* Package: sci-biology/augustus-3.4.0-r2:0 * 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/gentoo/commit/6c83a787829ad36a5cf7e165769ec5463c22bd60 (Sat Sep 3 22:19:50 UTC 2022) @@@@@ END @@@@@ @@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ This ebuild was merged (directly or as a dependency) because of the following commit: https://github.com/gentoo/gentoo/commit/405d411472329b890d43b44367b7874514c30379 @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.35 (python 3.10.6-final-0, default/linux/amd64/17.1, gcc-12.2.0, glibc-2.35-r8, 5.10.133-gentoo x86_64) ================================================================= System uname: Linux-5.10.133-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2650_v4_@_2.20GHz-with-glibc2.35 KiB Mem: 264024340 total, 159577260 free KiB Swap: 0 total, 0 free sh bash 5.1_p16-r2 ld GNU ld (Gentoo 2.38 p4) 2.38 app-misc/pax-utils: 1.3.5::gentoo app-shells/bash: 5.1_p16-r2::gentoo dev-lang/perl: 5.36.0::gentoo dev-lang/python: 3.8.13_p7::gentoo, 3.9.13_p5::gentoo, 3.10.6_p3::gentoo, 3.11.0_rc1_p1::gentoo dev-util/cmake: 3.24.1::gentoo dev-util/meson: 0.63.1::gentoo sys-apps/baselayout: 2.8-r2::gentoo sys-apps/openrc: 0.45.2::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.71-r1::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.38-r2::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/gcc: 12.2.0::gentoo sys-devel/gcc-config: 2.5-r1::gentoo sys-devel/libtool: 2.4.7::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.19::gentoo (virtual/os-headers) sys-libs/glibc: 2.35-r8::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-extra-opts: sync-rsync-verify-max-age: 24 sync-rsync-verify-metamanifest: yes ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* Artistic" AR="x86_64-pc-linux-gnu-ar" AS="x86_64-pc-linux-gnu-as" CBUILD="x86_64-pc-linux-gnu" CC="x86_64-pc-linux-gnu-gcc" CFLAGS="-O2 -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" CPP="x86_64-pc-linux-gnu-gcc -E" CXX="x86_64-pc-linux-gnu-g++" CXXFLAGS="-O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" DISTDIR="/var/tmp/portage/sci-biology/augustus-3.4.0-r2/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" FCFLAGS="-O2 -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 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" GCOV="x86_64-pc-linux-gnu-gcov" 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="en_US.utf8" LD="x86_64-pc-linux-gnu-ld" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0" MAKEOPTS="-j45" NM="x86_64-pc-linux-gnu-nm" OBJCOPY="x86_64-pc-linux-gnu-objcopy" OBJDUMP="x86_64-pc-linux-gnu-objdump" 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" RANLIB="x86_64-pc-linux-gnu-ranlib" READELF="x86_64-pc-linux-gnu-readelf" SHELL="/bin/bash" STRIP="x86_64-pc-linux-gnu-strip" 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 unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" USERLAND="GNU" Unset: ADDR2LINE, ARFLAGS, ASFLAGS, CCLD, CONFIG_SHELL, CPPFLAGS, CTARGET, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GPROF, INSTALL_MASK, LC_ALL, LEX, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS, SIZE, STRINGS, YACC, YFLAGS ############################## # emerge history (qlop -mv): # ############################## 2022-09-04T00:23:45 >>> virtual/fortran-0-r1 2022-09-04T00:23:39 >>> dev-util/boost-build-1.79.0-r1 2022-09-04T00:23:42 >>> sci-libs/htslib-1.15.1 2022-09-04T00:23:48 >>> sci-libs/gsl-2.7.1-r1 2022-09-04T00:23:54 >>> app-arch/lz4-1.9.4 2022-09-04T00:23:36 >>> sci-libs/suitesparseconfig-5.4.0 2022-09-04T00:23:51 >>> sci-libs/metis-5.1.0-r5 2022-09-04T00:24:18 >>> sci-libs/lapack-3.10.1 2022-09-04T00:23:57 >>> sci-biology/bamtools-2.5.2 2022-09-04T00:24:34 >>> sci-biology/samtools-1.15.1 2022-09-04T00:24:29 >>> dev-libs/boost-1.79.0 2022-09-04T00:24:44 >>> dev-db/mysql-connector-c-8.0.27-r1 2022-09-04T00:25:05 >>> sci-libs/btf-1.2.6 2022-09-04T00:25:02 >>> sci-libs/colamd-2.9.6 2022-09-04T00:25:08 >>> sci-libs/ccolamd-2.9.6 2022-09-04T00:25:11 >>> sci-libs/cxsparse-3.2.0 2022-09-04T00:25:14 >>> sci-libs/ldl-2.2.6 2022-09-04T00:25:17 >>> sci-libs/amd-2.4.6-r1 2022-09-04T00:25:20 >>> sci-libs/camd-2.4.6-r1 2022-09-04T00:25:31 >>> virtual/lapack-3.10 2022-09-04T00:25:35 >>> virtual/blas-3.8 2022-09-04T00:26:24 >>> sci-mathematics/lpsolve-5.5.2.0-r1 2022-09-04T00:26:54 >>> sci-libs/cholmod-3.0.13 2022-09-04T00:27:11 >>> sci-libs/spqr-2.0.9-r2 2022-09-04T00:27:17 >>> sci-libs/umfpack-5.7.9 2022-09-04T00:26:13 >>> dev-db/mysql++-3.3.0 2022-09-04T00:26:43 >>> sci-libs/klu-1.3.9-r2 2022-09-04T00:28:04 >>> sci-libs/suitesparse-5.4.0 2022-09-04T00:28:14 >>> sci-biology/augustus-3.4.0-r2 2022-09-04T00:35:31 >>> app-text/poppler-data-0.4.11 2022-09-04T00:35:42 >>> media-libs/tiff-4.4.0 2022-09-04T00:35:39 >>> app-arch/cpio-2.12-r1 2022-09-04T00:35:34 >>> media-fonts/baekmuk-fonts-2.2-r2 2022-09-04T00:35:49 >>> app-text/libpaper-1.1.28 2022-09-04T00:35:52 >>> media-libs/jbig2dec-0.19 2022-09-04T00:35:46 >>> media-libs/lcms-2.13.1 2022-09-04T00:35:55 >>> net-dns/libidn-1.41 2022-09-04T00:35:59 >>> media-fonts/arphicfonts-0.2.20080216.1-r2 2022-09-04T00:36:03 >>> media-libs/libjpeg-turbo-2.1.4 2022-09-04T00:36:07 >>> dev-lang/nasm-2.15.05 2022-09-04T00:36:10 >>> media-gfx/fontforge-20220308 2022-09-04T00:36:36 >>> app-arch/rpm2targz-2021.03.16 2022-09-04T00:37:00 >>> media-libs/openjpeg-2.5.0-r2 2022-09-04T00:37:24 >>> virtual/jpeg-100-r1 2022-09-04T00:37:37 >>> media-fonts/urw-fonts-2.4.9 2022-09-04T00:37:57 >>> app-text/ghostscript-gpl-9.55.0-r1 2022-09-04T00:38:08 >>> app-doc/doxygen-1.9.5 2022-09-04T00:38:18 >>> sci-biology/augustus-3.4.0-r2 2022-09-04T00:40:20 >>> dev-lang/python-exec-2.4.9 2022-09-04T00:40:20 >>> sys-devel/binutils-config-5.4.1 2022-09-04T00:40:20 >>> sys-devel/gcc-config-2.5-r1 ####################################### # 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-arch/bzip2-1.0.8-r1:0/1 -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 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app-portage/gemato-16.2:0 gpg 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-0.94.3:0 openmp qmanifest qtegrity -static app-shells/bash-5.1_p16-r2:0 -afs -bashlogger -examples -mem-scramble net nls -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-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-4.2-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/ghostscript-gpl-9.55.0-r1:0/9.55 -X -cups -dbus -gtk l10n_de -l10n_ja l10n_ko 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x11-libs/libXmu-1.1.3:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -doc ipv6 x11-libs/libXrender-0.9.10-r2:0 -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/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-0.40.0:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 -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-1.8.1:0 x11-misc/shared-mime-info-2.2:0 -test x11-misc/xdg-utils-1.1.3_p20210805:0 -dbus -doc -gnome ####################### # build.log # ####################### >>> Unpacking source... >>> Unpacking augustus-3.4.0.tar.gz to /var/tmp/portage/sci-biology/augustus-3.4.0-r2/work >>> Source unpacked in /var/tmp/portage/sci-biology/augustus-3.4.0-r2/work >>> Preparing source in /var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0 ... make -j45 LINK.cc=x86_64-pc-linux-gnu-g++ mkdir -p bin cd src && make make[1]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/src' x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o genbank.o genbank.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o properties.o properties.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o pp_profile.o pp_profile.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o pp_hitseq.o pp_hitseq.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o pp_scoring.o pp_scoring.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o statemodel.o statemodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o namgene.o namgene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o types.o types.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o gene.o gene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o evaluation.o evaluation.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o motif.o motif.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o geneticcode.o geneticcode.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o hints.o hints.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o extrinsicinfo.o extrinsicinfo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o projectio.o projectio.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o intronmodel.o intronmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o exonmodel.o exonmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o igenicmodel.o igenicmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o utrmodel.o utrmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o merkmal.o merkmal.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o vitmatrix.o vitmatrix.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o lldouble.o lldouble.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o mea.o mea.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o graph.o graph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o meaPath.o meaPath.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o exoncand.o exoncand.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o randseqaccess.o randseqaccess.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o fasta.o fasta.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o ncmodel.o ncmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o parser/parse.o parser/parse.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o scanner/lex.o scanner/lex.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o genomicMSA.o genomicMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o geneMSA.o geneMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o contTimeMC.o contTimeMC.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o codonevo.o codonevo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o compgenepred.o compgenepred.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o phylotree.o phylotree.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o orthograph.o orthograph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o orthoexon.o orthoexon.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o alignment.o alignment.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o speciesgraph.o speciesgraph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o codonMSA.o codonMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o train_logReg_param.o train_logReg_param.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o tokenizer.o tokenizer.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o sqliteDB.o sqliteDB.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o commontrain.o commontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o igenictrain.o igenictrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o introntrain.o introntrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o exontrain.o exontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o utrtrain.o utrtrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o dummy.o dummy.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ hints.cc: In function ‘std::istream& operator>>(std::istream&, Feature&)’: hints.cc:82:16: warning: â€-Wstringop-truncation][]] 82 | strncpy(copybuff, buff, 1014); | ^ x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o prepareAlign pp_prepare_align.cc x86_64-pc-linux-gnu-g++ -c -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE" > cxxflags x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 cp prepareAlign ../bin/ x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 cp load2sqlitedb ../bin/ cp load2db ../bin/ cp fastBlockSearch ../bin/ cp pp_simScore ../bin/ x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 x86_64-pc-linux-gnu-g++ -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 cp etraining ../bin/ cp getSeq ../bin/ cp augustus ../bin/ make[1]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/src' cd auxprogs && make make[1]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs' cd aln2wig; make; make[2]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/aln2wig' x86_64-pc-linux-gnu-gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c aln2wig.c aln2wig.c: In function ‘main’: aln2wig.c:454:41: warning: â€-Wstringop-truncation][]] 454 | strncpy(completedChromosomes[completedChromosomeCount-1],oldname,TOKEN_SIZE-1); | ^ aln2wig.c:460:41: warning: â€-Wstringop-truncation][]] 460 | strncpy(oldname,name,TOKEN_SIZE-1); | ^ aln2wig.c:327:41: warning: â€-Wstringop-truncation][]] 327 | strncpy(completedChromosomes[completedChromosomeCount-1],oldname,TOKEN_SIZE-1); | ^ aln2wig.c:334:41: warning: â€-Wstringop-truncation][]] 334 | strncpy(oldname,name,TOKEN_SIZE-1); | ^ x86_64-pc-linux-gnu-gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o aln2wig aln2wig.o mkdir -p ../../bin cp aln2wig ../../bin make[2]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/aln2wig' cd bam2hints; make; make[2]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/bam2hints' x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wall -O2 -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/list:63, from bam2hints.cc:9: In member function ‘std::_List_iterator< >::_Self std::_List_iterator< >::operator++(int) [with _Tp = hint_t]’, inlined from ‘void printHints(FILE*, const char*)’ at bam2hints.cc:326:121: /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/stl_list.h:297:28: warning: pointer used after â€-Wuse-after-free][]] 297 | _M_node = _M_node->_M_next; | ~~~~~~~~~^~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/x86_64-pc-linux-gnu/bits/c++allocator.h:33, from /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/allocator.h:46, from /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/list:61: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = std::_List_node]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = std::_List_node]’ at /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/alloc_traits.h:496:23, inlined from ‘void std::__cxx11::_List_base<_Tp, _Alloc>::_M_put_node(typename _Node_alloc_traits::pointer) [with _Tp = hint_t; _Alloc = std::allocator]’ at /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/stl_list.h:522:39, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = hint_t; _Alloc = std::allocator]’ at /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/stl_list.h:2024:13, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::erase(const_iterator) [with _Tp = hint_t; _Alloc = std::allocator]’ at /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/list.tcc:158:15, inlined from ‘void printHints(FILE*, const char*)’ at bam2hints.cc:334:26: /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/new_allocator.h:158:33: note: call to ‘void operator delete(void*, std::size_t)’ here 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wall -O2 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o bam2hints bam2hints.o -lbamtools -lz mkdir -p ../../bin cp bam2hints ../../bin make[2]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/bam2hints' cd compileSpliceCands; make; make[2]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/compileSpliceCands' x86_64-pc-linux-gnu-gcc -Wall -pedantic -ansi -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c compileSpliceCands.c x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o list.o list.c compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:216:9: warning: â€-Wstringop-overflow=][]] 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^ compileSpliceCands.c:216:9: note: length computed here 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function ‘parseLine’: compileSpliceCands.c:292:9: warning: â€-Wstringop-truncation][]] 292 | strncpy(d->name,tokens[0],LINEBUFFER); | ^ compileSpliceCands.c: In function ‘parseList’: compileSpliceCands.c:337:59: warning: â€-Wmaybe-uninitialized][]] 337 | if(isCompatibleStrand(left->strand,right->strand)) | ~~~~^~~~~~~~ compileSpliceCands.c:314:14: note: ‘left’ was declared here 314 | Data left; | ^~~~ compileSpliceCands.c: In function ‘main’: compileSpliceCands.c:563:17: warning: â€-Wmaybe-uninitialized][]] 563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c:416:18: note: ‘chromosomeLength’ was declared here 416 | long int chromosomeLength; | ^~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o compileSpliceCands compileSpliceCands.o list.o cp compileSpliceCands ../../bin/compileSpliceCands make[2]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/compileSpliceCands' cd filterBam; make; make[2]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/filterBam/src' x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools filterBam compiled with BAMTOOLS=/usr/include/bamtools In file included from filterBam.cc:17: /usr/include/bamtools/api/algorithms/Sort.h:64:18: warning: â€-Wdeprecated-declarations][]] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/string:48, from /usr/include/bamtools/api/BamReader.h:13, from filterBam.cc:14: /usr/lib/gcc/x86_64-pc-linux-gnu/12.2.0/include/g++-v12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-g++ -std=c++0x -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/filterBam/src' make[2]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/filterBam' cd homGeneMapping; make; make[2]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/homGeneMapping' (cd src; make) make[3]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/homGeneMapping/src' x86_64-pc-linux-gnu-g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -DBOOST -DM_SQLITE -o gene.o gene.cc -I../include x86_64-pc-linux-gnu-g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -DBOOST -DM_SQLITE -o genome.o genome.cc -I../include x86_64-pc-linux-gnu-g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -DBOOST -DM_SQLITE -o sqliteDB.o sqliteDB.cc -I../include x86_64-pc-linux-gnu-g++ -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -DBOOST -DM_SQLITE -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -I../include -lsqlite3 mkdir -p ../../../bin/ cp homGeneMapping ../../../bin/homGeneMapping make[3]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/homGeneMapping/src' make[2]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/homGeneMapping' cd joingenes; make; make[2]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/joingenes' x86_64-pc-linux-gnu-g++ -c -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wall -std=gnu++0x joingenes.cpp x86_64-pc-linux-gnu-g++ -c -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wall -std=gnu++0x jg_transcript.cpp x86_64-pc-linux-gnu-g++ -c -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wall -std=gnu++0x jg_ios.cpp jg_ios.cpp: In function ‘void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)’: jg_ios.cpp:251:14: warning: â€-Wstringop-truncation][]] 251 | strncpy(copybuff, buff, 1014); | ^ jg_ios.cpp:79:14: warning: â€-Wstringop-truncation][]] 79 | strncpy(copybuff, buff, 1014); | ^ jg_ios.cpp:148:16: warning: â€-Wstringop-truncation][]] 148 | strncpy(attribute, temp, 300); | ^ x86_64-pc-linux-gnu-g++ -O2 -pipe -march=x86-64 -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wall -std=gnu++0x -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 joingenes.o jg_transcript.o jg_ios.o -o joingenes mkdir -p ../../bin/ cp joingenes ../../bin/ make[2]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/joingenes' cd utrrnaseq/Debug; make all; make[2]: Entering directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/utrrnaseq/Debug' Building file: ../src/Compute_UTRs.cpp Building file: ../src/Genomic_Data.cpp Building file: ../src/Coord_Transform.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp" Invoking: GCC C++ Compiler Building file: ../src/Splice_Sites.cpp g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp" Invoking: GCC C++ Compiler Building file: ../src/Supporting_Methods.cpp g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp" /bin/sh: line 1: g++: command not found make[2]: *** [src/subdir.mk:40: src/Compute_UTRs.o] Error 127 make[2]: *** Waiting for unfinished jobs.... Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp" /bin/sh: line 1: g++: command not found Invoking: GCC C++ Compiler make[2]: *** [src/subdir.mk:41: src/Coord_Transform.o] Error 127 g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp" /bin/sh: line 1: g++: command not found make[2]: *** [src/subdir.mk:41: src/Genomic_Data.o] Error 127 /bin/sh: line 1: g++: command not found make[2]: *** [src/subdir.mk:41: src/Supporting_Methods.o] Error 127 /bin/sh: line 1: g++: command not found make[2]: *** [src/subdir.mk:41: src/Splice_Sites.o] Error 127 make[2]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs/utrrnaseq/Debug' make[1]: *** [Makefile:10: all] Error 2 make[1]: Leaving directory '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0/auxprogs' make: *** [Makefile:9: all] Error 2 * ERROR: sci-biology/augustus-3.4.0-r2::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/augustus-3.4.0-r2::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-biology/augustus-3.4.0-r2::gentoo'`. * The complete build log is located at '/var/log/emerge-log/build/sci-biology/augustus-3.4.0-r2:20220903-224106.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0' * S: '/var/tmp/portage/sci-biology/augustus-3.4.0-r2/work/Augustus-3.4.0'