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Bug 318605 - sci-chemistry/coot fails tests
Summary: sci-chemistry/coot fails tests
Status: RESOLVED NEEDINFO
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Justin Lecher (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2010-05-05 11:26 UTC by Diego Elio Pettenò (RETIRED)
Modified: 2010-06-30 18:54 UTC (History)
1 user (show)

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


Attachments
Build log (coot-0.6:20100505-073709.log,929.23 KB, text/plain)
2010-05-05 11:27 UTC, Diego Elio Pettenò (RETIRED)
Details

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Description Diego Elio Pettenò (RETIRED) gentoo-dev 2010-05-05 11:26:45 UTC
Portage 2.1.8.3 (default/linux/x86/10.0, gcc-4.5.0-asneeded, glibc-2.11.1-r0, 2.6.33.3 i686)
=================================================================
System uname: Linux-2.6.33.3-i686-Quad-Core_AMD_Opteron-tm-_Processor_2350-with-gentoo-2.0.1
Timestamp of tree: Tue, 04 May 2010 11:30:01 +0000
app-shells/bash:     4.1_p5
dev-java/java-config: 2.1.11
dev-lang/python:     2.6.5-r2, 3.1.2-r3
dev-python/pycrypto: 2.1.0
dev-util/cmake:      2.8.1-r1
sys-apps/baselayout: 2.0.1
sys-apps/openrc:     0.6.1-r1
sys-apps/sandbox:    2.2
sys-devel/autoconf:  2.13, 2.65
sys-devel/automake:  1.4_p6-r1, 1.5-r1, 1.6.3-r1, 1.7.9-r2, 1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.20.1
sys-devel/gcc:       4.5.0
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.2.6b
virtual/os-headers:  2.6.33
ACCEPT_KEYWORDS="x86 ~x86"
ACCEPT_LICENSE="*"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/X11/xkb /var/lib/hsqldb /var/qmail/alias /var/qmail/control /var/yp/Makefile"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /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"
DISTDIR="/var/cache/distfiles"
FEATURES="assume-digests distlocks fixpackages news parallel-fetch protect-owned sandbox sfperms split-log strict test test-fail-continue unmerge-orphans userfetch userpriv usersandbox"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1"
MAKEOPTS="-j14"
PKGDIR="/var/spool/portage/packages"
PORTAGE_COMPRESS=""
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/var/cache/portage/tree-tinderbox"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="acl berkdb bzip2 cli cracklib crypt cups cxx dri fortran gdbm gpm iconv ipv6 java5 java6 modules mudflap ncurses nls nostatic nptl nptlonly openmp pam pcre perl pppd python qt3support readline reflection ruby session spl ssl sysfs tcpd unicode vhosts x86 xorg zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1 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 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 auth_digest" ELIBC="glibc" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" RUBY_TARGETS="ruby18 jruby ruby19" 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_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PORTDIR_OVERLAY
Comment 1 Diego Elio Pettenò (RETIRED) gentoo-dev 2010-05-05 11:27:27 UTC
Created attachment 230449 [details]
Build log
Comment 2 Justin Lecher (RETIRED) gentoo-dev 2010-05-05 15:46:11 UTC
Do you have sci-libs/monomer-db installed and do you have CLIBD_MON in env?
Comment 3 Diego Elio Pettenò (RETIRED) gentoo-dev 2010-05-05 15:50:43 UTC
I have monomer-db… now… but if it's not in the deps I have no idea if I had it when this failed; as for the env, it _should_ be sourced before every merge…
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2010-05-05 15:57:23 UTC
(In reply to comment #3)
> I have monomer-db… now… but if it's not in the deps I have no idea if I had
> it when this failed; as for the env, it _should_ be sourced before every
> merge…
> 

actually the env comes from ccp4-libs, the files come from monomer-db and the prog which fails in the test from sci-chemistry/refmac. I definitely need to clean/fix that up.
Comment 5 Justin Lecher (RETIRED) gentoo-dev 2010-05-17 10:53:33 UTC
I added the missing var into the ebuild. Could you please try and test again?
Comment 6 Justin Lecher (RETIRED) gentoo-dev 2010-06-30 18:54:23 UTC
No response for six weeks, so setting to needinfo.