Bug 421777 – sci-biology/ncbi-tools++ fails to build with net-libs/gnutls-3

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Diego Elio Pettenò (RETIRED) 2012-06-18 13:47:35 UTC]

Portage 2.2.0_alpha110 (default/linux/amd64/10.0, gcc-4.7.1, glibc-2.15-r2, 3.4.2-hardened x86_64)
=================================================================
System uname: Linux-3.4.2-hardened-x86_64-AMD_Opteron-TM-_Processor_6272-with-gentoo-2.1
Timestamp of tree: Sat, 16 Jun 2012 07:30:01 +0000
app-shells/bash:          4.2_p29
dev-java/java-config:     2.1.11-r3
dev-lang/python:          2.7.3-r2, 3.2.3-r1
dev-util/cmake:           2.8.8-r3
dev-util/pkgconfig:       0.26
sys-apps/baselayout:      2.1-r1
sys-apps/openrc:          0.10.3
sys-apps/sandbox:         2.5
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.11.5, 1.12.1
sys-devel/binutils:       2.22-r1
sys-devel/gcc:            4.5.3-r2, 4.7.1
sys-devel/gcc-config:     1.7.3
sys-devel/libtool:        2.4.2
sys-devel/make:           3.82-r3
sys-kernel/linux-headers: 3.4 (virtual/os-headers)
sys-libs/glibc:           2.15-r2
Repositories: gentoo
Installed sets: 
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -ggdb -march=native -ftracer"
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/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo"
CXXFLAGS="-O2 -pipe -ggdb -march=native -ftracer"
DISTDIR="/var/cache/portage/distfiles"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles news parallel-fetch parse-eapi-ebuild-head protect-owned sandbox sfperms strict test test-fail-continue unknown-features-warn unmerge-orphans userfetch userpriv usersandbox"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j24"
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="/tmp"
PORTDIR="/var/cache/portage/tree"
PORTDIR_OVERLAY=""
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowex acl amd64 berkdb bzip2 cli cracklib crypt cups cxx dri ffmpeg fortran gdbm gpm iconv ipv6 mmx modules mudflap multilib ncurses nls nptl openmp pam pcre pppd qt3support readline session sse sse2 sse3 sse4 ssl ssse3 tcpd unicode vhosts xorg 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" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" PHP_TARGETS="php5-3" PYTHON_TARGETS="python3_2 python2_7" RUBY_TARGETS="ruby18 jruby ruby19 ree18" USERLAND="GNU" 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, LINGUAS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2012-11-19 10:39:53 UTC]

*** Bug 443902 has been marked as a duplicate of this bug. ***

[Comment 2 Manuel Rüger (RETIRED) 2014-04-27 22:49:41 UTC]

I suggest to pmask with gnutls-2.x 

sci-biology/ncbi-tools++
media-video/subcheck
sci-libs/rosetta-fragments
sci-biology/psipred
sci-chemistry/ccpn
sci-chemistry/ccpn-data
sci-chemistry/aria
sci-chemistry/mars

[Comment 3 Justin Lecher (RETIRED) 2014-05-14 12:09:48 UTC]

(In reply to Manuel Rüger from comment #2)
> I suggest to pmask with gnutls-2.x 
> 
> sci-biology/ncbi-tools++

You can go ahead here. I added the necessary subpackage to fullfill the dep.

> sci-libs/rosetta-fragments
> sci-biology/psipred
> sci-chemistry/ccpn
> sci-chemistry/ccpn-data
> sci-chemistry/aria
> sci-chemistry/mars

All sci revdeps are fixed

[Comment 4 Manuel Rüger (RETIRED) 2014-05-23 17:35:17 UTC]

# Manuel Rüger <[e-mail]> (23 May 2014)
# Fails to build with gnutls-3.
# See bug #421777
# Masked for removal in 30 days
sci-biology/ncbi-tools++

[Comment 5 Manuel Rüger (RETIRED) 2014-06-30 08:06:10 UTC]

Removed from the tree. Recent versions available in science-overlay.