Trying to emerge netbeans calls for jdom-jaxen, jdom and jaxen, this causes a circular dependency that does not allow me to emerge netbeans. Tryin to use emerge Reproducible: Always Steps to Reproduce: 1. emerge netbeans 2. emerge -O1 jaxen 3. Actual Results: emerge netbeans --- Invalid atom in /usr/portage/profiles/package.mask: app-admin/eselect-1.3.7 * IMPORTANT: 2 config files in '/etc/portage' need updating. These are the packages that would be merged, in order: Calculating dependencies * See the CONFIGURATION FILES section of the emerge * man page to learn how to update config files. .... done! [nomerge ] dev-util/netbeans-7.3:7.3 USE="-doc" LINGUAS="-af -ar -bg -ca -cs -de -el -es -fr -gl -hi_IN -id -it -ja -ko -lt -nl -pl -pt_BR -pt_PT -ro -ru -si -sq -sr -sv -ta_IN -tl -tr -vi -zh_CN -zh_TW" NETBEANS_MODULES="apisupport java javafx profiler websvccommon -cnd -dlight -enterprise -ergonomics -groovy -javacard -mobility -php -webcommon" [nomerge ] dev-java/netbeans-ide-7.3:7.3 [ebuild N ] dev-java/rhino-1.7.2-r2:1.6 USE="-doc -examples -source" 2,946 kB [ebuild N ] dev-java/xml-xmlbeans-1.0.4_pre20041217-r1:1 USE="-doc -source" 2,380 kB [ebuild N ] dev-java/freemarker-2.3.13-r1:2.3 USE="-doc -source" 2,087 kB [nomerge ] dev-util/netbeans-7.3:7.3 USE="-doc" LINGUAS="-af -ar -bg -ca -cs -de -el -es -fr -gl -hi_IN -id -it -ja -ko -lt -nl -pl -pt_BR -pt_PT -ro -ru -si -sq -sr -sv -ta_IN -tl -tr -vi -zh_CN -zh_TW" NETBEANS_MODULES="apisupport java javafx profiler websvccommon -cnd -dlight -enterprise -ergonomics -groovy -javacard -mobility -php -webcommon" [nomerge ] dev-java/netbeans-java-7.3:7.3 [nomerge ] dev-java/jdom-1.0-r4:1.0 USE="-doc -examples -source" [ebuild N ] dev-java/jdom-jaxen-1.0-r1:1.0 3,489 kB [ebuild N ] dev-java/jaxen-1.1.4-r1:1.1 USE="-doc -examples -source {-test}" 263 kB [ebuild N ] dev-util/netbeans-7.3:7.3 USE="-doc" LINGUAS="-af -ar -bg -ca -cs -de -el -es -fr -gl -hi_IN -id -it -ja -ko -lt -nl -pl -pt_BR -pt_PT -ro -ru -si -sq -sr -sv -ta_IN -tl -tr -vi -zh_CN -zh_TW" NETBEANS_MODULES="apisupport java javafx profiler websvccommon -cnd -dlight -enterprise -ergonomics -groovy -javacard -mobility -php -webcommon" 0 kB [ebuild N ] dev-java/netbeans-javafx-7.3:7.3 179,123 kB [ebuild N ] dev-java/netbeans-apisupport-7.3:7.3 0 kB [ebuild N ] dev-java/netbeans-profiler-7.3:7.3 0 kB [ebuild N ] dev-java/netbeans-nb-7.3:7.3 USE="-keychain" 20 kB [ebuild N ] dev-java/netbeans-java-7.3:7.3 36,082 kB [ebuild N ] dev-java/netbeans-websvccommon-7.3:7.3 0 kB [ebuild N ] dev-java/netbeans-ide-7.3:7.3 44,285 kB Total: 13 packages (13 new), Size of downloads: 270,670 kB * Error: circular dependencies: (dev-java/jaxen-1.1.4-r1::gentoo, ebuild scheduled for merge) depends on (dev-java/jdom-jaxen-1.0-r1::gentoo, ebuild scheduled for merge) (buildtime) (dev-java/jaxen-1.1.4-r1::gentoo, ebuild scheduled for merge) (buildtime) * Note that circular dependencies can often be avoided by temporarily * disabling USE flags that trigger optional dependencies. * IMPORTANT: 6 news items need reading for repository 'gentoo'. * Use eselect news to read news items. emerge -O1 jaxen --- Invalid atom in /usr/portage/profiles/package.mask: app-admin/eselect-1.3.7 * IMPORTANT: 2 config files in '/etc/portage' need updating. >>> Verifying ebuild manifests * IMPORTANT: 6 news items need reading for repository 'gentoo'. * Use eselect news to read news items. * See the CONFIGURATION FILES section of the emerge * man page to learn how to update config files. >>> Emerging (1 of 1) dev-java/jaxen-1.1.4-r1 * jaxen-1.1.4-src.tar.gz SHA256 SHA512 WHIRLPOOL size ;-) ... [ ok ] * Using: icedtea-bin-7 >>> Unpacking source... >>> Unpacking jaxen-1.1.4-src.tar.gz to /var/tmp/portage/dev-java/jaxen-1.1.4-r1/work >>> Source unpacked in /var/tmp/portage/dev-java/jaxen-1.1.4-r1/work >>> Preparing source in /var/tmp/portage/dev-java/jaxen-1.1.4-r1/work/jaxen-1.1.4 ... '/usr/portage/dev-java/jaxen/files/jaxen-1.1.4_maven1-build.xml' -> 'build.xml' >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-java/jaxen-1.1.4-r1/work/jaxen-1.1.4 ... Rewriting source attributes /var/tmp/portage/dev-java/jaxen-1.1.4-r1/temp/environment: line 1914: xml-rewrite-2.py: command not found * ERROR: dev-java/jaxen-1.1.4-r1::gentoo failed (configure phase): * xml-rewrite2 failed: ./build.xml * * Call stack: * ebuild.sh, line 93: Called src_configure * environment, line 4121: Called java-ant-2_src_configure * environment, line 1850: Called java-ant_bsfix * environment, line 1872: Called java-ant_bsfix_files './build.xml' * environment, line 1914: Called _bsfix_die 'xml-rewrite2 failed: ./build.xml' * environment, line 255: Called die * The specific snippet of code: * die ${1}; * * If you need support, post the output of `emerge --info '=dev-java/jaxen-1.1.4-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-java/jaxen-1.1.4-r1::gentoo'`. !!! When you file a bug report, please include the following information: GENTOO_VM=icedtea-bin-7 CLASSPATH="" JAVA_HOME="/opt/icedtea-bin-7.2.4.1" JAVACFLAGS="-source 1.4 -target 1.4" COMPILER="" and of course, the output of emerge --info =jaxen-1.1.4 * The complete build log is located at '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/temp/environment'. * Working directory: '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/work/jaxen-1.1.4' * S: '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/work/jaxen-1.1.4' >>> Failed to emerge dev-java/jaxen-1.1.4-r1, Log file: >>> '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/temp/build.log' * Messages for package dev-java/jaxen-1.1.4-r1: * ERROR: dev-java/jaxen-1.1.4-r1::gentoo failed (configure phase): * xml-rewrite2 failed: ./build.xml * * Call stack: * ebuild.sh, line 93: Called src_configure * environment, line 4121: Called java-ant-2_src_configure * environment, line 1850: Called java-ant_bsfix * environment, line 1872: Called java-ant_bsfix_files './build.xml' * environment, line 1914: Called _bsfix_die 'xml-rewrite2 failed: ./build.xml' * environment, line 255: Called die * The specific snippet of code: * die ${1}; * * If you need support, post the output of `emerge --info '=dev-java/jaxen-1.1.4-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-java/jaxen-1.1.4-r1::gentoo'`. * The complete build log is located at '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/temp/environment'. * Working directory: '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/work/jaxen-1.1.4' * S: '/var/tmp/portage/dev-java/jaxen-1.1.4-r1/work/jaxen-1.1.4' Portage 2.2.1 (default/linux/amd64/13.0/desktop, gcc-4.7.3, glibc-2.17, 3.10.9-gentoo x86_64) ================================================================= System uname: Linux-3.10.9-gentoo-x86_64-Intel-R-_Core-TM-_i7-3517U_CPU_@_1.90GHz-with-gentoo-2.2 KiB Mem: 8057628 total, 6176356 free KiB Swap: 8388604 total, 8388604 free Timestamp of tree: Wed, 28 Aug 2013 02:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.5-r2, 3.2.5-r2, 3.3.2-r2 dev-util/cmake: 2.8.11.1 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.11.6, 1.12.6, 1.14 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.7.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.10 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/sandbox.d /etc/terminfo" CXXFLAGS="-march=native -O2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j5" 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 cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac freetype gdbm gif gpm gtk iconv infinality ipv6 jpeg lcms ldap libnotify mad mmx mng modules mp3 mp4 mpeg mudflap multilib ncurses nls nptl nsplugin ogg opengl openmp pam pango pcre pdf png policykit ppds qt3support readline sdl session spell sse sse2 ssl startup-notification svg tcpd tiff truetype udev udevbindist udisks unicode upower usb vorbis wxwidgets x264 xcb xinerama 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" 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 ubx" INPUT_DEVICES="evdev synaptics" 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="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" RUBY_TARGETS="ruby19 ruby18" USERLAND="GNU" VIDEO_CARDS="intel" 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, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON
Same problem here when trying to install jabref. A workaround is to install =dev-java/jaxen-1.1.1 first and than update to latest unstable.
+ 30 Aug 2013; Tom Wijsman <TomWij@gentoo.org> -jaxen-1.1.4-r1.ebuild: + Remove revision bump which causes a circular dependency as seen in bug + #482750, bug reported by Camaron and Ted Tanberry; this revision bump was + introduced for bug #481112 where the dependency should be indirectly installed + because it is a dependency of the jdom dependency. Thank you for reporting.
