Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 499046 - sci-biology/cufflinks-1.3.0 failed to build with automake 1.14
Summary: sci-biology/cufflinks-1.3.0 failed to build with automake 1.14
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords: PATCH
Depends on:
Blocks:
 
Reported: 2014-01-23 14:23 UTC by Sergey Popov
Modified: 2014-02-05 08:17 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log (build.log,2.29 KB, text/plain)
2014-01-23 14:23 UTC, Sergey Popov
Details
automake.out (automake.out,8.67 KB, text/plain)
2014-01-23 14:24 UTC, Sergey Popov
Details
cufflinks-automake-1.14-fix.ebuild.patch (cufflinks-automake-1.14-fix.ebuild.patch,803 bytes, patch)
2014-01-23 14:26 UTC, Sergey Popov
Details | Diff

Note You need to log in before you can comment on or make changes to this bug.
Description Sergey Popov gentoo-dev 2014-01-23 14:23:10 UTC
Created attachment 368556 [details]
build.log

As per summary

emerge --info:
Portage 2.2.7 (default/linux/amd64/13.0/developer, gcc-4.7.3, glibc-2.17, 3.10.17-gentoo-BADO x86_64)
=================================================================
System uname: Linux-3.10.17-gentoo-BADO-x86_64-Intel-R-_Core-TM-_i7_CPU_950_@_3.07GHz-with-gentoo-2.2
KiB Mem:    12282408 total,   4317192 free
KiB Swap:          0 total,         0 free
Timestamp of tree: Wed, 22 Jan 2014 23:45:01 +0000
ld GNU ld (GNU Binutils) 2.23.2
ccache version 3.1.9 [disabled]
app-shells/bash:          4.2_p45
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.6, 3.2.5-r3
dev-util/ccache:          3.1.9-r3
dev-util/cmake:           2.8.12.1-r2
dev-util/pkgconfig:       0.28
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.11.6, 1.12.6, 1.13.4, 1.14
sys-devel/binutils:       2.23.2
sys-devel/gcc:            4.7.3-r1
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.12 (virtual/os-headers)
sys-libs/glibc:           2.17
Repositories: gentoo pinkbyte
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -fdiagnostics-show-option -frecord-gcc-switches"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt"
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="-O2 -pipe -fdiagnostics-show-option -frecord-gcc-switches"
DISTDIR="/bound/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going --autounmask-write=y --jobs=5"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms sign splitdebug strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirror.yandex.ru/gentoo-distfiles"
LANG="ru_RU.UTF-8"
LDFLAGS="-Wl,--hash-style=gnu -Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j9"
PKGDIR="/bound/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"
PORTDIR="/bound/portage"
PORTDIR_OVERLAY="/bound/overlays/pinkbyte"
USE="a52 aac acl amd64 bzip2 cairo cdda cdr cli cracklib cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gif gpm iconv ipv6 jpeg lcms mad mmx mng modules mp3 mp4 mpeg multilib ncurses nls nptl ogg openmp pam pango pcre pdf png ppds qt3support qt4 readline sdl session snmp spell sse sse2 ssl startup-notification svg tcpd threads truetype udev udisks unicode upower usb vorbis wxwidgets x264 xcb xml xv xvid 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" 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 ublox 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="ru ru_RU" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7" RUBY_TARGETS="ruby19 ruby18" 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"
USE_PYTHON="2.7"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC
Comment 1 Sergey Popov gentoo-dev 2014-01-23 14:24:02 UTC
Created attachment 368558 [details]
automake.out

automake.out, attached as requested by portage
Comment 2 Sergey Popov gentoo-dev 2014-01-23 14:26:14 UTC
Created attachment 368560 [details, diff]
cufflinks-automake-1.14-fix.ebuild.patch

Proposed fix for ebuild
Comment 3 Sergey Popov gentoo-dev 2014-02-05 08:17:09 UTC
+  05 Feb 2014; Sergey Popov <pinkbyte@gentoo.org> -cufflinks-1.3.0.ebuild,
+  +cufflinks-1.3.0-r1.ebuild, files/cufflinks-1.3.0-autotools.patch:
+  Revision bump: EAPI 5, add subslot to Boost dependency, fix compatibility
+  with Automake 1.14, wrt bug #499046. Drop old revision

I have incorporated fix into autotools patch.