* Package: sci-biology/unafold-3.8-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/b011c8b65a9c425e0b6a7e359fcf81d060b1f41d (Thu Mar 9 11:01:59 UTC 2023) @@@@@ END @@@@@ ################## # emerge --info: # ################## Portage 3.0.45.2 (python 3.11.2-final-0, default/linux/amd64/17.1, gcc-13, glibc-2.36-r7, 5.15.85-gentoo-dist x86_64) ================================================================= System uname: Linux-5.15.85-gentoo-dist-x86_64-AMD_EPYC_7513_32-Core_Processor-with-glibc2.36 KiB Mem: 263532996 total, 75686864 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Thu, 09 Mar 2023 11:01:58 +0000 sh bash 5.2_p15-r2 ld GNU ld (Gentoo 2.40 p3) 2.40.0 app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p15-r2::gentoo dev-lang/perl: 5.36.0-r2::gentoo dev-lang/python: 3.9.16_p2::gentoo, 3.10.10_p2::gentoo, 3.11.2_p1::gentoo dev-util/cmake: 3.25.3::gentoo dev-util/meson: 1.0.1::gentoo sys-apps/baselayout: 2.13-r1::gentoo sys-apps/openrc: 0.46::gentoo sys-apps/sandbox: 2.30-r1::gentoo sys-devel/autoconf: 2.71-r5::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.40-r3::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/gcc: 13.0.1_pre20230305::gentoo sys-devel/gcc-config: 2.10::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/llvm: 15.0.7::gentoo sys-devel/make: 4.4.1::gentoo sys-kernel/linux-headers: 6.2::gentoo (virtual/os-headers) sys-libs/glibc: 2.36-r7::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 volatile: True sync-rsync-verify-metamanifest: yes sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 sync-rsync-extra-opts: ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* unafold" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=x86-64 -pipe -pipe -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" CXXFLAGS="-O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0" DISTDIR="/var/tmp/portage/sci-biology/unafold-3.8-r1/distdir" EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -k -b" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE 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 -march=x86-64 -pipe -pipe -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 -march=x86-64 -pipe -pipe -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="en_US.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 debug 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, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, 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): # ############################## 2023-03-09T12:47:05 >>> sys-devel/llvm-common-15.0.7 2023-03-09T12:47:06 >>> sys-apps/hwdata-0.367 2023-03-09T12:47:06 >>> media-libs/libjpeg-turbo-2.1.5.1 2023-03-09T12:47:07 >>> x11-libs/libxshmfence-1.3.2 2023-03-09T12:47:07 >>> sys-libs/binutils-libs-2.40-r3 2023-03-09T12:47:08 >>> x11-libs/libXxf86vm-1.1.5 2023-03-09T12:47:08 >>> x11-libs/libXfixes-6.0.0 2023-03-09T12:47:09 >>> x11-libs/libXrender-0.9.11 2023-03-09T12:47:09 >>> media-libs/libglvnd-1.6.0 2023-03-09T12:47:11 >>> dev-lang/nasm-2.16.01 2023-03-09T12:47:10 >>> dev-python/pygments-2.14.0 2023-03-09T12:47:11 >>> dev-python/mako-1.2.4 2023-03-09T12:47:14 >>> x11-libs/libpciaccess-0.17 2023-03-09T12:47:19 >>> sys-devel/llvm-15.0.7 2023-03-09T12:47:23 >>> x11-libs/libXi-1.8 2023-03-09T12:47:25 >>> x11-libs/libXrandr-1.5.3 2023-03-09T12:47:27 >>> media-libs/gd-2.3.3-r3 2023-03-09T12:47:30 >>> dev-python/docutils-0.19 2023-03-09T12:47:39 >>> sys-devel/llvm-toolchain-symlinks-15-r1 2023-03-09T12:47:45 >>> x11-libs/libdrm-2.4.115 2023-03-09T12:47:48 >>> sys-devel/llvmgold-15 2023-03-09T12:47:51 >>> media-libs/mesa-23.0.0 2023-03-09T12:47:53 >>> virtual/opengl-7.0-r2 2023-03-09T12:47:56 >>> media-libs/glu-9.0.2 2023-03-09T12:47:58 >>> virtual/glu-9.0-r2 2023-03-09T12:48:00 >>> media-libs/freeglut-3.4.0 ####################################### # 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/floppy-0:0 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/root-0:0 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/usb-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-1.4.21:0 -doc -emacs -vim-syntax app-admin/perl-cleaner-2.30-r1:0 -pkgcore app-alternatives/awk-4:0 -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/sh-0:0 bash -busybox -dash -ksh -lksh -mksh 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-r4:0 -pic -static -verify-sig app-arch/libarchive-3.6.2-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 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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-ns-stylesheets-1.79.1:0 -ruby app-text/docbook-xsl-stylesheets-1.79.1-r3:0 -ruby app-text/manpager-1:0 app-text/opensp-1.5.2-r10:0 -doc nls -static-libs -test app-text/po4a-0.69:0 -test -test app-text/sgml-common-0.6.3-r7:0 app-text/xmlto-0.0.28-r10:0 -latex text dev-db/sqlite-3.41.0:3 -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-2.16.01:0 -doc dev-lang/perl-5.36.0-r2:0/5.36 -berkdb debug -doc gdbm ithreads -minimal -quadmath dev-lang/python-3.11.2_p1:3.11 -bluetooth -build ensurepip -examples gdbm -hardened -libedit -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig dev-lang/python-3.10.10_p2:3.10 -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_p2:3.9 -bluetooth -build ensurepip -examples gdbm -hardened -lto ncurses -pgo readline sqlite ssl -test -tk -valgrind -verify-sig xml dev-lang/python-exec-2.4.10:2 native-symlinks python_targets_pypy3 python_targets_python3_10 python_targets_python3_11 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_9 dev-lang/tcl-8.6.13-r1:0/8.6 -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 abi_x86_64 -abi_x86_x32 -cxx large -static-libs threads dev-libs/elfutils-0.189:0 -abi_mips_n32 -abi_mips_n64 -abi_mips_o32 -abi_s390_32 -abi_s390_64 -abi_x86_32 abi_x86_64 -abi_x86_x32 bzip2 -lzma nls -static-libs -test utils 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-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-1.8.4:0 x11-misc/shared-mime-info-2.2:0 -test x11-misc/xdg-utils-1.1.3_p20210805-r1:0 -dbus -doc -gnome ####################### # build.log # ####################### >>> Unpacking source... >>> Unpacking unafold-3.8.tar.bz2 to /var/tmp/portage/sci-biology/unafold-3.8-r1/work >>> Source unpacked in /var/tmp/portage/sci-biology/unafold-3.8-r1/work >>> Preparing source in /var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8 ... * Applying unafold-3.8-doc-version.patch ... [ ok ] * Applying unafold-3.8-autotools.patch ... [ ok ] * Applying unafold-3.8-clang16.patch ... [ ok ] * Running eautoreconf in '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' ... * Running 'aclocal --system-acdir=/var/tmp/portage/sci-biology/unafold-3.8-r1/temp/aclocal' ... [ ok ] * Running 'autoconf --force' ... [ ok ] * Running 'autoheader' ... [ ok ] * Running 'automake --add-missing --copy --foreign --force-missing' ... [ ok ] * Running elibtoolize in: unafold-3.8/ >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8 ... * econf: updating unafold-3.8/config.sub with /usr/share/gnuconfig/config.sub * econf: updating unafold-3.8/config.guess with /usr/share/gnuconfig/config.guess * econf: updating unafold-3.8/config/config.sub with /usr/share/gnuconfig/config.sub * econf: updating unafold-3.8/config/config.guess with /usr/share/gnuconfig/config.guess ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --datarootdir=/usr/share --disable-dependency-tracking --disable-silent-rules --docdir=/usr/share/doc/unafold-3.8-r1 --htmldir=/usr/share/doc/unafold-3.8-r1/html --libdir=/usr/lib64 --disable-coverage checking for a BSD-compatible install... /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to enable C11 features... none needed checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of x86_64-pc-linux-gnu-gcc... none checking whether ln -s works... yes checking for perl... /usr/bin/perl checking for gnuplot... no checking whether compiler needs -mieee... no checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for x86_64-pc-linux-gnu-pkg-config... (cached) /usr/bin/x86_64-pc-linux-gnu-pkg-config checking pkg-config is at least version 0.9.0... yes checking for GL... yes checking for GL/gl.h... yes checking for compiling a minimal OpenGL program... yes checking for linking a minimal OpenGL program... yes checking for library containing glutMainLoop... -lglut checking for GL/glut.h... yes checking for compiling a minimal GLUT program... yes checking for linking a minimal GLUT program... yes checking for gdlib-config... no checking for gdImageCreate in -lgd... yes checking for gdImageGif in -lgd... yes checking for gdImageJpeg in -lgd... yes checking for gdImagePng in -lgd... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fcntl.h... yes checking for ieeefp.h... no checking for libintl.h... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for an ANSI C-conforming const... yes checking whether scanf() understands "inf"... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating scripts/Makefile config.status: creating data/Makefile config.status: creating doc/Makefile config.status: creating tests/Makefile config.status: creating scripts/concentrations.pl config.status: creating scripts/concentrations-same.pl config.status: creating scripts/hybrid2.pl config.status: creating scripts/hybrid-2s.pl config.status: creating scripts/hybrid-ss-2s.pl config.status: creating scripts/hybrid-select.pl config.status: creating scripts/melt.pl config.status: creating scripts/plot2ann.pl config.status: creating scripts/h-num.pl config.status: creating scripts/ss-count.pl config.status: creating scripts/ct-energy-det.pl config.status: creating scripts/UNAFold.pl config.status: creating scripts/ITC-plot.pl config.status: creating scripts/vantHoff-plot.pl config.status: creating doc/hybrid.1 config.status: creating doc/hybrid-min.1 config.status: creating doc/hybrid-ss.1 config.status: creating doc/hybrid-ss-min.1 config.status: creating doc/hybrid-ss-noml.1 config.status: creating doc/hybrid-ss-simple.1 config.status: creating doc/hybrid-plot.1 config.status: creating doc/hybrid-plot-ng.1 config.status: creating doc/concentration.1 config.status: creating doc/concentration-same.1 config.status: creating doc/concentrations.pl.1 config.status: creating doc/concentrations-same.pl.1 config.status: creating doc/ensemble-dg.1 config.status: creating doc/ensemble-dg-same.1 config.status: creating doc/ensemble-ext.1 config.status: creating doc/ensemble-ext-same.1 config.status: creating doc/dG2dH.1 config.status: creating doc/dG2dS.1 config.status: creating doc/dG2Cp.1 config.status: creating doc/ct-energy.1 config.status: creating doc/hybrid2.pl.1 config.status: creating doc/hybrid2-x.pl.1 config.status: creating doc/hybrid2-min.pl.1 config.status: creating doc/hybrid2-min-x.pl.1 config.status: creating doc/hybrid2-2s.pl.1 config.status: creating doc/hybrid2-2s-x.pl.1 config.status: creating doc/ct-ext.1 config.status: creating doc/ct-uniq.1 config.status: creating doc/hybrid-2s.pl.1 config.status: creating doc/hybrid-ss-2s.pl.1 config.status: creating doc/ct-prob.1 config.status: creating doc/melt.pl.1 config.status: creating doc/plot2ann.pl.1 config.status: creating doc/h-num.pl.1 config.status: creating doc/ss-count.pl.1 config.status: creating doc/hybrid-select.pl.1 config.status: creating doc/ct2rnaml.1 config.status: creating doc/ct-energy-det.pl.1 config.status: creating doc/UNAFold.pl.1 config.status: creating doc/ITC-plot.pl.1 config.status: creating doc/vantHoff-plot.pl.1 config.status: creating config.h config.status: executing depfiles commands >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8 ... make -j16 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' Making all in src make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o getopt.o getopt.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o getopt1.o getopt1.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o energy.o energy.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o xmalloc.o xmalloc.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid.o hybrid.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DENERGY=int -DINTEGER -DPRECISION=1000 -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid_min-energy.o `test -f 'energy.c' || echo './'`energy.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DENERGY=int -DINTEGER -DPRECISION=1000 -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid_min-hybrid-min.o `test -f 'hybrid-min.c' || echo './'`hybrid-min.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid-ss.o hybrid-ss.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DENERGY=int -DINTEGER -DPRECISION=1000 -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid_ss_min-energy.o `test -f 'energy.c' || echo './'`energy.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DENERGY=int -DINTEGER -DPRECISION=1000 -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid_ss_min-hybrid-ss-min.o `test -f 'hybrid-ss-min.c' || echo './'`hybrid-ss-min.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid-ss-noml.o hybrid-ss-noml.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid-ss-simple.o hybrid-ss-simple.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid_plot-hybrid-plot.o `test -f 'hybrid-plot.c' || echo './'`hybrid-plot.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o hybrid_plot_ng-hybrid-plot-ng.o `test -f 'hybrid-plot-ng.c' || echo './'`hybrid-plot-ng.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o sbs.o sbs.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o concentration.o concentration.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o concentration-same.o concentration-same.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ensemble-dg.o ensemble-dg.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ensemble-dg-same.o ensemble-dg-same.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ensemble-ext.o ensemble-ext.c In file included from ensemble-ext.c:23: extinction.h: In function ‘loadExtinctionDat’: extinction.h:39:7: warning: ignoring return value of â€-Wunused-result][]] 39 | fscanf(file, "%*g%lg", &g_extinction[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ extinction.h:42:7: warning: ignoring return value of â€-Wunused-result][]] 42 | fscanf(file, "%lg%*g", &g_extinction[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ensemble-ext-same.o ensemble-ext-same.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o dG2Cp.o dG2Cp.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o dG2dH.o dG2dH.c In file included from ensemble-ext-same.c:23: extinction.h: In function ‘loadExtinctionDat’: extinction.h:39:7: warning: ignoring return value of â€-Wunused-result][]] 39 | fscanf(file, "%*g%lg", &g_extinction[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ extinction.h:42:7: warning: ignoring return value of â€-Wunused-result][]] 42 | fscanf(file, "%lg%*g", &g_extinction[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DENTROPY -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o dG2dS-dG2dH.o `test -f 'dG2dH.c' || echo './'`dG2dH.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ct-energy.o ct-energy.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ct-ext.o ct-ext.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ct-uniq.o ct-uniq.c In file included from ct-ext.c:9: extinction.h: In function ‘loadExtinctionDat’: extinction.h:39:7: warning: ignoring return value of â€-Wunused-result][]] 39 | fscanf(file, "%*g%lg", &g_extinction[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ extinction.h:42:7: warning: ignoring return value of â€-Wunused-result][]] 42 | fscanf(file, "%lg%*g", &g_extinction[i]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ct-prob.o ct-prob.c ct-prob.c: In function ‘main’: ct-prob.c:95:11: warning: ignoring return value of â€-Wunused-result][]] 95 | fgets(line, 80, ctFile); | ^~~~~~~~~~~~~~~~~~~~~~~ ct-prob.c:112:7: warning: ignoring return value of â€-Wunused-result][]] 112 | fgets(line, 80, plotFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -DPKGDATADIR=\"/usr/share/unafold/\" -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -c -o ct2rnaml.o ct2rnaml.c x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid-plot-ng hybrid_plot_ng-hybrid-plot-ng.o getopt.o getopt1.o xmalloc.o -lgd -lGL -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o concentration getopt.o getopt1.o xmalloc.o concentration.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o concentration-same getopt.o getopt1.o xmalloc.o concentration-same.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ensemble-dg getopt.o getopt1.o xmalloc.o ensemble-dg.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ensemble-dg-same getopt.o getopt1.o xmalloc.o ensemble-dg-same.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o dG2Cp getopt.o getopt1.o xmalloc.o dG2Cp.o -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o dG2dH getopt.o getopt1.o xmalloc.o dG2dH.o -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o dG2dS dG2dS-dG2dH.o getopt.o getopt1.o xmalloc.o -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ct-ext getopt.o getopt1.o ct-ext.o xmalloc.o -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ct-uniq ct-uniq.o xmalloc.o -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ct-prob getopt.o getopt1.o ct-prob.o xmalloc.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid-plot hybrid_plot-hybrid-plot.o getopt.o getopt1.o xmalloc.o -lglut -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ensemble-ext-same getopt.o getopt1.o xmalloc.o ensemble-ext-same.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ct2rnaml ct2rnaml.o xmalloc.o -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ensemble-ext getopt.o getopt1.o xmalloc.o ensemble-ext.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid getopt.o getopt1.o energy.o xmalloc.o hybrid.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o sbs getopt.o getopt1.o energy.o xmalloc.o sbs.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o ct-energy getopt.o getopt1.o energy.o xmalloc.o ct-energy.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid-min hybrid_min-energy.o hybrid_min-hybrid-min.o getopt.o getopt1.o xmalloc.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid-ss-noml getopt.o getopt1.o energy.o xmalloc.o hybrid-ss-noml.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid-ss-simple getopt.o getopt1.o energy.o xmalloc.o hybrid-ss-simple.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid-ss getopt.o getopt1.o energy.o xmalloc.o hybrid-ss.o -lm -lglut -lGL x86_64-pc-linux-gnu-gcc -O2 -march=x86-64 -pipe -pipe -frecord-gcc-switches -fno-diagnostics-color -fmessage-length=0 -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o hybrid-ss-min hybrid_ss_min-energy.o hybrid_ss_min-hybrid-ss-min.o getopt.o getopt1.o xmalloc.o -lm -lglut -lGL make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' Making all in data make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/data' /usr/bin/perl ../machine.pl inf rules/asint1x2.dg asint1x2.DG /usr/bin/perl ../machine.pl 0 rules/asint1x2.dh asint1x2.DH /usr/bin/perl ../machine.pl inf rules/dangle.dg dangle.DG /usr/bin/perl ../machine.pl 0 rules/dangle.dh dangle.DH /usr/bin/perl ../machine.pl inf rules/loop.dg loop.DG /usr/bin/perl ../machine.pl 0 rules/loop.dh loop.DH /usr/bin/perl ../machine.pl inf rules/miscloop.dg miscloop.DG /usr/bin/perl ../machine.pl 0 rules/miscloop.dh miscloop.DH /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches inf rules/sint2.dg sint2.DG /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches 0 rules/sint2.dh sint2.DH /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches inf rules/sint4.dg sint4.DG /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches 0 rules/sint4.dh sint4.DH /usr/bin/perl ../machine.pl inf rules/stack.dg stack.DG /usr/bin/perl ../machine.pl 0 rules/stack.dh stack.DH /usr/bin/perl ../machine.pl inf rules/tstackh.dg tstackh.DG /usr/bin/perl ../machine.pl 0 rules/tstackh.dh tstackh.DH /usr/bin/perl ../machine.pl inf rules/tstacki.dg tstacki.DG /usr/bin/perl ../machine.pl 0 rules/tstacki.dh tstacki.DH /usr/bin/perl ../machine.pl inf rules/tstacki23.dg tstacki23.DG /usr/bin/perl ../machine.pl 0 rules/tstacki23.dh tstacki23.DH /usr/bin/perl ../machine.pl inf rules/tstackm.dg tstackm.DG /usr/bin/perl ../machine.pl 0 rules/tstackm.dh tstackm.DH /usr/bin/perl ../machine.pl inf rules/tstacke.dg tstacke.DG /usr/bin/perl ../machine.pl 0 rules/tstacke.dh tstacke.DH /usr/bin/perl ../machine.pl inf rules/triloop.dg triloop.DG /usr/bin/perl ../machine.pl 0 rules/triloop.dh triloop.DH /usr/bin/perl ../machine.pl inf rules/tloop.dg tloop.DG /usr/bin/perl ../machine.pl 0 rules/tloop.dh tloop.DH /usr/bin/perl ../machine.pl inf rules/hexaloop.dg hexaloop.DG /usr/bin/perl ../machine.pl 0 rules/hexaloop.dh hexaloop.DH /usr/bin/perl ../machine.pl inf rules/asint1x2.dgd asint1x2.DGD /usr/bin/perl ../machine.pl 0 rules/asint1x2.dhd asint1x2.DHD /usr/bin/perl ../machine.pl inf rules/dangle.dgd dangle.DGD /usr/bin/perl ../machine.pl 0 rules/dangle.dhd dangle.DHD /usr/bin/perl ../machine.pl inf rules/loop.dgd loop.DGD /usr/bin/perl ../machine.pl 0 rules/loop.dhd loop.DHD /usr/bin/perl ../machine.pl inf rules/miscloop.dgd miscloop.DGD /usr/bin/perl ../machine.pl 0 rules/miscloop.dhd miscloop.DHD /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches --no-double-gu-close inf rules/sint2.dgd sint2.DGD /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches --no-double-gu-close 0 rules/sint2.dhd sint2.DHD /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches inf rules/sint4.dgd sint4.DGD /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-mismatches 0 rules/sint4.dhd sint4.DHD /usr/bin/perl ../machine.pl inf rules/stack.dgd stack.DGD /usr/bin/perl ../machine.pl 0 rules/stack.dhd stack.DHD /usr/bin/perl ../machine.pl inf rules/tstackh.dgd tstackh.DGD /usr/bin/perl ../machine.pl 0 rules/tstackh.dhd tstackh.DHD /usr/bin/perl ../machine.pl inf rules/tstacki.dgd tstacki.DGD /usr/bin/perl ../machine.pl 0 rules/tstacki.dhd tstacki.DHD /usr/bin/perl ../machine.pl inf rules/tstacki23.dgd tstacki23.DGD /usr/bin/perl ../machine.pl 0 rules/tstacki23.dhd tstacki23.DHD /usr/bin/perl ../machine.pl inf rules/tstackm.dgd tstackm.DGD /usr/bin/perl ../machine.pl 0 rules/tstackm.dhd tstackm.DHD /usr/bin/perl ../machine.pl inf rules/tstacke.dgd tstacke.DGD /usr/bin/perl ../machine.pl 0 rules/tstacke.dhd tstacke.DHD /usr/bin/perl ../machine.pl inf rules/triloop.dgd triloop.DGD /usr/bin/perl ../machine.pl 0 rules/triloop.dhd triloop.DHD /usr/bin/perl ../machine.pl inf rules/tloop.dgd tloop.DGD /usr/bin/perl ../machine.pl 0 rules/tloop.dhd tloop.DHD /usr/bin/perl ../machine.pl inf rules/hexaloop.dgd hexaloop.DGD /usr/bin/perl ../machine.pl 0 rules/hexaloop.dhd hexaloop.DHD /usr/bin/perl ../machine.pl inf rules/asint1x2.dat asint1x2.DAT /usr/bin/perl ../machine.pl inf rules/dangle.dat dangle.DAT /usr/bin/perl ../machine.pl inf rules/loop.dat loop.DAT /usr/bin/perl ../machine.pl inf rules/miscloop.dat miscloop.DAT /usr/bin/perl ../machine.pl --no-wc-mismatches --no-gu-close inf rules/sint2.dat sint2.DAT /usr/bin/perl ../machine.pl --no-wc-mismatches inf rules/sint4.dat sint4.DAT /usr/bin/perl ../machine.pl --no-gu-gu-stacks inf rules/stack.dat stack.DAT /usr/bin/perl ../machine.pl inf rules/tstackh.dat tstackh.DAT /usr/bin/perl ../machine.pl inf rules/tstacki.dat tstacki.DAT /usr/bin/perl ../machine.pl inf rules/tstacki23.dat tstacki23.DAT /usr/bin/perl ../machine.pl inf rules/tstackm.dat tstackm.DAT /usr/bin/perl ../machine.pl inf rules/tstacke.dat tstacke.DAT /usr/bin/perl ../machine.pl inf rules/triloop.dat triloop.DAT /usr/bin/perl ../machine.pl inf rules/tloop.dat tloop.DAT /usr/bin/perl ../machine.pl inf rules/hexaloop.dat hexaloop.DAT /usr/bin/perl ../machine.pl inf rules/extinction.dat extinction.DAT /usr/bin/perl ../machine.pl --null-energies inf rules/asint1x2.dg asint1x2.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/dangle.dg dangle.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/loop.dg loop.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/miscloop.dg miscloop.NUL /usr/bin/perl ../machine.pl --null-energies --no-wc-mismatches --no-gu-mismatches inf rules/sint2.dg sint2.NUL /usr/bin/perl ../machine.pl --null-energies --no-wc-mismatches --no-gu-mismatches inf rules/sint4.dg sint4.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/stack.dg stack.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/tstackh.dg tstackh.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/tstacki.dg tstacki.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/tstackm.dg tstackm.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/tstacke.dg tstacke.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/triloop.dg triloop.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/tloop.dg tloop.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/hexaloop.dg hexaloop.NUL /usr/bin/perl ../machine.pl --null-energies inf rules/asint1x2.dgd asint1x2.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/dangle.dgd dangle.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/loop.dgd loop.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/miscloop.dgd miscloop.NULD /usr/bin/perl ../machine.pl --null-energies --no-wc-mismatches --no-gu-mismatches inf rules/sint2.dgd sint2.NULD /usr/bin/perl ../machine.pl --null-energies --no-wc-mismatches --no-gu-mismatches inf rules/sint4.dgd sint4.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/stack.dgd stack.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/tstackh.dgd tstackh.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/tstacki.dgd tstacki.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/tstacki23.dgd tstacki23.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/tstackm.dgd tstackm.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/tstacke.dgd tstacke.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/triloop.dgd triloop.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/tloop.dgd tloop.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/hexaloop.dgd hexaloop.NULD /usr/bin/perl ../machine.pl --null-energies inf rules/asint1x2.dat asint1x2.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/dangle.dat dangle.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/loop.dat loop.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/miscloop.dat miscloop.NULDAT /usr/bin/perl ../machine.pl --null-energies --no-wc-mismatches --no-gu-close inf rules/sint2.dat sint2.NULDAT /usr/bin/perl ../machine.pl --null-energies --no-wc-mismatches inf rules/sint4.dat sint4.NULDAT /usr/bin/perl ../machine.pl --null-energies --no-gu-gu-stacks inf rules/stack.dat stack.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/tstackh.dat tstackh.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/tstacki.dat tstacki.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/tstacki23.dat tstacki23.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/tstackm.dat tstackm.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/tstacke.dat tstacke.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/triloop.dat triloop.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/tloop.dat tloop.NULDAT /usr/bin/perl ../machine.pl --null-energies inf rules/hexaloop.dat hexaloop.NULDAT make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/data' Making all in scripts make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' Making all in doc make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/doc' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/doc' Making all in tests make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/tests' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/tests' make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' >>> Source compiled. >>> Test phase [not enabled]: sci-biology/unafold-3.8-r1 >>> Install sci-biology/unafold-3.8-r1 into /var/tmp/portage/sci-biology/unafold-3.8-r1/image make -j16 DESTDIR=/var/tmp/portage/sci-biology/unafold-3.8-r1/image install Making install in src make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c hybrid hybrid-min hybrid-ss hybrid-ss-min hybrid-ss-noml hybrid-ss-simple hybrid-plot hybrid-plot-ng sbs concentration concentration-same ensemble-dg ensemble-dg-same ensemble-ext ensemble-ext-same dG2Cp dG2dH dG2dS ct-energy ct-ext ct-uniq ct-prob ct2rnaml '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin' make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/src' Making install in data make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/data' make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/data' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/unafold' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c -m 644 asint1x2.DG asint1x2.DH dangle.DG dangle.DH loop.DG loop.DH miscloop.DG miscloop.DH sint2.DG sint2.DH sint4.DG sint4.DH stack.DG stack.DH tstackh.DG tstackh.DH tstacki.DG tstacki.DH tstacki23.DG tstacki23.DH tstackm.DG tstackm.DH tstacke.DG tstacke.DH triloop.DG triloop.DH tloop.DG tloop.DH hexaloop.DG hexaloop.DH asint1x2.DGD asint1x2.DHD dangle.DGD dangle.DHD loop.DGD loop.DHD miscloop.DGD miscloop.DHD sint2.DGD sint2.DHD '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/unafold' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c -m 644 sint4.DGD sint4.DHD stack.DGD stack.DHD tstackh.DGD tstackh.DHD tstacki.DGD tstacki.DHD tstacki23.DGD tstacki23.DHD tstackm.DGD tstackm.DHD tstacke.DGD tstacke.DHD triloop.DGD triloop.DHD tloop.DGD tloop.DHD hexaloop.DGD hexaloop.DHD asint1x2.DAT dangle.DAT loop.DAT miscloop.DAT sint2.DAT sint4.DAT stack.DAT tstackh.DAT tstacki.DAT tstacki23.DAT tstackm.DAT tstacke.DAT triloop.DAT tloop.DAT hexaloop.DAT extinction.DAT asint1x2.NUL dangle.NUL loop.NUL miscloop.NUL '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/unafold' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c -m 644 sint2.NUL sint4.NUL stack.NUL tstackh.NUL tstacki.NUL tstacki23.DAT tstackm.NUL tstacke.NUL triloop.NUL tloop.NUL hexaloop.NUL asint1x2.NULD dangle.NULD loop.NULD miscloop.NULD sint2.NULD sint4.NULD stack.NULD tstackh.NULD tstacki.NULD tstacki23.NULD tstackm.NULD tstacke.NULD triloop.NULD tloop.NULD hexaloop.NULD asint1x2.NULDAT dangle.NULDAT loop.NULDAT miscloop.NULDAT sint2.NULDAT sint4.NULDAT stack.NULDAT tstackh.NULDAT tstacki.NULDAT tstacki23.NULDAT tstackm.NULDAT tstacke.NULDAT triloop.NULDAT tloop.NULDAT '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/unafold' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c -m 644 hexaloop.NULDAT '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/unafold' make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/data' make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/data' Making install in scripts make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c concentrations.pl concentrations-same.pl hybrid2.pl hybrid-2s.pl hybrid-ss-2s.pl hybrid-select.pl melt.pl plot2ann.pl h-num.pl ss-count.pl ct-energy-det.pl UNAFold.pl ITC-plot.pl vantHoff-plot.pl '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin' make install-exec-hook make[3]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' cd /var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin && ln -s -f hybrid2.pl hybrid2-x.pl cd /var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin && ln -s -f hybrid2.pl hybrid2-min.pl cd /var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin && ln -s -f hybrid2.pl hybrid2-min-x.pl cd /var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin && ln -s -f hybrid2.pl hybrid2-2s.pl cd /var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/bin && ln -s -f hybrid2.pl hybrid2-2s-x.pl make[3]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/scripts' Making install in doc make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/doc' make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/doc' make[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/man/man1' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c -m 644 hybrid.1 hybrid-min.1 hybrid-ss.1 hybrid-ss-min.1 hybrid-ss-noml.1 hybrid-ss-simple.1 hybrid-plot.1 hybrid-plot-ng.1 concentration.1 concentration-same.1 concentrations.pl.1 concentrations-same.pl.1 ensemble-dg.1 ensemble-dg-same.1 ensemble-ext.1 ensemble-ext-same.1 dG2dH.1 dG2dS.1 dG2Cp.1 ct-energy.1 hybrid2.pl.1 hybrid2-x.pl.1 hybrid2-min.pl.1 hybrid2-min-x.pl.1 hybrid2-2s.pl.1 hybrid2-2s-x.pl.1 ct-ext.1 ct-uniq.1 hybrid-2s.pl.1 hybrid-ss-2s.pl.1 ct-prob.1 melt.pl.1 plot2ann.pl.1 h-num.pl.1 ss-count.pl.1 hybrid-select.pl.1 ct2rnaml.1 ct-energy-det.pl.1 UNAFold.pl.1 ITC-plot.pl.1 '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/man/man1' /usr/lib/portage/python3.11/ebuild-helpers/xattr/install -c -m 644 vantHoff-plot.pl.1 '/var/tmp/portage/sci-biology/unafold-3.8-r1/image/usr/share/man/man1' make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/doc' make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/doc' Making install in tests make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/tests' make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/tests' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/tests' make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/tests' make[1]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' make[2]: Entering directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' make[2]: Nothing to be done for 'install-exec-am'. make[2]: Nothing to be done for 'install-data-am'. make[2]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' make[1]: Leaving directory '/var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8' >>> Completed installing sci-biology/unafold-3.8-r1 into /var/tmp/portage/sci-biology/unafold-3.8-r1/image * Final size of build directory: 8120 KiB (7.9 MiB) * Final size of installed tree: 2320 KiB (2.2 MiB) * QA Notice: Found the following implicit function declarations in configure logs: * /var/tmp/portage/sci-biology/unafold-3.8-r1/work/unafold-3.8/config.log:406 - finite * Check that no features were accidentally disabled. * See https://wiki.gentoo.org/wiki/Modern_C_porting. strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version /usr/bin/hybrid /usr/bin/hybrid-min /usr/bin/hybrid-ss /usr/bin/hybrid-ss-noml /usr/bin/hybrid-ss-min /usr/bin/hybrid-ss-simple /usr/bin/hybrid-plot /usr/bin/hybrid-plot-ng /usr/bin/concentration /usr/bin/sbs /usr/bin/ensemble-dg /usr/bin/concentration-same /usr/bin/ensemble-dg-same /usr/bin/ensemble-ext /usr/bin/ensemble-ext-same /usr/bin/dG2Cp /usr/bin/dG2dH /usr/bin/dG2dS /usr/bin/ct-energy /usr/bin/ct-ext /usr/bin/ct-uniq /usr/bin/ct-prob /usr/bin/ct2rnaml >>> Done.