'emerge biopython' fails with: >>> Emerging (2 of 3) sci-biology/biopython-1.62 from science !!! Fetched file: biopython-1.62.tar.gz VERIFY FAILED! !!! Reason: Insufficient data for checksum verification !!! Got: !!! Expected: MD5 RMD160 SHA1 SHA256 SHA512 WHIRLPOOL * Fetch failed for 'sci-biology/biopython-1.62', Log file: * '/var/tmp/portage/sci-biology/biopython-1.62/temp/build.log' root@leopard:/root(58)# emerge --info biopython Portage 2.2.6 (default/linux/amd64/13.0, gcc-4.7.3, glibc-2.17, 3.11.0-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.11.0-gentoo-x86_64-Intel-R-_Core-TM-_i7-2600_CPU_@_3.40GHz-with-gentoo-2.2 KiB Mem: 8123156 total, 3619740 free KiB Swap: 0 total, 0 free Timestamp of tree: Wed, 18 Sep 2013 12:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.2_p45 dev-java/java-config: 2.2.0 dev-lang/python: 2.7.5-r2, 3.2.5-r2, 3.3.2-r2 dev-util/cmake: 2.8.11.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13, 2.69 sys-devel/automake: 1.10.3, 1.11.6, 1.12.6, 1.13.4, 1.14 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.7.3 sys-devel/gcc-config: 1.8 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.11 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo science sunrise x11 sage-on-gentoo x-portage g-cpan g-octave 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" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" 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-php5.3/ext-active/ /etc/php/apache2-php5.5/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.5/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=native -O2 -pipe" 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="-O2 -pipe" 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" LC_ALL="" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j9" 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_leopard" PORTDIR_OVERLAY="/var/lib/layman/science /var/lib/layman/sunrise /var/lib/layman/x11 /var/lib/layman/sage-on-gentoo /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 bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli cmake consolekit cracklib crypt css cuda 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 ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpm fpx fuse g3dvl gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp git glade glib glpk gml gmp gnome gnome-keyring gnome-print gnuplot gnutls gold gphoto2 gpm grammar graphics graphtft graphviz grass gsl gstreamer gtk gtk3 gudev guile hddtemp hdf hdf5 hdri html http httpd hvm hwdb iconv icq icu id3 id3tag ide imagemagick imap inotify introspection ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kate kdepim kdrive kerberos keymap kpathsea kvm ladspa lame lapack latex lcms ldap lensfun libffi libkms libnotify libsamplerate live lm_sensors lua lzma lzo mad mail maildir mapnik math matroska media-library mercurial mikmod mmx mmxext mng mod modules mono motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib multimedia musepack musicbrainz mysql mysqli nautilus ncurses netcdf netpbm network networking networkmanager nfs nls nntp nptl nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ofa ogdi ogg openexr opengl openmp openvg pam pango pcre pda pdf perl plasma plotutils plugins png podcast policykit portaudio posix postgres postscript ppds preview-latex proj projectm projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime raw readline reiserfs reports rhythmbox 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 sockets sound soup sox speex spell sql sqlite sse sse2 sse4 ssl stlport subtitles subversion sudo suexec svg svm swig systemd szip t1lib tcl tcpd tex tex4ht texmacs tgif theora thesaurus threads thunderbird tidy tiff tk tools truetype udev udisks unicode usb userlocales utempter v4l vaapi vala valgrind vdpau video virt-network virtualbox visio vorbis vpx wav webdav webdav-serf webkit wmf wxwidgets x264 xa xattr xcb xemacs xetex xext xft xine xml xmlreader xmlrpc xpm xv xvid xvmc yaml youtube zlib zvbi" ABI_X86="64" 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" 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 dm lvm mdraid 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="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 ruby websvccommon xml" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_2" QEMU_SOFTMMU_TARGETS="arm i386 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby19 ruby18" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, SYNC, USE_PYTHON ================================================================= Package Settings ================================================================= sci-biology/biopython-1.61 was built with the following: USE="mysql postgres" PYTHON_TARGETS="python2_7 -python2_6"
Please use the version in the tree.
What can I do that 'emerge -uvDN world' takes biopython-1.62 f(In reply to Justin Lecher from comment #1) > Please use the version in the tree. What can I do that 'emerge -uvDN world' takes biopython-1.62 from the standard tree instead of the science overlay? >>> Emerging (1 of 1) sci-biology/biopython-1.62 from science !!! Fetched file: biopython-1.62.tar.gz VERIFY FAILED! !!! Reason: Insufficient data for checksum verification !!! Got: !!! Expected: MD5 RMD160 SHA1 SHA256 SHA512 WHIRLPOOL * Fetch failed for 'sci-biology/biopython-1.62', Log file: * '/var/tmp/portage/sci-biology/biopython-1.62/temp/build.log' >>> Failed to emerge sci-biology/biopython-1.62, Log file: >>> '/var/tmp/portage/sci-biology/biopython-1.62/temp/build.log' root@leopard:/root(9)# ll /usr/portage/sci-biology/biopython/ total 29 -rw-r--r-- 1 portage portage 1423 Dec 14 2012 biopython-1.57.ebuild -rw-r--r-- 1 portage portage 1426 Dec 14 2012 biopython-1.58.ebuild -rw-r--r-- 1 portage portage 1426 Dec 14 2012 biopython-1.59.ebuild -rw-r--r-- 1 portage portage 1314 Jul 2 15:01 biopython-1.61.ebuild -rw-r--r-- 1 portage portage 1286 Sep 17 18:07 biopython-1.62.ebuild -rw-r--r-- 1 portage portage 11257 Sep 17 18:31 ChangeLog drwxr-xr-x 2 portage portage 1024 Jan 31 2012 files/ -rw-r--r-- 1 portage portage 5270 Sep 17 18:31 Manifest -rw-r--r-- 1 portage portage 166 Apr 26 12:31 metadata.xml root@leopard:/root(10)# ll /var/lib/layman/science/sci-biology/biopython/ total 12 -rw-r--r-- 1 root root 1358 Sep 13 14:22 biopython-1.62.ebuild -rw-r--r-- 1 root root 301 Sep 13 14:22 ChangeLog -rw-r--r-- 1 root root 166 Sep 13 14:22 metadata.xml
Put the following in your package.mask: sci-biology/biopython::science
(In reply to Francois Bissey from comment #3) > Put the following in your package.mask: > sci-biology/biopython::science Thanks Francois, but one 'layman -S' later biopython disappeared from /var/lib/layman/sci-biology.
I am not surprised. But you can keep it in mind, you can mask an overlay with ::$overlay_name and the main tree with ::gentoo
