hmmer fails to build in the patch phase. Reproducible: Always Steps to Reproduce: 1.emerge hmmer 2. 3. Portage 2.1.10.65 (default/linux/amd64/10.0/desktop/kde, gcc-4.5.3, glibc-2.14.1-r3, 3.3.8-gentoo x86_64) ================================================================= System uname: Linux-3.3.8-gentoo-x86_64-Intel-R-_Core-TM-_i7_CPU_930_@_2.80GHz-with-gentoo-2.1 Timestamp of tree: Thu, 28 Jun 2012 13:15:01 +0000 app-shells/bash: 4.2_p20 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.5.4-r4, 2.7.3-r2, 3.2.3 dev-util/cmake: 2.8.7-r5 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1-r1 sys-apps/openrc: 0.9.8.4 sys-apps/sandbox: 2.5 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.11.1 sys-devel/binutils: 2.21.1-r1 sys-devel/gcc: 4.5.3-r2 sys-devel/gcc-config: 1.6 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82-r1 sys-kernel/linux-headers: 3.4 (virtual/os-headers) sys-libs/glibc: 2.14.1-r3 Repositories: gentoo science x-portage ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=core2 -mtune=generic -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /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=core2 -mtune=generic -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="pt_BR.UTF-8" LDFLAGS="-Wl,--as-needed" LINGUAS="pt_BR en" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/science /usr/local/portage" SYNC="rsync://rsync.br.gentoo.org/gentoo-portage" USE="X a52 aac acl acpi additions alsa amd64 bash-completion berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr dvdread emacs embedded emboss encode exif extensions extras fam ffmpeg fftw firefox flac fortran ftp gcj gdbm ggc gif gimp gpm gtk gzip hwdb iconv icu imagemagick ipv6 java jpeg kde kipi kpathsea lapack latex lcms ldap libnotify mad midi minizip mmx mng modules motif mp3 mp4 mpeg mudflap multilib ncurses nls nptl nsplugin nss nvidia ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds pppd python qt3support qt4 readline reiserfs samba sdl semantic-desktop session spell sse sse2 ssl startup-notification svg synlink tar tcpd tetex threads tiff tk truetype type1 udev udisks unicode upower usb vorbis wxwidgets x264 xcb xcomposite xft xinerama xml xorg xscreensaver xulrunner xv xvid zip zlib" 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" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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 ubx" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="pt_BR en" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="nvidia" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ####################### build.log####################################### [32;01m * [39;49;00mPackage: sci-biology/hmmer-3.0 [32;01m * [39;49;00mRepository: gentoo [32;01m * [39;49;00mMaintainer: sci-biology@gentoo.org [32;01m * [39;49;00mUSE: amd64 consolekit elibc_glibc kernel_linux multilib policykit sse threads userland_GNU [32;01m * [39;49;00mFEATURES: sandbox >>> Unpacking source... >>> Unpacking hmmer-3.0.tar.gz to /var/tmp/portage/sci-biology/hmmer-3.0/work >>> Source unpacked in /var/tmp/portage/sci-biology/hmmer-3.0/work >>> Preparing source in /var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0 ... [32;01m*[0m Applying hmmer-3.0-fix_tests.patch ... [A[138C [34;01m[ [32;01mok[34;01m ][0m [32;01m*[0m Applying hmmer-3.0-perl-5.16.patch ... [31;01m*[0m Failed Patch: hmmer-3.0-perl-5.16.patch ! [31;01m*[0m ( /usr/portage/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch ) [31;01m*[0m [31;01m*[0m Include in your bugreport the contents of: [31;01m*[0m [31;01m*[0m /var/tmp/portage/sci-biology/hmmer-3.0/temp/hmmer-3.0-perl-5.16.patch.out [31;01m*[0m ERROR: sci-biology/hmmer-3.0 failed (prepare phase): [31;01m*[0m Failed Patch: hmmer-3.0-perl-5.16.patch! [31;01m*[0m [31;01m*[0m Call stack: [31;01m*[0m ebuild.sh, line 85: Called src_prepare [31;01m*[0m environment, line 2092: Called epatch '/usr/portage/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch' '/usr/portage/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch' [31;01m*[0m environment, line 837: Called epatch '/usr/portage/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch' [31;01m*[0m environment, line 996: Called die [31;01m*[0m The specific snippet of code: [31;01m*[0m die "Failed Patch: ${patchname}!"; [31;01m*[0m [31;01m*[0m If you need support, post the output of `emerge --info '=sci-biology/hmmer-3.0'`, [31;01m*[0m the complete build log and the output of `emerge -pqv '=sci-biology/hmmer-3.0'`. [31;01m*[0m The complete build log is located at '/var/tmp/portage/sci-biology/hmmer-3.0/temp/build.log'. [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-biology/hmmer-3.0/temp/environment'. [31;01m*[0m Working directory: '/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0' [31;01m*[0m S: '/var/tmp/portage/sci-biology/hmmer-3.0/work/hmmer-3.0'
Appending /newaches/gentoo/cvs/gentoo-x86 to PORTDIR_OVERLAY... >>> Downloading 'ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz' --2012-06-28 17:41:25-- ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz => `/world/distfiles/hmmer-3.0.tar.gz' Resolving selab.janelia.org (selab.janelia.org)... 128.177.18.22 Connecting to selab.janelia.org (selab.janelia.org)|128.177.18.22|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/software/hmmer3/3.0 ... done. ==> SIZE hmmer-3.0.tar.gz ... 3952015 ==> PASV ... done. ==> RETR hmmer-3.0.tar.gz ... done. Length: 3952015 (3.8M) (unauthoritative) 100%[==========================================================================================>] 3,952,015 1.52M/s in 2.5s 2012-06-28 17:41:28 (1.52 MB/s) - `/world/distfiles/hmmer-3.0.tar.gz' saved [3952015] * hmmer-3.0.tar.gz RMD160 SHA1 SHA256 size ;-) ... [ ok ] * checking ebuild checksums ;-) ... [ ok ] * checking auxfile checksums ;-) ... [ ok ] * checking miscfile checksums ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking hmmer-3.0.tar.gz to /home/jer/portage/sci-biology/hmmer-3.0/work >>> Source unpacked in /home/jer/portage/sci-biology/hmmer-3.0/work >>> Preparing source in /home/jer/portage/sci-biology/hmmer-3.0/work/hmmer-3.0 ... * Applying hmmer-3.0-fix_tests.patch ... [ ok ] * Applying hmmer-3.0-perl-5.16.patch ... * Failed Patch: hmmer-3.0-perl-5.16.patch ! * ( /newaches/gentoo/cvs/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch ) * * Include in your bugreport the contents of: * * /home/jer/portage/sci-biology/hmmer-3.0/temp/hmmer-3.0-perl-5.16.patch.out * ERROR: sci-biology/hmmer-3.0 failed (prepare phase): * Failed Patch: hmmer-3.0-perl-5.16.patch! * * Call stack: * ebuild.sh, line 85: Called src_prepare * environment, line 2026: Called epatch '/newaches/gentoo/cvs/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-fix_tests.patch' '/newaches/gentoo/cvs/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch' * environment, line 771: Called epatch '/newaches/gentoo/cvs/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16.patch' * environment, line 930: Called die * The specific snippet of code: * die "Failed Patch: ${patchname}!"; * * If you need support, post the output of `emerge --info '=sci-biology/hmmer-3.0'`, * the complete build log and the output of `emerge -pqv '=sci-biology/hmmer-3.0'`. * The complete build log is located at '/keeps/gentoo/emergelogs/wieneke/sci-biology:hmmer-3.0:20120628-154124.log'. * For convenience, a symlink to the build log is located at '/home/jer/portage/sci-biology/hmmer-3.0/temp/build.log'. * The ebuild environment file is located at '/home/jer/portage/sci-biology/hmmer-3.0/temp/environment'. * Working directory: '/home/jer/portage/sci-biology/hmmer-3.0/work/hmmer-3.0' * S: '/home/jer/portage/sci-biology/hmmer-3.0/work/hmmer-3.0'
the VCS tags got screwed, thanks for reporting. + 28 Jun 2012; Justin Lecher <jlec@gentoo.org> files/hmmer-3.0-perl-5.16.patch: + Fix patch, screwed VCS tags, #423983 +
