I have bicatali's overlay installed and working. A recent emerge --sync revealed a new stable portage (2.1.10.3) was available and the recommendation was to install it before proceeding with updates. I emerged the new portage and then tried to update world (emerge -puDN world). The result was blocked packages that I could not resolve by masking packages. I then downgraded from portage-2.1.10.3 to portage-2.1.9.42 and an emerge -puDN world had NO blocked packages. After updating world and completing revdep-rebuild I updated to portage-2.1.10.3. An emerge -puDN world then revealed the same blocked packages that were present originally. Reproducible: Always Steps to Reproduce: 1.install bicatali's overlay 2.install portage-2.1.10.3 3.emerge -puDN world Actual Results: Calculating dependencies... done! [ebuild N ] app-admin/eselect-blas-0.1 [ebuild U ~] sci-libs/blas-reference-20070226-r2 [3.3.1-r1] USE="-doc%" [blocks B ] app-admin/eselect-blas ("app-admin/eselect-blas" is blocking sci-libs/lapack-reference-3.3.1-r1, sci-libs/blas-reference-3.3.1-r1, sci-libs/gsl-1.15-r1, sci-libs/cblas-reference-20110218) * Error: The above package list contains packages which cannot be * installed at the same time on the same system. (sci-libs/cblas-reference-20110218::bicatali, installed) pulled in by >=sci-libs/cblas-reference-20110218 required by (virtual/cblas-2.0::bicatali, installed) sci-libs/cblas-reference required by @selected (app-admin/eselect-blas-0.1::gentoo, ebuild scheduled for merge) pulled in by app-admin/eselect-blas required by (sci-libs/blas-reference-20070226-r2::gentoo, ebuild scheduled for merge) (sci-libs/lapack-reference-3.3.1-r1::bicatali, installed) pulled in by >=sci-libs/lapack-reference-3.3 required by (virtual/lapack-3.3::bicatali, installed) sci-libs/lapack-reference required by @selected (sci-libs/gsl-1.15-r1::bicatali, installed) pulled in by >=sci-libs/gsl-1.15 required by (sci-mathematics/sage-4.7-r2::sage-on-gentoo, installed) sci-libs/gsl required by @selected sci-libs/gsl required by (media-gfx/inkscape-0.48.0::gentoo, installed) For more information about Blocked Packages, please refer to the following section of the Gentoo Linux x86 Handbook (architecture is irrelevant): http://www.gentoo.org/doc/en/handbook/handbook-x86.xml?full=1#blocked Expected Results: There should not be an attempt to install app-admin/eselect-blas-0.1 and sci-libs/blas-reference-20070226-r2. The expected behavior is provided when portage-2.1.9.42 is installed. masking app-admin/eselect-blas-0.1 does not resolve the issue for then I get The following mask changes are necessary to proceed: #required by sci-libs/blas-reference-20070226-r2, required by virtual/blas-2.0, required by sci-libs/umfpack-5.2.0, required by @selected, required by @world (argument) # /etc/portage/package.mask: >=app-admin/eselect-blas-0.1 For reference, I have virtual/blas-2.0 and app-admin/eselect-1.2.15-r1 from bicatali's overlay installed. Here is my emerge --info: Portage 2.1.10.3 (default/linux/amd64/10.0/desktop, gcc-4.4.5, glibc-2.12.2-r0, 2.6.36-gentoo-r5 x86_64) ================================================================= System uname: Linux-2.6.36-gentoo-r5-x86_64-Dual-Core_AMD_Opteron-tm-_Processor_2216-with-gentoo-2.0.2 Timestamp of tree: Sun, 17 Jul 2011 20:15:01 +0000 ccache version 2.4 [enabled] app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.5.4-r4, 2.6.6-r2, 2.7.1-r1::sage-on-gentoo, 3.1.3-r1 dev-util/ccache: 2.4-r9 dev-util/cmake: 2.8.4-r1 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.0.2 sys-apps/openrc: 0.8.3-r1 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.5::<unknown repository>, 1.6.3::<unknown repository>, 1.7.9-r1, 1.8.5-r3::<unknown repository>, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.20.1-r1 sys-devel/gcc: 4.1.2, 4.3.4, 4.4.5 sys-devel/gcc-config: 1.4.1-r1 sys-devel/libtool: 2.2.10 sys-devel/make: 3.82 sys-kernel/linux-headers: 2.6.36.1 (virtual/os-headers) sys-libs/glibc: 2.12.2 Repositories: gentoo desktop-effects science sunrise x11 sage-on-gentoo bicatali local-overlay ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA googleearth AdobeFlash-10 AdobeFlash-10.1" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=opteron -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/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=opteron -O2 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs ccache collision-protect distlocks ebuild-locks fixlafiles fixpackages multilib-strict news parallel-fetch protect-owned sandbox sfperms splitdebug 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="en" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_EXTRA_OPTS="--delete-after --timeout=500" 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/desktop-effects /var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/x11 /var/lib/layman/sage-on-gentoo /var/lib/layman/bicatali /usr/local/portage" SYNC="rsync://rsync.namerica.gentoo.org/gentoo-portage" USE="3dnow X Xaw3d a52 aac aalib acl acpi alsa amd64 apache2 audiofile bash-completion berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit cracklib crypt cups cxx dbus dri dts dvd dvdr emboss encode exif fam firefox flac fortran gdbm gdu gif gphoto2 gpm gstreamer gtk iconv ieee1394 imlib ipv6 java jpeg lcms ldap lesstif libnotify lm_sensors mad midi mmx mng modules motif mozilla mp3 mp4 mpeg mudflap multilib ncurses nls nptl nptlonly nsplugin ogg opengl openmp oss pam pango pcre pdf perl png policykit ppds pppd python qt3support qt4 radius readline sdl session spell sse sse2 ssl startup-notification svg sysfs tcl tcpd tiff tk truetype udev unicode usb vorbis x264 xcb xml xorg xulrunner xv xvid zlib" 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" 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" CALLIGRA_FEATURES="braindump flow karbon kexi kpresenter krita tables words" 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 keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en" PHP_TARGETS="php5-3" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nvidia fbdev vesa vga nv" 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
It has nothing to do with portage os the overlay. The packages are quite different. Here your solution unemerge everything which has to do with blas/lapck aand comes from the tree from your system. E.g. sci-libs/blas-reference, app-admin/eselect-blas etc add following to your /etc/portage/package.mask >sci-libs/blas-reference-10 and then go ahead again.
This did work. I must say I had considered removing everything (blas-reference, cblas-reference, lapack-reference and gsl) as suggested but didn't think the Blocking information pointed in this direction. And I would never have thought of adding >sci-libs/blas-reference-10 to package.mask since the overlay profile has all the portage blas-reference masked. Updating world wouldn't go without it. Isn't this a Bug or something? In fact, if I comment out the above in package.mask after a world update then the Blocking error returns on subsequent attempts to update world.
(In reply to comment #2) > This did work. I must say I had considered removing everything (blas-reference, > cblas-reference, lapack-reference and gsl) as suggested but didn't think the > Blocking information pointed in this direction. And I would never have thought > of adding > > >sci-libs/blas-reference-10 > > to package.mask since the overlay profile has all the portage blas-reference > masked. Updating world wouldn't go without it. Isn't this a Bug or something? > In fact, if I comment out the above in package.mask after a world update then > the Blocking error returns on subsequent attempts to update world. Masking somehting in the overlay should work for a normal emerge. I cannot tell ou why this isn't working for the bicatali overlay.
An interesting question would be whether or not it affects only bicatali's overlay. It should work out of the box and not need to add the block in the local package.mask (I don't think removing stuff was necessary before the masking - that's only if you were migrating to the overlay). Steve, are R-2.12+ properly masked because of the sage-on-gentoo overlay?
(In reply to comment #4) > An interesting question would be whether or not it affects only bicatali's > overlay. It should work out of the box and not need to add the block in the > local package.mask (I don't think removing stuff was necessary before the > masking - that's only if you were migrating to the overlay). > > Steve, are R-2.12+ properly masked because of the sage-on-gentoo overlay? I believe you are correct about removing stuff before the masking. Yes, all R-2.12+ stuff is masked here because of sage-on-gentoo.
I keep forgetting that commenting doesn't add me to CC, and this hasn't been assigned to science so I don't receive it as part of the alias either. So portage 2.2.0_alpha46 here: eix m4ri [I] sci-libs/m4ri Available versions: (~)20090512!m[1] (~)20100221!m[1] (~)20100701!m[2] (~)20100701!m[3] (~)20100817!m[2] (~)20100817!m[3] [M](~)20110613!m[2] [M](~)20110613!m[3] [M]**99999999!m[2] [M]**99999999!m[3] {debug openmp sse2 static-libs} Installed versions: 20100817!m[3](09:50:41 07/23/11)(sse2 -debug -openmp -static-libs) Homepage: http://m4ri.sagemath.org/ Description: Method of four russian for inversion (M4RI)) [1] "science" /var/lib/layman/science [2] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo [3] "sage" /home/francois/Work/Overlays/Gentoo-sage Notice that m4ri-20110613+ is package masked from the sage-on-gentoo overlay and eix reports it correctly. However: emerge -puDv world These are the packages that would be merged, in order: Calculating dependencies ... done! [ebuild U ~] sci-libs/m4ri-20110613 [20100817] USE="sse2 -debug -openmp -static-libs" 0 kB [1] [ebuild U ] dev-libs/libevent-2.0.12 [2.0.10] USE="-static-libs -test" 804 kB [0] [ebuild U ~] app-admin/eselect-1.2.16-r1 [1.2.15-r1] USE="-bash-completion -doc" 166 kB [2] Total: 3 packages (3 upgrades), Size of downloads: 969 kB Portage tree and overlays: [0] /usr/portage [1] /home/francois/Work/Overlays/Gentoo-sage [2] /var/lib/layman/bicatali So portage wants to update something that's package masked in the sage-on-gentoo overlay. I made sure there wasn't anything interfering in package unmask too. Adding a line in /etc/portage/package.mask worked. Curiously R is indeed masked properly, as if the problem only applies to overlay ebuilds.
portage-2.1.10.3 here. I don't have m4ri in my local overlay and there is no issue. However, if I copy the sage-on-gentoo sci-libs/m4ri folder to my local overlay and update eix then the issue appears: eix m4ri [I] sci-libs/m4ri Available versions: (~)20090512!m[1] (~)20100221!m[1] (~)20100701!m[2] (~)20100701!m[3] (~)20100817!m[2] (~)20100817!m[3] [M](~)20110613!m[2] [M](~)20110613!m[3] [M]**99999999!m[2] [M]**99999999!m[3] {debug openmp sse2 static-libs} Installed versions: 20100817!m[2](07:13:52 PM 07/22/2011)(openmp sse2 -debug -static-libs) Homepage: http://m4ri.sagemath.org/ Description: Method of four russian for inversion (M4RI) [1] "science" /var/lib/layman/science [2] "sage-on-gentoo" /var/lib/layman/sage-on-gentoo [3] "local-overlay" /usr/local/portage emerge -puDv world These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ~] sci-libs/m4ri-20110613 [20100817] USE="openmp sse2 -debug -static-libs" 441 kB [1=>2] Total: 1 package (1 upgrade), Size of downloads: 441 kB Portage tree and overlays: [0] /usr/portage [1] /var/lib/layman/sage-on-gentoo [2] /usr/local/portage Removing m4ri-20110613.ebuild from my local overlay fixed the problem. Therefore, even though eix reported m4ri-20110613 from my local overlay as being package masked, it really wasn't! There does appear to be some ambiguity in how package masked stuff is being handled.
