[Bio-linux-dev] Upgrade to Bio-Linux 7 (at last)

[Tony Travis]

On 26/09/12 17:45, Tony Travis wrote:
> [...]
> I'll look into it and see if I can come up with a fix.

Hi, Tim.

No fix yest, but here's some info that might help:

Bye,

   Tony.

> The following packages have unmet dependencies.
>  bio-linux-qiime : Depends: qiime (>= 1.3.0) but it is not going to be installed
> E: Unable to correct problems, you have held broken packages.
> Not all packages installed properly - exiting.
> root at bifx-rta:/usr/local/src/NEBC/Bio-Linux-upgrade# apt-cache policy qiime
> qiime:
>   Installed: (none)
>   Candidate: 1.4.0-0ubuntu2
>   Version table:
>      1.4.0-0ubuntu2 0
>         500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
>      1.3.0-3 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages
>      1.3.0-0ubuntu6 0
>         500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
>      1.3.0-0ubuntu5 0
>         500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
>      1.2.1-ubuntu5 0
>         500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
> root at bifx-rta:/usr/local/src/NEBC/Bio-Linux-upgrade# aptitude install qiime
> The following NEW packages will be installed:
>   qiime{b}
> The following packages are RECOMMENDED but will NOT be installed:
>   cd-hit chimeraslayer python-matplotlib
> 0 packages upgraded, 1 newly installed, 0 to remove and 7 not upgraded.
> Need to get 4,214 kB of archives. After unpacking 17.5 MB will be used.
> The following packages have unmet dependencies:
>  qiime : Depends: libffi5 (>= 3.0.4) which is a virtual package.
>          Depends: libgmp3c2 but it is not going to be installed.
>          Depends: python2.6 which is a virtual package.
>          Depends: python-pynast but it is not going to be installed.
> open: 110; closed: 326; defer: 82; conflict: 340                                                                                   oThe following actions will resolve these dependencies:
>
>        Remove the following packages:
> 1)       bio-linux-assembly-conversion-tools
> 2)       bio-linux-happy
> 3)       bio-linux-nrdb
> 4)       bio-linux-ocount
> 5)       bio-linux-staden
> 6)       bluez-alsa:i386
> 7)       glib-networking:i386
> 8)       gstreamer0.10-plugins-base:i386
> 9)       gstreamer0.10-plugins-good:i386
> 10)      gstreamer0.10-x:i386
> 11)      gtk2-engines:i386
> 12)      gtk2-engines-murrine:i386
> 13)      gtk2-engines-oxygen:i386
> 14)      gtk2-engines-pixbuf:i386
> 15)      gvfs:i386
> 16)      gvfs-libs:i386
> 17)      ia32-libs
> 18)      ia32-libs-multiarch:i386
> 19)      ibus-gtk:i386
> 20)      libaa1:i386
> 21)      libacl1:i386
> 22)      libao4:i386
> 23)      libasn1-8-heimdal:i386
> 24)      libasound2:i386
> 25)      libasound2-plugins:i386
> 26)      libasyncns0:i386
> 27)      libatk1.0-0:i386
> 28)      libattr1:i386
> 29)      libaudio2:i386
> 30)      libaudiofile1:i386
> 31)      libavahi-client3:i386
> 32)      libavahi-common3:i386
> 33)      libavc1394-0:i386
> 34)      libbz2-1.0:i386
> 35)      libc6:i386
> 36)      libcaca0:i386
> 37)      libcairo-gobject2:i386
> 38)      libcairo2:i386
> 39)      libcanberra-gtk-module:i386
> 40)      libcanberra-gtk0:i386
> 41)      libcanberra0:i386
> 42)      libcap2:i386
> 43)      libcapi20-3:i386
> 44)      libcdparanoia0:i386
> 45)      libcomerr2:i386
> 46)      libcroco3:i386
> 47)      libcups2:i386
> 48)      libcupsimage2:i386
> 49)      libcurl3:i386
> 50)      libdatrie1:i386
> 51)      libdb5.1:i386
> 52)      libdbus-1-3:i386
> 53)      libdbus-glib-1-2:i386
> 54)      libdrm-intel1:i386
> 55)      libdrm-nouveau1a:i386
> 56)      libdrm-radeon1:i386
> 57)      libdrm2:i386
> 58)      libdv4:i386
> 59)      libesd0:i386
> 60)      libexif12:i386
> 61)      libexpat1:i386
> 62)      libffi6:i386
> 63)      libflac8:i386
> 64)      libfontconfig1:i386
> 65)      libfreetype6:i386
> 66)      libgail-common:i386
> 67)      libgail18:i386
> 68)      libgcc1:i386
> 69)      libgconf-2-4:i386
> 70)      libgcrypt11:i386
> 71)      libgd2-xpm:i386
> 72)      libgdbm3:i386
> 73)      libgdk-pixbuf2.0-0:i386
> 74)      libgettextpo0:i386
> 75)      libgl1-mesa-dri:i386
> 76)      libgl1-mesa-glx:i386
> 77)      libglapi-mesa:i386
> 78)      libglib2.0-0:i386
> 79)      libglu1-mesa:i386
> 80)      libgnome-keyring0:i386
> 81)      libgnutls26:i386
> 82)      libgomp1:i386
> 83)      libgpg-error0:i386
> 84)      libgphoto2-2:i386
> 85)      libgphoto2-port0:i386
> 86)      libgpm2:i386
> 87)      libgssapi-krb5-2:i386
> 88)      libgssapi3-heimdal:i386
> 89)      libgstreamer-plugins-base0.10-0:i386
> 90)      libgstreamer0.10-0:i386
> 91)      libgtk2.0-0:i386
> 92)      libgudev-1.0-0:i386
> 93)      libhcrypto4-heimdal:i386
> 94)      libheimbase1-heimdal:i386
> 95)      libheimntlm0-heimdal:i386
> 96)      libhx509-5-heimdal:i386
> 97)      libibus-1.0-0:i386
> 98)      libice6:i386
> 99)      libidn11:i386
> 100)     libiec61883-0:i386
> 101)     libieee1284-3:i386
> 102)     libjack-jackd2-0:i386
> 103)     libjasper1:i386
> 104)     libjpeg-turbo8:i386
> 105)     libjpeg8:i386
> 106)     libjson0:i386
> 107)     libk5crypto3:i386
> 108)     libkeyutils1:i386
> 109)     libkrb5-26-heimdal:i386
> 110)     libkrb5-3:i386
> 111)     libkrb5support0:i386
> 112)     liblcms1:i386
> 113)     libldap-2.4-2:i386
> 114)     libllvm3.0:i386
> 115)     libltdl7:i386
> 116)     libmad0:i386
> 117)     libmikmod2:i386
> 118)     libmng1:i386
> 119)     libmpg123-0:i386
> 120)     libmysqlclient18:i386
> 121)     libncurses5:i386
> 122)     libncursesw5:i386
> 123)     libnspr4:i386
> 124)     libnss3:i386
> 125)     libodbc1:i386
> 126)     libogg0:i386
> 127)     libopenal1:i386
> 128)     liborc-0.4-0:i386
> 129)     libp11-kit0:i386
> 130)     libpango1.0-0:i386
> 131)     libpciaccess0:i386
> 132)     libpcre3:i386
> 133)     libpixman-1-0:i386
> 134)     libpng12-0:i386
> 135)     libproxy1:i386
> 136)     libpulse-mainloop-glib0:i386
> 137)     libpulse0:i386
> 138)     libpulsedsp:i386
> 139)     libqt4-dbus:i386
> 140)     libqt4-declarative:i386
> 141)     libqt4-designer:i386
> 142)     libqt4-network:i386
> 143)     libqt4-opengl:i386
> 144)     libqt4-qt3support:i386
> 145)     libqt4-script:i386
> 146)     libqt4-scripttools:i386
> 147)     libqt4-sql:i386
> 148)     libqt4-sql-mysql:i386
> 149)     libqt4-svg:i386
> 150)     libqt4-test:i386
> 151)     libqt4-xml:i386
> 152)     libqt4-xmlpatterns:i386
> 153)     libqtcore4:i386
> 154)     libqtgui4:i386
> 155)     libqtwebkit4:i386
> 156)     libraw1394-11:i386
> 157)     libroken18-heimdal:i386
> 158)     librsvg2-2:i386
> 159)     librsvg2-common:i386
> 160)     librtmp0:i386
> 161)     libsamplerate0:i386
> 162)     libsane:i386
> 163)     libsasl2-2:i386
> 164)     libsasl2-modules:i386
> 165)     libsdl-image1.2:i386
> 166)     libsdl-mixer1.2:i386
> 167)     libsdl-net1.2:i386
> 168)     libsdl-ttf2.0-0:i386
> 169)     libsdl1.2debian:i386
> 170)     libselinux1:i386
> 171)     libshout3:i386
> 172)     libslang2:i386
> 173)     libsm6:i386
> 174)     libsndfile1:i386
> 175)     libsoup-gnome2.4-1:i386
> 176)     libsoup2.4-1:i386
> 177)     libspeex1:i386
> 178)     libspeexdsp1:i386
> 179)     libsqlite3-0:i386
> 180)     libssl0.9.8:i386
> 181)     libssl1.0.0:i386
> 182)     libstdc++5:i386
> 183)     libstdc++6:i386
> 184)     libtag1-vanilla:i386
> 185)     libtag1c2a:i386
> 186)     libtasn1-3:i386
> 187)     libtdb1:i386
> 188)     libthai0:i386
> 189)     libtheora0:i386
> 190)     libtiff4:i386
> 191)     libtinfo5:i386
> 192)     libudev0:i386
> 193)     libunistring0:i386
> 194)     libusb-0.1-4:i386
> 195)     libuuid1:i386
> 196)     libv4l-0:i386
> 197)     libv4lconvert0:i386
> 198)     libvisual-0.4-0:i386
> 199)     libvisual-0.4-plugins:i386
> 200)     libvorbis0a:i386
> 201)     libvorbisenc2:i386
> 202)     libvorbisfile3:i386
> 203)     libwavpack1:i386
> 204)     libwind0-heimdal:i386
> 205)     libwrap0:i386
> 206)     libx11-6:i386
> 207)     libx11-xcb1:i386
> 208)     libxau6:i386
> 209)     libxaw7:i386
> 210)     libxcb-glx0:i386
> 211)     libxcb-render0:i386
> 212)     libxcb-shm0:i386
> 213)     libxcb1:i386
> 214)     libxcomposite1:i386
> 215)     libxcursor1:i386
> 216)     libxdamage1:i386
> 217)     libxdmcp6:i386
> 218)     libxext6:i386
> 219)     libxfixes3:i386
> 220)     libxft2:i386
> 221)     libxi6:i386
> 222)     libxinerama1:i386
> 223)     libxml2:i386
> 224)     libxmu6:i386
> 225)     libxp6:i386
> 226)     libxpm4:i386
> 227)     libxrandr2:i386
> 228)     libxrender1:i386
> 229)     libxslt1.1:i386
> 230)     libxss1:i386
> 231)     libxt6:i386
> 232)     libxtst6:i386
> 233)     libxv1:i386
> 234)     libxxf86vm1:i386
> 235)     odbcinst1debian2:i386
> 236)     xaw3dg:i386
> 237)     zlib1g:i386
>
>        Keep the following packages at their current version:
> 238)     qiime [Not Installed]
>
>        Leave the following dependencies unresolved:
> 239)     libcanberra-gtk0:i386 recommends libcanberra-gtk-module:i386
> 240)     libncurses5:i386 recommends libgpm2:i386
> 241)     libncursesw5:i386 recommends libgpm2:i386
> 242)     libslang2:i386 recommends libpng12-0:i386
> 243)     libgl1-mesa-glx:i386 recommends libgl1-mesa-dri:i386 (>= 7.2)
> 244)     libgphoto2-2:i386 recommends udev:i386 (>= 0.175)
> 245)     libgphoto2-2:i386 recommends libgphoto2-l10n:i386 (>= 2.4.13-1ubuntu1.2)
> 246)     libqt4-dbus:i386 recommends qdbus:i386 (= 4:4.8.1-0ubuntu4.2)
> 247)     libqtgui4:i386 recommends libcups2:i386
> 248)     ia32-libs-multiarch:i386 recommends libgl1-mesa-glx:i386
> 249)     ia32-libs-multiarch:i386 recommends libgl1-mesa-dri:i386
>
>
> Accept this solution? [Y/n/q/?]