth -build ensurepip -examples gdbm -hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml dev-lang/python-3.9.16:3.9 -bluetooth -build ensurepip -examples gdbm -hardened -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml dev-lang/python-3.8.16:3.8 -bluetooth -build ensurepip -examples gdbm -hardened -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig -wininst xml dev-lang/python-exec-2.4.9:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 -test dev-lang/python-exec-conf-2.4.6:2 python_targets_pypy3 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 dev-lang/tcl-8.6.13:0/8.6 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -debug threads dev-libs/boehm-gc-8.2.2-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 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virtual/perl-ExtUtils-CBuilder-0.280.236-r1:0 virtual/perl-ExtUtils-Install-2.200.0-r1:0 virtual/perl-ExtUtils-MakeMaker-7.640.0:0 virtual/perl-ExtUtils-Manifest-1.730.0-r1:0 virtual/perl-ExtUtils-ParseXS-3.450.0:0 virtual/perl-File-Path-2.180.0-r1:0 virtual/perl-File-Spec-3.840.0:0 virtual/perl-File-Temp-0.231.100:0 virtual/perl-Getopt-Long-2.520.0-r1:0 virtual/perl-IO-1.500.0:0 virtual/perl-IO-Compress-2.106.0:0 virtual/perl-IO-Socket-IP-0.410.0-r1:0 virtual/perl-JSON-PP-4.70.0:0 virtual/perl-libnet-3.140.0:0 ssl virtual/perl-MIME-Base64-3.160.0-r1:0 virtual/perl-Module-Metadata-1.0.37-r2:0 virtual/perl-parent-0.238.0-r2:0 virtual/perl-Parse-CPAN-Meta-2.150.10-r6:0 virtual/perl-Perl-OSType-1.10.0-r6:0 virtual/perl-podlators-4.140.0-r3:0 virtual/perl-Scalar-List-Utils-1.620.0:0 virtual/perl-Storable-3.260.0:0 virtual/perl-Sys-Syslog-0.360.0-r2:0 virtual/perl-Test-Harness-3.440.0:0 virtual/perl-Test-Simple-1.302.190:0 virtual/perl-Text-ParseWords-3.310.0:0 virtual/perl-Time-Local-1.300.0-r1:0 virtual/perl-version-0.992.900:0 virtual/perl-XSLoader-0.310.0:0 virtual/pkgconfig-2-r1:0 virtual/service-manager-1-r1:0 virtual/ssh-0-r1:0 -minimal virtual/tmpfiles-0-r3:0 virtual/ttf-fonts-1-r2:0 virtual/udev-217-r5:0 virtual/w3m-1:0 www-client/pybugz-0.13-r2:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 www-client/w3m-0.5.3_p20220429-r1:0 -X -fbcon -gdk-pixbuf -gpm -imlib l10n_ja -lynxkeymap nls -nntp ssl unicode -xface x11-apps/xprop-1.2.6:0 x11-apps/xset-1.2.5:0 x11-base/xcb-proto-1.15.2:0 python_targets_python3_10 -python_targets_python3_11 python_targets_python3_8 python_targets_python3_9 x11-base/xorg-proto-2022.2:0 -test x11-libs/cairo-1.17.6:0 -X -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -aqua -debug -gles2-only -gles3 glib -gtk-doc -opengl -test x11-libs/libICE-1.1.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 x11-libs/libSM-1.2.3-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc ipv6 uuid x11-libs/libX11-1.8.2-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -test x11-libs/libXau-1.0.11:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libxcb-1.15-r1:0/1.12 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -doc -selinux -test xkb x11-libs/libXdmcp-1.1.4-r1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libXext-1.3.5:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libXmu-1.1.4:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc x11-libs/libXt-1.2.1:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc -test x11-libs/pixman-0.42.2:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -cpu_flags_arm_iwmmxt -cpu_flags_arm_iwmmxt2 -cpu_flags_arm_neon -cpu_flags_ppc_altivec cpu_flags_x86_mmxext cpu_flags_x86_sse2 cpu_flags_x86_ssse3 -loongson2f -static-libs -test x11-libs/xtrans-1.4.0:0 -doc x11-misc/compose-tables-1.8.2:0 x11-misc/shared-mime-info-2.2:0 -test x11-misc/xdg-user-dirs-0.18:0 -gtk x11-misc/xdg-utils-1.1.3_p20210805-r1:0 -dbus -doc -gnome ####################### # build.log # ####################### >>> Unpacking source... >>> Unpacking wise2.4.0alpha.tar.gz to /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work >>> Unpacking wise-2.4.0_alpha-patchset.tar.bz2 to /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha ... * Applying wise-2.4.0_alpha-glibc-2.10.patch ... [ ok ] * Applying wise-2.4.0_alpha-cflags.patch ... [ ok ] * Applying wise-api.tex.patch ... patching file api.tex Hunk #4 succeeded at 5551 with fuzz 1 (offset 496 lines). [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha ... make -j16 -C src all make: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src' (cd base ; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread `pkg-config glib-2.0 --cflags`" libwisebase.a ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/base' clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseconfig.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestring.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseerror.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisememman.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisefile.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiserandom.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisetime.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wiseoverlay.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include wisestreaminterface.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include commandline.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include linesubs.c wisefile.dy:72:33: warning: format specifies type 'int' but the argument has type 'FILE *' (aka 'struct _IO_FILE *') [-Wformat] fprintf(stderr,"Closing %d\n",ofp); ~~ ^~~ 1 warning generated. ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/base' (cd HMMer2 ; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread `pkg-config glib-2.0 --cflags`" libhmmer.a ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/HMMer2' clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alphabet.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c core_algorithms.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c debug.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emit.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c emulation.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c histogram.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c hmmio.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c mathsupport.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c masks.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c misc.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c modelmakers.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan7.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c plan9.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c prior.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c tophits.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c trace.c prior.c:102:12: warning: call to undeclared library function 'strcmp' with type 'int (const char *, const char *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; ^ prior.c:102:12: note: include the header or explicitly provide a declaration for 'strcmp' alphabet.c:236:9: warning: logical not is only applied to the left hand side of this bitwise operator [-Wlogical-not-parentheses] if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { ^ ~ alphabet.c:236:9: note: add parentheses after the '!' to evaluate the bitwise operator first if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { ^ ( ) alphabet.c:236:9: note: add parentheses around left hand side expression to silence this warning if (! ainfo->sqinfo[idx].flags & SQINFO_LEN) { ^ ( ) clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c aligneval.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c alignio.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c cluster.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c dayhoff.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c file.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c getopt.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c gnuregex.c 1 warning generated. clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c interleaved.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c iupac.c gnuregex.c:795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_set_syntax (syntax) ^ gnuregex.c:1175:37: warning: passing arguments to 'at_begline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] || at_begline_loc_p (pattern, p, syntax)) ^ gnuregex.c:1190:37: warning: passing arguments to 'at_endline_loc_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] || at_endline_loc_p (p, pend, syntax)) ^ gnuregex.c:1296:21: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump, b, laststart); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1301:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (maybe_pop_jump, b, laststart - 3); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1310:13: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (keep_string_p ? on_failure_keep_string_jump ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1324:17: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (dummy_failure_jump, laststart, laststart + 6); ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1407:39: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] = compile_range (&p, pend, translate, syntax, b); ^ gnuregex.c:1418:41: warning: passing arguments to 'compile_range' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] ret = compile_range (&p, pend, translate, syntax, b); ^ gnuregex.c:1616:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ gnuregex.c:1629:19: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump_past_alt, fixup_alt_jump, b - 1); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1636:17: warning: add explicit braces to avoid dangling else [-Wdangling-else] else ^ gnuregex.c:1686:15: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (on_failure_jump, begalt, b + 6); ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1707:17: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump_past_alt, fixup_alt_jump, b); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1801:22: warning: passing arguments to 'insert_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP (jump, laststart, b + 3); ^ gnuregex.c:911:14: note: expanded from macro 'INSERT_JUMP' insert_op1 (op, loc, (to) - (loc) - 3, b) ^ gnuregex.c:1826:22: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] INSERT_JUMP2 (succeed_n, laststart, ^ gnuregex.c:915:14: note: expanded from macro 'INSERT_JUMP2' insert_op2 (op, loc, (to) - (loc) - 3, arg, b) ^ gnuregex.c:1835:33: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op2 (set_number_at, laststart, 5, lower_bound, b); ^ gnuregex.c:1846:26: warning: passing arguments to 'store_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP2 (jump_n, b, laststart + 5, ^ gnuregex.c:907:13: note: expanded from macro 'STORE_JUMP2' store_op2 (op, loc, (to) - (loc) - 3, arg) ^ gnuregex.c:1864:37: warning: passing arguments to 'insert_op2' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op2 (set_number_at, laststart, b - laststart, ^ gnuregex.c:1958:42: warning: passing arguments to 'group_in_compile_stack' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (group_in_compile_stack (compile_stack, c1)) ^ 1 warning generated. gnuregex.c:2024:5: warning: passing arguments to 'store_op1' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] STORE_JUMP (jump_past_alt, fixup_alt_jump, b); ^ gnuregex.c:903:13: note: expanded from macro 'STORE_JUMP' store_op1 (op, loc, (to) - (loc) - 3) ^ gnuregex.c:1049:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regex_compile (pattern, size, syntax, bufp) ^ gnuregex.c:2050:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] store_op1 (op, loc, arg) ^ gnuregex.c:2063:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] store_op2 (op, loc, arg1, arg2) ^ gnuregex.c:2078:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op1 (op, loc, arg, end) ^ gnuregex.c:2097:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] insert_op2 (op, loc, arg1, arg2, end) ^ gnuregex.c:2118:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] at_begline_loc_p (pattern, p, syntax) ^ gnuregex.c:2137:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] at_endline_loc_p (p, pend, syntax) ^ gnuregex.c:2159:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] group_in_compile_stack (compile_stack, regnum) ^ gnuregex.c:2187:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] compile_range (p_ptr, pend, translate, syntax, b) ^ clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c msf.c gnuregex.c:2519:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_compile_fastmap (bufp) ^ gnuregex.c:2804:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_set_registers (bufp, regs, num_regs, starts, ends) ^ gnuregex.c:2821:33: warning: expression which evaluates to zero treated as a null pointer constant of type 'regoff_t *' (aka 'int *') [-Wnon-literal-null-conversion] regs->start = regs->end = (regoff_t) 0; ^~~~~~~~~~~~ gnuregex.c:2831:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_search (bufp, string, size, startpos, range, regs) ^ gnuregex.c:2864:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_search_2 (bufp, string1, size1, string2, size2, startpos, range, regs, stop) ^ gnuregex.c:3123:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_match (bufp, string, size, pos, regs) ^ gnuregex.c:3148:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] re_match_2 (bufp, string1, size1, string2, size2, pos, regs, stop) ^ gnuregex.c:3604:43: warning: passing arguments to 'group_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] = group_match_null_string_p (&p1, pend, reg_info); ^ gnuregex.c:3752:31: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^~~~~~~~~~~~~~~~~~~ gnuregex.c:3752:54: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^~~~~~~~~~~~~~~~~ clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c revcomp.c gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3758:19: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c selex.c gnuregex.c:3822:38: warning: passing arguments to 'bcmp_translate' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] ? bcmp_translate (d, d2, mcnt, translate) ^ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3905:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:3958:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (p + mcnt, d, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4064:13: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (sdummy, pdummy, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4097:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2394:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4110:11: warning: cast to 'fail_stack_elt_t' (aka 'unsigned char *') from smaller integer type 'unsigned int' [-Wint-to-pointer-cast] PUSH_FAILURE_POINT (0, 0, -2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2397:5: note: expanded from macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_ITEM (highest_active_reg); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2315:42: note: expanded from macro 'PUSH_FAILURE_ITEM' fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2482:14: note: expanded from macro 'POP_FAILURE_POINT' high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:4278:11: warning: cast to smaller integer type 'unsigned int' from 'fail_stack_elt_t' (aka 'unsigned char *') [-Wpointer-to-int-cast] POP_FAILURE_POINT (d, p, ^~~~~~~~~~~~~~~~~~~~~~~~ gnuregex.c:2485:13: note: expanded from macro 'POP_FAILURE_POINT' low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sqerror.c interleaved.c:165:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:165:32: note: did you mean to compare the result of 'strncmp' instead? if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ ~ ) interleaved.c:165:60: note: explicitly cast the argument to size_t to silence this warning if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ (size_t)( ) clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sqio.c interleaved.c:240:82: warning: size argument in 'strncmp' call is a comparison [-Wmemsize-comparison] if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ~~~~~~~~~~~~~~~~~~~~~~^~~~ interleaved.c:240:32: note: did you mean to compare the result of 'strncmp' instead? if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ ~ ) interleaved.c:240:60: note: explicitly cast the argument to size_t to silence this warning if (expected_name != NULL && strncmp(buf, expected_name, strlen(expected_name) == 0)) ^ (size_t)( ) gnuregex.c:4394:48: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!alt_match_null_string_p (p1, p1 + mcnt - 3, ^ gnuregex.c:4424:44: warning: passing arguments to 'alt_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!alt_match_null_string_p (p1, p1 + mcnt, reg_info)) ^ gnuregex.c:4439:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!common_op_match_null_string_p (&p1, end, reg_info)) ^ gnuregex.c:4344:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] group_match_null_string_p (p, end, reg_info) ^ gnuregex.c:4475:46: warning: passing arguments to 'common_op_match_null_string_p' without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] if (!common_op_match_null_string_p (&p1, end, reg_info)) ^ gnuregex.c:4453:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] alt_match_null_string_p (p, end, reg_info) ^ gnuregex.c:4490:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] common_op_match_null_string_p (p, end, reg_info) ^ gnuregex.c:4578:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] bcmp_translate (s1, s2, len, translate) ^ gnuregex.c:4720:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regcomp (preg, pattern, cflags) ^ gnuregex.c:4795:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regexec (preg, string, nmatch, pmatch, eflags) ^ gnuregex.c:4860:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regerror (errcode, preg, errbuf, errbuf_size) ^ gnuregex.c:4904:1: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C2x [-Wdeprecated-non-prototype] regfree (preg) ^ clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_ctype.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_math.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c sre_string.c sqio.c:1033:9: warning: comparison of array 'sp' equal to a null pointer is always false [-Wtautological-pointer-compare] if (sp==NULL || *sp=='\0') ^~ ~~~~ clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c stack.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c translate.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c types.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c weight.c 2 warnings generated. 1 warning generated. 67 warnings generated. ar rcv libhmmer.a alphabet.o core_algorithms.o debug.o emit.o emulation.o histogram.o hmmio.o mathsupport.o masks.o misc.o modelmakers.o plan7.o plan9.o prior.o tophits.o trace.o aligneval.o alignio.o cluster.o dayhoff.o file.o getopt.o gnuregex.o interleaved.o iupac.o msf.o revcomp.o selex.o sqerror.o sqio.o sre_ctype.o sre_math.o sre_string.o stack.o translate.o types.o weight.o a - alphabet.o a - core_algorithms.o a - debug.o a - emit.o a - emulation.o a - histogram.o a - hmmio.o a - mathsupport.o a - masks.o a - misc.o a - modelmakers.o a - plan7.o a - plan9.o a - prior.o a - tophits.o a - trace.o a - aligneval.o a - alignio.o a - cluster.o a - dayhoff.o a - file.o a - getopt.o a - gnuregex.o a - interleaved.o a - iupac.o a - msf.o a - revcomp.o a - selex.o a - sqerror.o a - sqio.o a - sre_ctype.o a - sre_math.o a - sre_string.o a - stack.o a - translate.o a - types.o a - weight.o if test -x /bin/ranlib; then /bin/ranlib libhmmer.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libhmmer.a; else exit 0; fi if test -x ranlib; then ranlib libhmmer.a; else exit 0; fi chmod 644 libhmmer.a make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/HMMer2' (cd dynlibsrc ; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread `pkg-config glib-2.0 --cflags`" libdyna.a ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/dynlibsrc' clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ packaln.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ aln.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dnamatrix.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ probability.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ alnrange.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ alnconvert.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ basematrix.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shattermatrix.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ matrixdebug.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dpenvelope.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dbsearchimpl.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dprunimpl.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexsequence.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexevalset.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ complexconsensi.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequence.c dpenvelope.dy:68:1: warning: non-void function does not return a value in all control paths [-Wreturn-type] } ^ aln.dy:867:65: warning: data argument not used by format string [-Wformat-extra-args] fprintf(ofp," {%3.2f} ",(double)(*score_to_double)(cuml),cuml); ~~~~~~~~~~~~ ^ clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequencestream.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ seqalign.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hitlist.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsp.c 1 warning generated. clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hspstream.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codon.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ compmat.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codonmatrix.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ codonmapper.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ sequencedb.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hscore.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ seqlookup.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ arrayseqlookup.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genericindexresult.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ linkedlist_lookpos.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ singlenumberspace.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ histogram.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ searchstatinterface.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ searchstatlookup.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteindb.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ protein.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ pairbase.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ pairbaseseq.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomicdb.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ randommodel.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ randomdb.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomic.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ cdna.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ cdnadb.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dna.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ embl.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ genomicregion.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ gene.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ transcript.c 1 warning generated. clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ translation.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ btcanvas.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ asciibtcanvas.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dynlibcross.c ar ru libdyna.a packaln.o aln.o dnamatrix.o probability.o alnrange.o alnconvert.o basematrix.o shattermatrix.o matrixdebug.o dpenvelope.o dbsearchimpl.o dprunimpl.o complexsequence.o complexevalset.o complexconsensi.o sequence.o sequencestream.o seqalign.o hitlist.o hsp.o hspstream.o codon.o compmat.o codonmatrix.o codonmapper.o sequencedb.o hscore.o seqlookup.o arrayseqlookup.o genericindexresult.o linkedlist_lookpos.o singlenumberspace.o histogram.o searchstatinterface.o searchstatlookup.o proteindb.o protein.o pairbase.o pairbaseseq.o genomicdb.o randommodel.o randomdb.o genomic.o cdna.o cdnadb.o dna.o embl.o genomicregion.o gene.o transcript.o translation.o btcanvas.o asciibtcanvas.o dynlibcross.o ar: creating libdyna.a if test -x /bin/ranlib; then /bin/ranlib libdyna.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna.a; else exit 0; fi make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/dynlibsrc' (cd dynlibsrc ; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread `pkg-config glib-2.0 --cflags`" libdyna_glib.a ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/dynlibsrc' clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ subseqhash.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ intallocator.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteinstreamedindex.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shadowseq.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ shadowseqindex.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsphandler.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hspscaninterface.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsp2hitscan.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsplookupscan.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ hsplookupthreaded.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ proteinindexcons.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ dnaindexcons.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ staticseq.c subseqhash.dy:111:29: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] if( g_hash_table_lookup(h,(gconstpointer)seq_number) == NULL ) { ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:128:85: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] return new_linkedl_SeqLookupResultInterface((SeqLookupPos *)g_hash_table_lookup(h,(gconstpointer)seq_number)); ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:160:54: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:161:29: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] g_hash_table_insert(h,(gpointer)seq_number,p); ^~~~~~~~~~~~~~~~~~~~ subseqhash.dy:188:52: warning: cast to 'gconstpointer' (aka 'const void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] if((ret = (SeqLookupPos *) g_hash_table_lookup(h,(gconstpointer)seq_number)) == NULL ) { ^~~~~~~~~~~~~~~~~~~~~~~~~ subseqhash.dy:189:27: warning: cast to 'gpointer' (aka 'void *') from smaller integer type 'int' [-Wint-to-void-pointer-cast] g_hash_table_insert(h,(gpointer)seq_number,p); ^~~~~~~~~~~~~~~~~~~~ shadowseqindex.dy:285:59: warning: format specifies type 'double' but the argument has type 'unsigned long' [-Wformat] fprintf(ofp,"Head memory %d [%.2f Mbytes]\n",total_head,(total_head*sizeof(ShadowArraySeqHead))/100000); ~~~~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ %.2lu hsplookupthreaded.dy:160:3: warning: call to undeclared function 'gettimeofday'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] gettimeofday(&t1,NULL); ^ hsp2hitscan.dy:210:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:211:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:212:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:213:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ hsplookupthreaded.dy:211:41: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] fprintf(stderr,"Got seq %d numbers\n",current); ~~ ^~~~~~~ %ld hsplookupthreaded.dy:259:55: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] fprintf(stderr,"retrieved array with %d elements\n",current_oph); ~~ ^~~~~~~~~~~ %ld hsp2hitscan.dy:274:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:275:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:276:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:277:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:287:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:288:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:289:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:290:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:303:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_utime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:304:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_utime.tv_sec/1000, ^~~~~~~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:305:4: warning: format specifies type 'int' but the argument has type '__time_t' (aka 'long') [-Wformat] use.ru_stime.tv_sec, ^~~~~~~~~~~~~~~~~~~ hsp2hitscan.dy:306:4: warning: format specifies type 'int' but the argument has type 'long' [-Wformat] use.ru_stime.tv_sec/1000 ^~~~~~~~~~~~~~~~~~~~~~~~ hsplookupthreaded.dy:561:1: warning: non-void function does not return a value [-Wreturn-type] } ^ 6 warnings generated. 1 warning generated. 16 warnings generated. 4 warnings generated. ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o proteinindexcons.o dnaindexcons.o staticseq.o ar: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/dynlibsrc' (cd external ; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread `pkg-config glib-2.0 --cflags`" all ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/external' (cd mott; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include " all) make[2]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/external/mott' clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c -o mott_api.o mott_api.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -c -o gaplib.o gaplib.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c mott_api.c:64:3: warning: call to undeclared library function 'free' with type 'void (void *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] free(freq0); ^ mott_api.c:64:3: note: include the header or explicitly provide a declaration for 'free' mott_api.c:179:16: warning: call to undeclared library function 'calloc' with type 'void *(unsigned long, unsigned long)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin; ^ mott_api.c:179:16: note: include the header or explicitly provide a declaration for 'calloc' mott_api.c:207:12: warning: call to undeclared library function 'toupper' with type 'int (int)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] freq[toupper(seq[n])]++; ^ mott_api.c:207:12: note: include the header or explicitly provide a declaration for 'toupper' 3 warnings generated. ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi make[2]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/external/mott' make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/external' (cd socket ; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread `pkg-config glib-2.0 --cflags`" libwisesocket.a ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/socket' clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ functionserver.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ functionclient.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ anonobj.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ transferinterface.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ directsocketwrite.c functionclient.dy:193:24: warning: incompatible pointer types passing 'struct sockaddr_in *' to parameter of type 'const struct sockaddr *' [-Wincompatible-pointer-types] connect(out->socket, &server, sizeof(server)); ^~~~~~~ /usr/include/sys/socket.h:126:52: note: passing argument to parameter '__addr' here extern int connect (int __fd, __CONST_SOCKADDR_ARG __addr, socklen_t __len); ^ 1 warning generated. ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/socket' (cd dnaindex ; make CC="clang" CFLAGS="-O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread `pkg-config glib-2.0 --cflags`" all ) make[1]: Entering directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/dnaindex' clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c clang -O2 -g0 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -pthread -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c kmer_assembly_untangler.dy:52:65: warning: cast to smaller integer type 'int' from 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wpointer-to-int-cast] fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base); ^~~~~~~~~~~~~~~~~~ kmer_assembly.dy:365:88: warning: format specifies type 'long' but the argument has type 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wformat] fprintf(stderr," ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len); ~~~ ^~~ kmer_assembly.dy:367:36: warning: more '%' conversions than data arguments [-Wformat-insufficient-args] fprintf(stderr," [%ld] is %d label\n",kal->sequence_label[i]); ~^ kmer_assembly_error.dy:351:127: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat] fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos); ~~ ^~~~~~~~~~~~ kmer_assembly_untangler.dy:568:75: warning: incompatible pointer types passing 'long[10000]' to parameter of type 'int *' [-Wincompatible-pointer-types] lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len); ^~~~~~~~~~~~~~~~~ ./kmer_assembly_untangler.h:174:116: note: passing argument to parameter 'start_label' here void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len); ^ compressed_protein_index.dy:223:10: error: incompatible pointer to integer conversion returning 'void *' from a function with result type 'boolean' (aka 'int') [-Wint-conversion] return NULL; ^~~~ /usr/lib/llvm/15/bin/../../../../lib/clang/15.0.6/include/stddef.h:89:16: note: expanded from macro 'NULL' # define NULL ((void*)0) ^~~~~~~~~~ 1 error generated. make[1]: *** [makefile:80: compressed_protein_index.o] Error 1 make[1]: *** Waiting for unfinished jobs.... 2 warnings generated. 1 warning generated. 2 warnings generated. make[1]: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src/dnaindex' make: *** [makefile:86: realall] Error 2 make: Leaving directory '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha/src' * ERROR: sci-biology/wise-2.4.0_alpha-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/wise-2.4.0_alpha-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/wise-2.4.0_alpha-r1::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-biology/wise-2.4.0_alpha-r1:20221215-064008.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha' * S: '/var/tmp/portage/sci-biology/wise-2.4.0_alpha-r1/work/wise2.4.0alpha'