Currently package.use.mask says # Justin Lecher <jlec@gentoo.org> (17 Nov 2010) # Upstream didn't release patches for aria yet >=sci-chemistry/cns-1.3 aria sci-chemistry/aria depends on >=sci-chemistry/cns-1.2.1-r3[aria,openmp] sci-chemistry/cns has PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )" so having aria-2.3.1 and cns-1.2.1-r5[aria] installed should be a valid solution. Nevertheless portage tells me: # emerge -uvaDN world system These are the packages that would be merged, in reverse order: Calculating dependencies... done! It may be possible to solve this problem by using package.mask to prevent one of those packages from being selected. However, it is also possible that conflicting dependencies exist such that they are impossible to satisfy simultaneously. If such a conflict exists in the dependencies of two different packages, then those packages can not be installed simultaneously. You may want to try a larger value of the --backtrack option, such as --backtrack=30, in order to see if that will solve this conflict automatically. For more information, see MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook. !!! All ebuilds that could satisfy ">=sci-chemistry/cns-1.2.1-r3[aria,openmp]" have been masked. !!! One of the following masked packages is required to complete your request: - sci-chemistry/cns-1.2.1-r5 (masked by: ) - sci-chemistry/cns-1.2.1-r4 (masked by: ) - sci-chemistry/cns-1.2.1-r3 (masked by: ) (dependency required by "sci-chemistry/aria-2.3.1" [installed]) (dependency required by "@selected") (dependency required by "@world" [argument]) For more information, see the MASKED PACKAGES section in the emerge man page or refer to the Gentoo Handbook. So both the dependency detection and the mask reason go wrong here.
Portage 2.1.9.24 (default/linux/amd64/10.0, gcc-4.5.1-asneeded, glibc-2.12.1-r3, 2.6.35-gentoo-r12 x86_64) ================================================================= System uname: Linux-2.6.35-gentoo-r12-x86_64-Intel-R-_Core-TM-_i7_CPU_860_@_2.80GHz-with-gentoo-2.0.1 Timestamp of tree: Thu, 18 Nov 2010 11:15:02 +0000 distcc 3.1 x86_64-pc-linux-gnu [disabled] ccache version 2.4 [enabled] app-shells/bash: 4.1_p7 dev-java/java-config: 2.1.11-r1 dev-lang/python: 2.6.6-r1, 3.1.2-r4 dev-util/ccache: 2.4-r8 dev-util/cmake: 2.8.1-r2 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.6.4 sys-apps/sandbox: 2.3-r1 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.6.3-r1, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.5.1 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4 sys-devel/make: 3.81-r2 virtual/os-headers: 2.6.35 (sys-kernel/linux-headers) ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -march=core2 -frecord-gcc-switches -mssse3 -mcx16 -mmmx -msse4 -g -Wall -Wimplicit-function-declaration -Wmissing-include-dirs" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/nano/ /usr/share/openvpn/easy-rsa /var/lib/hsqldb /var/spool/torque" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /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 -march=core2 -frecord-gcc-switches -mssse3 -mcx16 -mmmx -msse4 -g -Wall -Wmissing-include-dirs -Wenum-compare" DISTDIR="/usr/portage/distfiles" EMERGE_DEFAULT_OPTS="-t --jobs=12 --load-average=12 --keep-going" FEATURES="assume-digests binpkg-logs buildsyspkg ccache collision-protect distlocks fixlafiles fixpackages news noinfo parallel-fetch protect-owned sandbox sfperms sign split-log splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe -march=core2 -frecord-gcc-switches -mssse3 -mcx16 -mmmx -msse4 -g -Wall" GENTOO_MIRRORS=" http://gentoo.j-schmitz.net/mirror/ ftp://ftp.gentoo.mesh-solutions.com/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gentoo ftp://ftp.tu-clausthal.de/pub/linux/gentoo/" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-O1,--hash-style=gnu,--sort-common" LINGUAS="en" MAKEOPTS="-j12 -l12" PKGDIR="/usr/portage/packages" PORTAGE_COMPRESS="lzma" PORTAGE_COMPRESS_FLAGS="-z -9 -f -S .lzma -v" 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/science /data/local/sunrise/sunrise /data/local/sunrise/reviewed /data/local/dummy /data/local/last-hope" SYNC="rsync://rsync.j-schmitz.net/gentoo-portage" USE="64bit 7zip X acpi additions alsa amd64 arpwarp bash-completion berkdb branding bzip2 c++ cairo cblas ccache cleartype cli command-args corefonts cracklib cups cupsddk custom-optimization cxx dbus dri dts exif fbcondecor fortran gdbm gif glibc-omitfp gmp gnome gnome-keyring gpm graphics gstreamer gtk hddtemp iconv icu java javascript jpeg kqemu lapack lcms ldap libnotify libsexy lm_sensors lzma mailtrain md5sum mmx modules mp3 mudflap multilib multiuser nagios-dns nagios-ntp nagios-ping nagios-ssh nano-syntax ncurses network-cron nis nls nptl nptlonly nsplugin objc objc++ opengl openmp openntpd pam pcre pdf perl png pppd pymol python qt-static qt3support readline rrdcgi rrdtool science sensord session smp sqlite sqlite3 sse sse2 ssl startup-notification svg sysfs system-sqlite tcpd threads tiff truetype type1 unicode x264 xcb xcomposite xinerama xorg xulrunner zlib" ALSA_CARDS="hda-intel" 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 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" 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="en" PHP_TARGETS="php5-2" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia" 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_RSYNC_EXTRA_OPTS
I verified this with 2.2.0_alpha4
Please post --debug output for the same command that produced the above output.
Created attachment 254731 [details] debug.log
Probably because cns[aria] has PDEPEND on aria and aria DEPENDs on cns[aria], which should logically be okay. In the moment it should not be allowed to emerge cns-1.3 if you want to use aria.
I will remove the PDEPEND, which isn't needed anyways. I don't why I put it there.
It was the PDEPEND which causes this problem. But in my opinion it was a correct depedency tree.
(In reply to comment #7) > It was the PDEPEND which causes this problem. But in my opinion it was a > correct depedency tree. > That's not true. It still exists.
It seems like the bug could be related to backtracking. Can you mask >=sci-libs/cctbx-2010.03.29.2334-r2 in order to solve the slot conflict (which triggers backracking), and see if it that makes it behave better?
NO, only the blocking reporting cctbx <-> pointless is gone
Do you have the required aria and openmp USE flags enabled? If not, does it behave correctly if you enable them? Please post the output of 'emerge -pv =sci-chemistry/cns-1.3'.
These are the packages that would be merged, in reverse order: Calculating dependencies ... done! [ebuild fU ] sci-chemistry/cns-1.3 [1.2.1-r5] USE="debug openmp (-aria*)" 0 kB Total: 1 package (1 upgrade), Size of downloads: 0 kB Fetch Restriction: 1 package What is strange, that aria should block it as it requires cns[aria].
(In reply to comment #12) > [ebuild fU ] sci-chemistry/cns-1.3 [1.2.1-r5] USE="debug openmp (-aria*)" Now I see that the following in profiles/base/package.use.mask: >=sci-chemistry/cns-1.3 aria So, apparently the code that shows the masking message doesn't handle masked flags correctly.
This fixes the main issue, so that the installed sci-chemistry/cns-1.3 is selected if it happened to be installed with the aria flag enabled (before it got masked): http://git.overlays.gentoo.org/gitweb/?p=proj/portage.git;a=commit;h=31edc4fcbb9138e523d09db2844c5835577a831b However, I think that -N should trigger a downgrade to a version that does not have the flag masked. I'll see about fixing that too.
(In reply to comment #14) > However, I think that -N should trigger a downgrade to a version that does not > have the flag masked. I'll see about fixing that too. Well, it downgrades if I add --deep=1 to my options, and I guess that's good enough.
The is in 2.2.0_alpha5, but I'll leave this bug open until it's in an unmasked release.
Confirmed, it works with alpha5.
Thanks for testing. This is fixed in 2.1.9.25.
