I do not understand why is that but it sees current mpich2 ebuilds do not provide virtual/mpi. Therefore, clustalw-mpi attempts to install lam-mpi which gets blocked. I would be willing to test fixed ebuilds on x86 and amd64 arch with mpich2 installed. # emerge -uN clustalw-mpi Calculating dependencies... done! [ebuild N ] sys-cluster/lam-mpi-7.1.2 USE="crypt fortran -debug -pbs -xmpi" [ebuild N ] sci-biology/clustalw-mpi-0.13 USE="mpi_njtree -static_pairalign" [blocks B ] sys-cluster/lam-mpi (is blocking sys-cluster/mpich2-1.0.6) [blocks B ] sys-cluster/mpich2 (is blocking sys-cluster/lam-mpi-7.1.2) # # emerge --info Portage 2.1.4.4 (default/linux/amd64/2008.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo-r4-default x86_64) ================================================================= System uname: 2.6.24-gentoo-r4-default x86_64 Intel(R) Core(TM)2 Quad CPU Q6600 @ 2.40GHz Timestamp of tree: Fri, 06 Jun 2008 19:00:01 +0000 distcc 2.18.3 x86_64-pc-linux-gnu (protocols 1 and 2) (default port 3632) [disabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.4.4-r13 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /var/bind /var/spool/torque" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/udev/rules.d" CXXFLAGS="-O2 -march=nocona -fomit-frame-pointer -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks metadata-transfer sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://gentoo.mirror.web4u.cz/" LINGUAS="en cs cz" MAKEOPTS="-j1" PKGDIR="/usr/portage/packages" 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="/nfslarge/usr/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="R X Xaw3d acl acpi amd64 apache2 bash-completion bcmath berkdb blas boost bzip2 cblas clamav cli colordiff compress cpio cracklib crypt cscope css ctype curl curlwrappers cxx dbus djbfft emboss enblend encode enscript expat fam fortran ftp gcj gd gdbm gif glibc-compat20 glibc-omitfp glitz glut gmp gnuplot gnutls gpm graphviz gs gtk gtkhtml hal icc iconv ifc inifile innodb isdnlog ithreads java javascript jbig jikes jpeg jpeg2k kdtree lapack lcms libedit libwww lzo lzw maildir mhash midi mime ming mjpeg mmap mmx mng mod_python modperl modplug mozilla moznoirc mpeg mpi mpi_njtree mudflap mule multilib mxdatetime mysql mysqli ncurses netcdf netpbm network nntp nptl nptlonly numeric openmp pam pcntl pcre pdf perl plotutils png pnm postproc postscript ppds pppd procmail pymol python rar raw readline reflection reiserfs rpm rtc scp seamonkey server session sftp sift smime sndfile sockets spl srt sse sse2 sse3 ssl svg svgz sysfs sysvipc tcl tcpd threads tiff transcode unicode urandom userlocales uuencode vim-syntax vim-with-x wmf xanim xfs xinetd xml xorg xpm xslt xv xvid zip 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 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 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" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="en cs cz" USERLAND="GNU" VIDEO_CARDS="nv" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
mpich2 is part of the mpi virtual and hence should be fine as a dependency of clustalw-mpi. However, since clustalw-mpi is only keyworded x86 you must have done something to the ebuild to be able to emerge it on amd64. Can you make sure you didn't accidentally change some dependencies and that your portage tree is up to date. Thanks, Markus
Yes, I just unmasked clustalw-mpi with the hope I could compile and use it and report back. But I got stuck as I have reported.
Ping. ;-)
It seems the ebuild "as is" works also on ~amd64. Please add this arch to the list. I successfully compiled against mpich2-1.0.8-1. I definitely have no lam-mpi installed: # emerge -pv clustalw-mpi These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-biology/clustalw-mpi-0.13 USE="-mpi_njtree -static_pairalign" 0 kB # emerge -pv mpich2 These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sys-cluster/mpich2-1.0.8-r1 USE="cxx -debug -doc -fortran -mpi-threads -pvfs2 -romio -threads" 0 kB [?=>1] Total: 1 package (1 reinstall), Size of downloads: 0 kB Portage tree and overlays: [0] /nfslarge/usr/portage [1] /nfslarge/usr/portage/local #
Package correctly depends on virtual/mpi which is correct. Please open a new bug if you're requesting keywords.
