'emerge gromacs' fails with: ... -r3/work >>> Source unpacked in /var/tmp/portage/sci-chemistry/gromacs-4.5.3-r3/work >>> Preparing source in /var/tmp/portage/sci-chemistry/gromacs-4.5.3-r3/work/gromacs-4.5.3 ... * mdrun uses only threads OR mpi, and gromacs favours the * use of mpi over threads, so a mpi-version of mdrun will * be compiled. If you want to run mdrun on shared memory * machines only, you can safely disable mpi * QA: File or directory "/var/tmp/portage/sci-chemistry/gromacs-4.5.3-r3/work/gromacs-4.5.3_upstream20110217.patch.bz2" does not exist. * QA: Check your PATCHES array or add missing file/directory. * ERROR: sci-chemistry/gromacs-4.5.3-r3 failed (prepare phase): Reproducible: Always root@caiman:/root(18)# emerge --info =sci-chemistry/gromacs-4.5.3-r3 Portage 2.1.9.40 (default/linux/amd64/10.0, gcc-4.5.2, glibc-2.13-r1, 2.6.37-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.37-gentoo-x86_64-AMD_Phenom-tm-_II_X6_1090T_Processor-with-gentoo-2.0.1 Timestamp of tree: Sat, 19 Feb 2011 07:30:01 +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: 2.5 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: 4.5.2 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=amdfam10 -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-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/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=amdfam10 -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="-j7" 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/sunrise /var/lib/layman/x11 /var/lib/layman/science /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="3dnow 3dnowext 64bit R X Xaw3d a52 aac abiword acl acpi afs alsa amd64 amrr ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion berkdb blas blast boo boost bzip2 cairo cdda cddb cdf cdio cdparanoia cgi chm cli consolekit cracklib crypt cups curl cxx daap db dbase dbi dbm dbus devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dv dvb dvd dvdr dvi eds elf emacs emboss emf empathy encode epiphany evo examples exif expat extensions extra extras fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago gd gdal gdbm gdu gedit geoip geolocation geos gfortran gimp ginac git glade gmp gmtsuppl gnokii gnome gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gtk guile hddtemp hdf hdf5 hdri http httpd hvm iconv id3 imagemagick innodb inotify ipv6 ithreads jadetex jbig jpeg jpeg2k kdrive kpathsea kqemu kvm lapack latex latex3 ldap lensfun libffi libgda libnotify lm_sensors lua math matroska mkl mmx mmxext mng modules mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pam pcre pdf perl plotutils plugins png policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings q16 q32 qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdl semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4a ssl stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter v4l2 video virtualbox vorbis wav webdav webdav-serf webkit wmf wxwidgets xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml zlib zvbi" 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 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="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="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" USERLAND="GNU" VIDEO_CARDS="radeon ati 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 root@caiman:/root(19)# emerge -pqv =sci-chemistry/gromacs-4.5.3-r3 [ebuild U ] sci-chemistry/gromacs-4.5.3-r3 [4.5.3-r2] USE="X bash-completion blas doc fftw gsl lapack mpi single-precision sse sse2 threads xml (-altivec) -dmalloc -double-precision -fkernels -static-libs -test -zsh-completion"
If I list the directory I see: root@condor:/root(37)# ll /var/tmp/portage/sci-chemistry/gromacs-4.5.3-r3/work total 4652 drwxr-xr-x 11 root root 4096 Nov 9 22:16 gromacs-4.5.3/ -rw-r--r-- 1 root root 4746088 Feb 19 11:48 gromacs-4.5.3_upstream20110217.patch root@caiman:/root(21)# ll /var/tmp/portage/sci-chemistry/gromacs-4.5.3-r3/work total 4641 drwxr-xr-x 11 root root 720 Nov 9 22:16 gromacs-4.5.3/ -rw-r--r-- 1 root root 4746088 Feb 19 11:47 gromacs-4.5.3_upstream20110217.patch
Fixed the issue, the patch was unpacked automatically!
There will be a new version of gromacs in the portage tree?
