Bug 527224 – sci-chemistry/pdb2pqr-1.9.0-r1 - Change USE: -python_targets_python2_7, this change violates use flag constraints defined by sci-chemistry/pdb2pqr-1.9.0-r1: 'any-of ( python_targets_python2_7 )'

• Status: RESOLVED TEST-REQUEST
• Product: Gentoo Linux

[Description Juergen Rose 2014-10-28 13:00:35 UTC]

'emerge -v1 pdb2pqr' fails with:

root@gepard:/root(27)# emerge -v1 pdb2pqr

These are the packages that would be merged, in order:

Calculating dependencies... done!

emerge: there are no ebuilds built with USE flags to satisfy "sci-chemistry/apbs[python_targets_python2_7(-)?,-python_single_target_python2_7(-),-mpi]".
!!! One of the following packages is required to complete your request:
- sci-chemistry/apbs-1.4.1::gentoo (Change USE: -python_single_target_python2_7, this change violates use flag constraints defined by sci-chemistry/apbs-1.4.1: 'mpi? ( !python ) python_single_target_python2_7? ( python_targets_python2_7 ) exactly-one-of ( python_single_target_python2_7 )')
- sci-chemistry/pdb2pqr-1.9.0-r1::gentoo (Change USE: -python_targets_python2_7, this change violates use flag constraints defined by sci-chemistry/pdb2pqr-1.9.0-r1: 'any-of ( python_targets_python2_7 )')
(dependency required by "sci-chemistry/pdb2pqr-1.9.0-r1" [ebuild])
(dependency required by "pdb2pqr" [argument])


I did not set USE: -python_targets_python2_7:

root@gepard:/root(28)# grep pdb2pqr /etc/portage/package.use 
#required by sci-chemistry/apbs-1.3-r3, required by sci-chemistry/pdb2pqr-1.7.0-r2[pdb2pka], required by sci-chemistry/mgltools-molkit-1.5.6_rc2, required by sci-chemistry/mgltools-autodocktools-1.5.6_rc2, required by sci-chemistry/mgltools-1.5.6_rc2, required by mgltools (argument)
#required by sci-chemistry/pdb2pqr-1.7.0-r2[pdb2pka], required by sci-chemistry/mgltools-molkit-1.5.6_rc2, required by sci-chemistry/mgltools-autodocktools-1.5.6_rc2, required by sci-chemistry/mgltools-1.5.6_rc2, required by mgltools (argument)


root@gepard:/root(29)# emerge --info
Portage 2.2.14 (python 2.7.8-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-4.8.3, glibc-2.19-r1, 3.17.1-gentoo-r1 x86_64)
=================================================================
System uname: Linux-3.17.1-gentoo-r1-x86_64-Intel-R-_Core-TM-_i7_CPU_M_620_@_2.67GHz-with-gentoo-2.2
KiB Mem:     3903236 total,   1696824 free
KiB Swap:   12582908 total,  11932424 free
Timestamp of tree: Tue, 28 Oct 2014 12:30:01 +0000
ld GNU ld (Gentoo 2.24 p1.4) 2.24
distcc 3.1 x86_64-pc-linux-gnu [disabled]
app-shells/bash:          4.3_p30
dev-java/java-config:     2.2.0
dev-lang/perl:            5.20.1-r2
dev-lang/python:          2.7.8, 3.3.5-r1, 3.4.2
dev-util/cmake:           3.0.2
dev-util/pkgconfig:       0.28-r2
sys-apps/baselayout:      2.2
sys-apps/openrc:          0.13.2
sys-apps/sandbox:         2.6-r1
sys-devel/autoconf:       2.13, 2.69
sys-devel/automake:       1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 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:           4.1-r1
sys-kernel/linux-headers: 3.17 (virtual/os-headers)
sys-libs/glibc:           2.19-r1
Repositories: gentoo sage-on-gentoo science sunrise x11 ago tlp local g-cpan g-octave
Installed sets: @system
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA PUEL Intel-SDP dlj-1.1 skype-eula skype-4.0.0.7-copyright googleearth AdobeFlash-11.x cadsoft Oracle-BCLA-JavaSE MakeMKV-EULA NVIDIA-CUDA Nero-AAC-EULA GIMPS"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core2 -mtune=generic -Os -pipe -msse3 -msse4 -mcx16 -msahf -mpopcnt -mpreferred-stack-boundary=6"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /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/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/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 -mtune=generic -Os -pipe -msse3 -msse4 -mcx16 -msahf -mpopcnt -mpreferred-stack-boundary=6"
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 xattr"
FFLAGS="-march=core2 -mtune=generic -Os -pipe -msse3 -msse4 -mcx16 -msahf -mpopcnt -mpreferred-stack-boundary=6"
GENTOO_MIRRORS="http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror http://ftp-stud.fht-esslingen.de/pub/Mirrors/gentoo/ ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo ftp://ftp.easynet.nl/mirror/gentoo/ "
LANG="en_US.UTF-8"
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_gepard"
PORTDIR_OVERLAY="/var/lib/layman/sage-on-gentoo /var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/x11 /var/lib/layman/ago /var/lib/layman/tlp /usr/local/portage /var/lib/cpan /var/lib/g-octave"
USE="64bit R X Xaw3d a52 aac acl acpi admin afs alsa amd64 ao apache2 apng applet archive armadillo arpack asf aspell atlas audacious audiofile automap automount bash-completion berkdb blas blast bluetooth bluray boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake colord cracklib crypt css cups curl cxx daap db dbi dbm dbus declarative designer devhelp device-mapper dga dia dirac djvu doc dot dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds egl elf emacs emboss emf encode epiphany evo examples exif expat extensions extra extras faac faad fam ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glamor glib glpk gml gmp gnome gnome-keyring gnome-online-accounts gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gsm gstreamer gtk gtk3 gudev guile hdaps hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java java6 jbig jit john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack laptop latex lcms ldap lensfun libffi libkms libnotify libsamplerate libsecret lirc live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mkl mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking nfs nls nntp nptl nsplugin ntfs ntp numpy obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf pdl2 perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl schroedinger science sdk sdl secure-delete semantic-desktop server session shout sip slang slp smart smbclient smp sms sndfile snmp soap socialweb sockets sound soup sox speex spell sql sqlite sse sse2 sse4 sse4_1 sse4_2 ssl ssse3 startup-notification stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs theora thesaurus thinkpad threads thunderbird tidy tiff tk tools truetype udev udisks unicode upower usb utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx vtk wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xa xattr xcb xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" ALSA_CARDS="intel8x0" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_core authn_dbm authn_default authn_file authz_core 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 lbmethod_byrequests log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif slotmem_shm so socache_shmcb speling status unique_id unixd userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="canon fuji ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CURL_SSL="nss" DRACUT_MODULES="caps lvm syslog" DVB_CARDS="usb-wt220u" 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 synaptics void" KERNEL="linux" LCD_DEVICES="cfontz hd44780 mtxorb ncurses X lcd2usb lcdlinux png usblcd" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de fr ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="nouveau displaylink" 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, SYNC, USE_PYTHON

[Comment 1 Justin Lecher (RETIRED) 2014-10-28 15:35:35 UTC]

Please resync, it should be fixed in apbs-1.4.1-r1

[Comment 2 Juergen Rose 2014-10-29 15:26:06 UTC]

(In reply to Justin Lecher from comment #1)
> Please resync, it should be fixed in apbs-1.4.1-r1

Sadly 'emerge apbs-1.4.1-r1' fails due to bug 527344.