ebwt_search_backtrack.h:772:11: warning: variable ‘foundTarget’ set but not used [-Wunused-but-set-variable] bool foundTarget = false; ^ In file included from ebwt_build.cpp:11:0: ebwt.h: At global scope: ebwt.h:3948:19: error: redeclaration of ‘void Ebwt<TStr>::joinToDisk(std::vector<FileBuf*>&, std::vector<RefRecord>&, std::vector<unsigned int>&, uint32_t, const RefReadInParams&, TStr&, std::ostream&, std::ostream&, uint32_t)’ may not have default arguments [-fpermissive] uint32_t seed = 0) ^ In file included from SeqAn-1.1/seqan/sequence.h:57:0, from SeqAn-1.1/seqan/index.h:27, from ebwt_build.cpp:5: $ cat ./info.txt ----------------------------------------------------------------- This is an stable amd64 chroot image (named amd64-kde-stable_20151021-204100) at a hardened host acting as a tinderbox. ----------------------------------------------------------------- Portage 2.2.20.1 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/kde, gcc-4.9.3, glibc-2.21-r1, 4.1.7-hardened-r1 x86_64) ================================================================= System uname: Linux-4.1.7-hardened-r1-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 16164644 total, 3054152 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Wed, 28 Oct 2015 00:21:55 +0000 sh bash 4.3_p39 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.3_p39::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.20.2::gentoo dev-lang/python: 2.7.10::gentoo, 3.4.3::gentoo dev-util/cmake: 3.3.1-r1::gentoo dev-util/pkgconfig: 0.28-r2::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.17::gentoo sys-apps/sandbox: 2.6-r1::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69::gentoo sys-devel/automake: 1.9.6-r4::gentoo, 1.10.3-r1::gentoo, 1.11.6-r1::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.7.3::gentoo sys-devel/libtool: 2.4.6::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 3.18::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r1::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: 1 local location: /usr/local/portage masters: gentoo priority: 2 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /etc/grs/systems.conf /etc/stunnel/stunnel.conf /usr/lib64/fax /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb /var/spool/fax/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/var/tmp/distfiles" EMERGE_DEFAULT_OPTS="--deep --color=n --nospinner --tree --quiet-build --accept-properties=-interactive --accept-restrict=-fetch" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac acl acpi alsa amd64 berkdb bindist bluetooth branding bzip2 cairo cdda cdr clang cli consolekit cracklib crypt cups cxx dbus declarative dnssec dri dts dvb dvd dvdr emboss encode exif fam ffmpeg firefox flac fortran fpm gdbm gif glamor gpm gtk iconv inifile ipv6 jadetex jpeg kde kerberos kipi kvm lcms libnotify libvirtd logrotate mad mbox mmx mmxext mng modules mp3 mp4 mpeg multilib multimedia multitarget mysql mysqli ncurses nls nptl nss odbc ogg opengl openmp pam pango pax_kernel pcre pdf phonon pkcs11 png policykit ppds pulseaudio pyqt4 qml qt3support qt4 qt5 readline scripts sdl seccomp semantic-desktop session smartcard spell sqlite sse sse2 sse4 ssl startup-notification svg system-icu system-libvpx system-sqlite tcl tcpd thinkpad tiff tk tls truetype udev udisks uml unicode upower usb v4l vaapi vorbis wxwidgets x264 xa xattr xcb xcomposite xinerama xinetd xml xmp xscreensaver xslt xv xvid xz zenmap zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
Created attachment 415634 [details] emerge-history.txt
Created attachment 415636 [details] environment
Created attachment 415638 [details] sci-biology:bowtie-0.12.8:20151028-020235.log
commit 369678cffc9f7ecae414f3800f01a2c2251e8669 Author: Justin Lecher <jlec@gentoo.org> Date: Sat Dec 26 19:02:47 2015 +0100 sci-biology/bowtie: Drop old obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=564320 Package-Manager: portage-2.2.26 Signed-off-by: Justin Lecher <jlec@gentoo.org> https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=369678cffc9f7ecae414f3800f01a2c2251e8669
