Bug 514432

Summary:	sci-biology/beast-mcmc-1.7.5 fails to build: Buildfile: build_BEAST_MCMC.xml does not exist!
Product:	Gentoo Linux	Reporter:	Patrick Lauer <patrick>
Component:	New packages	Assignee:	Gentoo Science Biology related packages <sci-biology>
Status:	RESOLVED FIXED
Severity:	normal	CC:	hasufell, java, toralf, treecleaner
Priority:	Normal
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	648050

Description Patrick Lauer gentoo-dev

2014-06-22 10:27:06 UTC

* Package:    sci-biology/beast-mcmc-1.7.5
 * Repository: gentoo
 * Maintainer: sci-biology
 * USE:        amd64 elibc_glibc kernel_linux userland_GNU
 * FEATURES:   preserve-libs sandbox userpriv usersandbox
 * Using: icedtea-bin-7
>>> Unpacking source...
>>> Unpacking beast-mcmc-1.7.5.tar.xz to /var/tmp/portage/sci-biology/beast-mcmc-1.7.5/work
>>> Source unpacked in /var/tmp/portage/sci-biology/beast-mcmc-1.7.5/work
>>> Preparing source in /var/tmp/portage/sci-biology/beast-mcmc-1.7.5/work/beast_release_1_7_5 ...
removed ‘colt.jar’
removed ‘junit-4.4.jar’
removed ‘itext-1.4.5.jar’
removed ‘jdom.jar’
removed ‘mtj.jar’
removed ‘commons-math-2.2.jar’
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/beast-mcmc-1.7.5/work/beast_release_1_7_5 ...
cElementTree rewriter
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/beast-mcmc-1.7.5/work/beast_release_1_7_5 ...
 * Using following ANT_TASKS: ant-junit4
Buildfile: build_BEAST_MCMC.xml does not exist!
Build failed
 * ERROR: sci-biology/beast-mcmc-1.7.5::gentoo failed (compile phase):
 *   eant failed

Portage 2.2.10 (default/linux/amd64/13.0/desktop/kde, gcc-4.8.3, glibc-2.19-r1, 3.15.0-gentoo x86_64)
=================================================================
System uname: Linux-3.15.0-gentoo-x86_64-AMD_Phenom-tm-_II_X4_965_Processor-with-gentoo-2.2
KiB Mem:     7919000 total,    295532 free
KiB Swap:   25165812 total,  24807036 free
Timestamp of tree: Unknown
ld GNU ld (Gentoo 2.24 p1.4) 2.24
app-shells/bash:          4.2_p47
dev-java/java-config:     2.2.0
dev-lang/python:          2.7.6-r1, 3.2.5-r4, 3.3.5, 3.4.0
dev-util/cmake:           2.8.12.2-r1
dev-util/pkgconfig:       0.28-r1
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.12.4
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.69
sys-devel/automake:       1.11.6, 1.14.1
sys-devel/binutils:       2.24-r3
sys-devel/gcc:            4.8.3
sys-devel/gcc-config:     1.8
sys-devel/libtool:        2.4.2-r1
sys-devel/make:           4.0-r1
sys-kernel/linux-headers: 3.15 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /var/lib/hsqldb"
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"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="-j2"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs buildpkg config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync parallel-fetch preserve-libs protect-owned sandbox sfperms split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://mirrors.163.com/gentoo/ ftp://ftp.kaist.ac.kr/gentoo/ http://ftp.kaist.ac.kr/pub/gentoo/ http://gentoo.mirrors.hoobly.com/ http://gentoo.mirrors.easynews.com/linux/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4"
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"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY=""
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus declarative dri dts dvd dvdr emboss encode exif fam ffmpeg firefox flac fortran gbm gd gdbm gif glade gpm gtk iconv icu ipv6 java jpeg kde kipi lapack lcms ldap libkms libnotify mad mmx mng modules mp3 mp4 mpeg multilib ncurses nls nptl objc ogg opengl openmp pam pango pcre pdf phonon plasma png policykit ppds python qt3support qt4 readline sdl semantic-desktop session spell sqlite sse sse2 ssl startup-notification svg tcpd threads tiff truetype udev udisks unicode upower usb vorbis wxwidgets x264 xa xcb xcomposite xinerama xml xscreensaver xv xvfb 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" 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" 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" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3 php5-4" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2 pypy python3_3 python3_4" RUBY_TARGETS="ruby19 ruby20" 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:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON

Comment 1 Toralf Förster gentoo-dev

2016-07-04 13:18:57 UTC

*** Bug 565754 has been marked as a duplicate of this bug. ***

Comment 2 Toralf Förster gentoo-dev

2016-11-26 08:46:59 UTC

still true

Comment 3 Pacho Ramos gentoo-dev

2018-02-26 09:48:01 UTC

still doesn't build

Comment 4 Larry the Git Cow gentoo-dev

2018-04-15 10:34:17 UTC

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=57b9f13f0c8719e04a011b071e0096f660ed706e

commit 57b9f13f0c8719e04a011b071e0096f660ed706e
Author:     Mikle Kolyada <zlogene@gentoo.org>
AuthorDate: 2018-04-15 10:33:19 +0000
Commit:     Mikle Kolyada <zlogene@gentoo.org>
CommitDate: 2018-04-15 10:33:19 +0000

    sci-biology/beast-mcmc: remove last rited package
    
    Closes: https://bugs.gentoo.org/514432

 sci-biology/beast-mcmc/Manifest                   |  1 -
 sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild | 85 -----------------------
 sci-biology/beast-mcmc/beast-mcmc-9999.ebuild     | 80 ---------------------
 sci-biology/beast-mcmc/metadata.xml               | 11 ---
 4 files changed, 177 deletions(-)