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Bug 353933 - conflict of amarok and bioperl blocks 'emerge -uvD world' via embedded USE flag
Summary: conflict of amarok and bioperl blocks 'emerge -uvD world' via embedded USE flag
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: [OLD] Unspecified (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Portage team
URL:
Whiteboard:
Keywords: InVCS
Depends on:
Blocks: 349307
  Show dependency tree
 
Reported: 2011-02-07 07:32 UTC by Juergen Rose
Modified: 2011-02-15 19:01 UTC (History)
1 user (show)

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


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Description Juergen Rose 2011-02-07 07:32:07 UTC
With my current settings in /etc/portage/packages.use:

dev-db/mysql innodb test -berkdb embedded
virtual/mysql embedded

'emerge -uvDN world' fails with:

emerge: there are no ebuilds built with USE flags to satisfy "=virtual/mysql-5.1[-embedded]".
!!! One of the following packages is required to complete your request:
- virtual/mysql-5.1 (Change USE: -embedded)
(dependency required by "dev-perl/DBD-mysql-4.18-r1" [ebuild])
(dependency required by "sci-biology/biosql-1.0.1[mysql]" [installed])
(dependency required by "sci-biology/bioperl-db-1.6.0" [installed])
(dependency required by "sci-biology/bioperl-1.6.1[db]" [installed])
(dependency required by "@selected" [set])
(dependency required by "@world" [argument])


If I remove virtual/mysql embedded from /etc/portage/package.use 
'emerge -uvDN world' fails with:


 * Error: The above package list contains packages which cannot be
 * installed at the same time on the same system.

  (dev-db/mysql-5.1.53, installed) pulled in by
    dev-db/mysql required by (sci-geosciences/grass-6.4.0, installed)
    >=dev-db/mysql-5.1.50-r3[embedded] required by (media-sound/amarok-2.4.0, installed)

  (dev-db/mariadb-5.1.50, ebuild scheduled for merge) pulled in by
    =dev-db/mariadb-5.1*[-embedded,-static] required by (virtual/mysql-5.1, ebuild scheduled for merge)


If I remove additional the embedded USE flag from dev-db/mysql 
'emerge -uvDN world' fails with:



emerge: there are no ebuilds built with USE flags to satisfy ">=dev-db/mysql-5.1.50-r3[embedded]".
!!! One of the following packages is required to complete your request:
- dev-db/mysql-5.1.53 (Change USE: +embedded)
(dependency required by "media-sound/amarok-2.4.0[player,embedded]" [installed])
(dependency required by "@selected" [set])
(dependency required by "@world" [argument])

There is probably some connection to Bug 335433.





Reproducible: Always




root@orca:/usr/local/portage/sci-libs/gdal(39)# emerge --info
Portage 2.1.9.36 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.13-r0, 2.6.37-gentoo x86_64)
=================================================================
System uname: Linux-2.6.37-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_W3520_@_2.67GHz-with-gentoo-2.0.1
Timestamp of tree: Mon, 07 Feb 2011 06:30:01 +0000
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.7.1, 3.1.3
dev-util/cmake:      2.8.3-r1
sys-apps/baselayout: 2.0.1-r1
sys-apps/openrc:     0.7.0
sys-apps/sandbox:    2.4
sys-devel/autoconf:  2.13, 2.68
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.21
sys-devel/gcc:       4.4.5, 4.5.2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.4-r1
sys-devel/make:      3.82
virtual/os-headers:  2.6.36.1 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
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-php5.3/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.3/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="-march=core2 -msse4 -mcx16 -msahf -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS=""
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j9"
PKGDIR="/usr/portage/packages"
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="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/java-overlay /var/lib/layman/sunrise /var/lib/layman/arcon /var/lib/layman/science /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fpx fts3 fuse galago gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd hvm iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric nvidia obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora thinkpad threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets x264 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" 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 auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="canon" 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="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="nv nvidia nouveau vesa" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Comment 1 Torsten Veller (RETIRED) gentoo-dev 2011-02-07 07:58:28 UTC
The "embedded" useflag was added to DBD-mysql-4.18-r1 and it must be the same as virtual/mysql. So adding
| dev-perl/DBD-mysql embedded
to /etc/portage/packages.use should fix your problem.

If that is the problem, then the portage output isn't useful and we should forward the bug to the portage maintainers.
Comment 2 Juergen Rose 2011-02-07 09:56:42 UTC
Hello Torsten,

thanks, works!
Comment 3 Torsten Veller (RETIRED) gentoo-dev 2011-02-07 10:19:39 UTC
Can the portage output below be improved? (Sorry, if this is a dup.)

The output only partially supports useflag settings.
It prints "dev-db/mariadb-5.1.50[perl]" (with useflag) and 
then "dev-perl/DBD-mysql-4.18-r1" (without useflag).
DBD-mysql-4.18-r1 depends on virtual/mysql[embedded=].



emerge: there are no ebuilds built with USE flags to satisfy "=virtual/mysql-5.1[-embedded]".
!!! One of the following packages is required to complete your request:
- virtual/mysql-5.1 (Change USE: -embedded)
(dependency required by "dev-perl/DBD-mysql-4.18-r1" [ebuild])
(dependency required by "dev-db/mariadb-5.1.50[perl]" [installed])
(dependency required by "@selected" [set])
(dependency required by "@world" [argument])
Comment 4 Zac Medico gentoo-dev 2011-02-07 11:22:12 UTC
(In reply to comment #3)
I reproduced that emerge output, and this should partially fix it:

http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=a60acb9f203f56af8225dc7dda7c453a12fd6372

With this patch, I get different output:

emerge: there are no ebuilds built with USE flags to satisfy "=dev-db/mariadb-5.1*[embedded=,static=]".
!!! One of the following packages is required to complete your request:
- dev-db/mariadb-5.1.50 (Change USE: +embedded)
- virtual/mysql-5.1 (Change USE: -embedded)
(dependency required by "virtual/mysql-5.1" [ebuild])
(dependency required by "dev-perl/DBD-mysql-4.18-r1" [ebuild])
(dependency required by "dev-db/mariadb-5.1.50[perl]" [ebuild])

As noted in the commit message, there is a remaining issue involving interaction between this code and extract_affecting_use().
Comment 5 Zac Medico gentoo-dev 2011-02-07 11:54:58 UTC
I fixed the code a bit more:

http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=7e735aaa79ed26901c66b9444e4098b320abc2d5

And now the output looks like this:

emerge: there are no ebuilds built with USE flags to satisfy "=virtual/mysql-5.1[embedded=]".
!!! One of the following packages is required to complete your request:
- virtual/mysql-5.1 (Change USE: -embedded)
- dev-perl/DBD-mysql-4.18-r1 (Change USE: +embedded)
(dependency required by "dev-perl/DBD-mysql-4.18-r1" [ebuild])
(dependency required by "dev-db/mariadb-5.1.50[perl]" [ebuild])
Comment 6 Zac Medico gentoo-dev 2011-02-12 00:17:57 UTC
(In reply to comment #4)
> As noted in the commit message, there is a remaining issue involving
> interaction between this code and extract_affecting_use().

It's fixed to work with extract_affecting_use() now:

http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=5b16e0d800f34dc90cdd8c505172ad16b97f0af4
Comment 7 Zac Medico gentoo-dev 2011-02-12 00:21:18 UTC
After the last commit, output looks like this:

emerge: there are no ebuilds built with USE flags to satisfy "virtual/mysql[embedded=]".
!!! One of the following packages is required to complete your request:
- virtual/mysql-5.1 (Change USE: -embedded)
- dev-perl/DBD-mysql-4.18-r1 (Change USE: +embedded)
(dependency required by "dev-perl/DBD-mysql-4.18-r1" [ebuild])
(dependency required by "dev-db/mariadb-5.1.50[perl]" [ebuild])
Comment 8 Torsten Veller (RETIRED) gentoo-dev 2011-02-12 04:57:51 UTC
I think it's much better. Thanks
Comment 9 Zac Medico gentoo-dev 2011-02-15 19:01:23 UTC
This is fixed in 2.1.9.40 and 2.2.0_alpha24.