Bug#667599: dolfin-dev: fails to upgrade from squeeze - apt does not find an upgrade path
Ana Guerrero
ana at debian.org
Wed Feb 27 08:46:29 UTC 2013
On Tue, Feb 26, 2013 at 03:47:22PM +0100, Sylvestre Ledru wrote:
> On 25/02/2013 11:44, Andreas Beckmann wrote:
> > Followup-For: Bug #667599
> > Control: tag -1 patch
> >
> > Hi,
> >
> > after having tested a lot of modifications, I think I found a solution
> > that provides smoother hdf5 upgrade paths from squeeze.
> >
> > As that is primarily an apt bug in squeeze, we need to work around it
> > somehow.
> >
> > I'm not sure if this also solves the issue switching from mpi to serial
> > variant during upgrades.
> Excellent. Many thanks.
>
> Ana is currently testing your fix. I upload it as soon as I have her go!
Bad news, it doesn't fully work. A couple of cases:
A) Minimal installation of Squeeze (actually a cowbuilder instance) where
it's installed libhdf5-serial-1.8.4 and libhdf5-serial-dev. After the upgrade to
wheezy, libhdf5-7 from Wheezy is installed while libhdf5-serial-1.8.4 from
Squeeze is kept and the -dev package has been removed:
# dpkg -l | grep hdf5
ii hdf5-helpers 1.8.8-9.1 amd64 Hierarchical Data Format 5 (HDF5) - Helper tools
ii libhdf5-7 1.8.8-9.1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-serial-1.8.4 1.8.4-patch1-2 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
(see test1-missing-serial-dev.txt)
The same problem exists with the *openmpi* version.
B) Minimal installation of Squeeze where it's installed
libhdf5-openmpi-1.8.4 and r-cran-hdf5. After the upgrade to Wheezy,
libhdf5-7 from Wheezy is installed (the serial version) while
hdf5-openmpi-1.8.4 from Squeeze is kept. r-cran-hdf5 is updated fine.
# dpkg -l | grep hdf5
ii libhdf5-7 1.8.8-9.1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-openmpi-1.8.4 1.8.4-patch1-2 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version
ii r-cran-hdf5 1.6.10-1+b1 amd64 GNU R package interfacing the NCSA HDF5 library
(see test2.txt)
Ana
-------------- next part --------------
c7test:/home/ana# cowbuilder --login
-> Copying COW directory
forking: rm -rf /var/cache/pbuilder/build//cow.14707
forking: cp -al /var/cache/pbuilder/base.cow /var/cache/pbuilder/build//cow.14707
I: removed stale ilistfile /var/cache/pbuilder/build//cow.14707/.ilist
-> Invoking pbuilder
forking: pbuilder login --buildplace /var/cache/pbuilder/build//cow.14707 --no-targz --internal-chrootexec chroot /var/cache/pbuilder/build//cow.14707 cow-shell
W: /root/.pbuilderrc does not exist
I: Running in no-targz mode
I: copying local configuration
I: mounting /proc filesystem
I: mounting /dev/pts filesystem
I: Mounting /var/cache/pbuilder/ccache
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: entering the shell
root at c7test:/# apt-get install libhdf5-serial-1.8.4 libhdf5-serial-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
libgfortran3 libjpeg62 libjpeg62-dev zlib1g-dev
Suggested packages:
libhdf5-doc
The following NEW packages will be installed:
libgfortran3 libhdf5-serial-1.8.4 libhdf5-serial-dev libjpeg62 libjpeg62-dev zlib1g-dev
0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/4594 kB of archives.
After this operation, 24.5 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
Selecting previously deselected package libgfortran3.
(Reading database ... 11950 files and directories currently installed.)
Unpacking libgfortran3 (from .../libgfortran3_4.4.5-8_amd64.deb) ...
Selecting previously deselected package libhdf5-serial-1.8.4.
Unpacking libhdf5-serial-1.8.4 (from .../libhdf5-serial-1.8.4_1.8.4-patch1-2_amd64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously deselected package libjpeg62.
Unpacking libjpeg62 (from .../libjpeg62_6b1-1_amd64.deb) ...
Selecting previously deselected package libjpeg62-dev.
Unpacking libjpeg62-dev (from .../libjpeg62-dev_6b1-1_amd64.deb) ...
Selecting previously deselected package libhdf5-serial-dev.
Unpacking libhdf5-serial-dev (from .../libhdf5-serial-dev_1.8.4-patch1-2_amd64.deb) ...
Setting up libgfortran3 (4.4.5-8) ...
Setting up libhdf5-serial-1.8.4 (1.8.4-patch1-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up libjpeg62 (6b1-1) ...
Setting up libjpeg62-dev (6b1-1) ...
Setting up libhdf5-serial-dev (1.8.4-patch1-2) ...
root at c7test:/# vim /etc/apt/sources.list
root at c7test:/# apt-get update
Ign file: ./ Release.gpg
Ign file:/tmp/Mirror/ ./ Translation-en
Ign file: ./ Release
Ign file: ./ Packages
Get:1 http://debian wheezy Release.gpg [836 B]
Get:2 http://debian/debian/ wheezy/main Translation-en [3870 kB]
Get:3 http://debian wheezy Release [223 kB]
Get:4 http://debian wheezy/main amd64 Packages [5872 kB]
Fetched 9966 kB in 1s (6470 kB/s)
Reading package lists... Done
root at c7test:/# apt-get -d dist-upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be REMOVED:
libhdf5-serial-dev
The following NEW packages will be installed:
cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base hdf5-helpers libapt-inst1.5 libapt-pkg4.12 libclass-isa-perl libdb5.1
libgcrypt11 libgmp10 libgnutls26 libgpg-error0 libhdf5-7 libidn11 libitm1 libjpeg8 liblzma5 libmount1 libmpc2
libp11-kit0 libpam-modules-bin libquadmath0 libsemanage-common libsemanage1 libstdc++6-4.7-dev libswitch-perl
libtasn1-3 libtinfo5 libustr-1.0-1 multiarch-support
The following packages will be upgraded:
apt apt-utils base-files base-passwd bash binutils bsdutils bzip2 coreutils cowbuilder cowdancer cpp cpp-4.4 dash
debconf debconf-i18n debian-archive-keyring debianutils debootstrap diffutils dpkg dpkg-dev e2fslibs e2fsprogs
eatmydata findutils g++ g++-4.4 gcc gcc-4.4 gcc-4.4-base gnupg gpgv grep gzip hostname initscripts insserv libacl1
libattr1 libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcomerr2 libdpkg-perl libgcc1 libgdbm3
libgfortran3 libgomp1 libgpm2 libjpeg62 libjpeg62-dev liblocale-gettext-perl libmpfr4 libncurses5 libpam-modules
libpam-runtime libpam0g libreadline6 libselinux1 libsepol1 libslang2 libss2 libstdc++6 libstdc++6-4.4-dev
libtext-charwidth-perl libtext-iconv-perl libusb-0.1-4 libuuid1 linux-libc-dev login lsb-base make mawk mount
ncurses-base ncurses-bin passwd patch pbuilder perl perl-base perl-modules readline-common sed sensible-utils
sysv-rc sysvinit sysvinit-utils tar tzdata util-linux vim vim-common vim-runtime wget xz-utils zlib1g zlib1g-dev
102 upgraded, 31 newly installed, 1 to remove and 0 not upgraded.
Need to get 25.2 MB/104 MB of archives.
After this operation, 42.3 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
WARNING: The following packages cannot be authenticated!
hdf5-helpers libhdf5-7
Install these packages without verification [y/N]? y
Get:1 http://debian/debian/ wheezy/main multiarch-support amd64 2.13-38 [150 kB]
Get:2 http://debian/debian/ wheezy/main libc6-dev amd64 2.13-38 [2660 kB]
Get:3 http://debian/debian/ wheezy/main libc-dev-bin amd64 2.13-38 [224 kB]
Get:4 http://debian/debian/ wheezy/main libc-bin amd64 2.13-38 [1269 kB]
Get:5 http://debian/debian/ wheezy/main libc6 amd64 2.13-38 [4339 kB]
Get:6 http://debian/debian/ wheezy/main sysvinit-utils amd64 2.88dsf-41 [99.5 kB]
Get:7 http://debian/debian/ wheezy/main sysv-rc all 2.88dsf-41 [81.4 kB]
Get:8 http://debian/debian/ wheezy/main initscripts amd64 2.88dsf-41 [94.1 kB]
Get:9 http://debian/debian/ wheezy/main perl-modules all 5.14.2-18 [3442 kB]
Get:10 http://debian/debian/ wheezy/main perl amd64 5.14.2-18 [4424 kB]
Get:11 http://debian/debian/ wheezy/main perl-base amd64 5.14.2-18 [1537 kB]
Get:12 http://debian/debian/ wheezy/main sysvinit amd64 2.88dsf-41 [133 kB]
Get:13 http://debian/debian/ wheezy/main libapt-inst1.5 amd64 0.9.7.7 [166 kB]
Get:14 http://debian/debian/ wheezy/main apt-utils amd64 0.9.7.7 [377 kB]
Get:15 http://debian/debian/ wheezy/main libgnutls26 amd64 2.12.20-4 [617 kB]
Get:16 http://debian/debian/ wheezy/main vim amd64 2:7.3.547-7 [841 kB]
Get:17 http://debian/debian/ wheezy/main vim-runtime all 2:7.3.547-7 [4607 kB]
Get:18 http://debian/debian/ wheezy/main vim-common amd64 2:7.3.547-7 [163 kB]
Fetched 25.2 MB in 0s (55.8 MB/s)
Download complete and in download only mode
root at c7test:/# apt-get dist-upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be REMOVED:
libhdf5-serial-dev
The following NEW packages will be installed:
cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base hdf5-helpers libapt-inst1.5 libapt-pkg4.12 libclass-isa-perl libdb5.1
libgcrypt11 libgmp10 libgnutls26 libgpg-error0 libhdf5-7 libidn11 libitm1 libjpeg8 liblzma5 libmount1 libmpc2
libp11-kit0 libpam-modules-bin libquadmath0 libsemanage-common libsemanage1 libstdc++6-4.7-dev libswitch-perl
libtasn1-3 libtinfo5 libustr-1.0-1 multiarch-support
The following packages will be upgraded:
apt apt-utils base-files base-passwd bash binutils bsdutils bzip2 coreutils cowbuilder cowdancer cpp cpp-4.4 dash
debconf debconf-i18n debian-archive-keyring debianutils debootstrap diffutils dpkg dpkg-dev e2fslibs e2fsprogs
eatmydata findutils g++ g++-4.4 gcc gcc-4.4 gcc-4.4-base gnupg gpgv grep gzip hostname initscripts insserv libacl1
libattr1 libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcomerr2 libdpkg-perl libgcc1 libgdbm3
libgfortran3 libgomp1 libgpm2 libjpeg62 libjpeg62-dev liblocale-gettext-perl libmpfr4 libncurses5 libpam-modules
libpam-runtime libpam0g libreadline6 libselinux1 libsepol1 libslang2 libss2 libstdc++6 libstdc++6-4.4-dev
libtext-charwidth-perl libtext-iconv-perl libusb-0.1-4 libuuid1 linux-libc-dev login lsb-base make mawk mount
ncurses-base ncurses-bin passwd patch pbuilder perl perl-base perl-modules readline-common sed sensible-utils
sysv-rc sysvinit sysvinit-utils tar tzdata util-linux vim vim-common vim-runtime wget xz-utils zlib1g zlib1g-dev
102 upgraded, 31 newly installed, 1 to remove and 0 not upgraded.
Need to get 0 B/104 MB of archives.
After this operation, 42.3 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
WARNING: The following packages cannot be authenticated!
hdf5-helpers libhdf5-7
Install these packages without verification [y/N]? y
Extracting templates from packages: 100%
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Current default time zone: 'Etc/UTC'
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Preparing to replace initscripts 2.88dsf-13.1+squeeze1 (using .../initscripts_2.88dsf-41_amd64.deb) ...
Removing unmodified and obsolete conffile /etc/default/bootlogd ...
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Upgrading unmodified configuration file /etc/default/rcS ...
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Installing new version of config file /etc/init.d/bootlogs ...
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Installing new version of config file /etc/init.d/mountall.sh ...
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Installing new version of config file /etc/init.d/mountnfs.sh ...
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Installing new version of config file /etc/network/if-up.d/mountnfs ...
guest environment detected: Linking /run to /var/run
guest environment detected: Linking /run/lock to /var/lock
guest environment detected: Linking /dev/shm to /run/shm
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Updating /etc/profile to current default.
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Setting up bash (4.2+dfsg-0.1) ...
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update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
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Setting up gzip (1.5-1.1) ...
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Setting up login (1:4.1.5.1-1) ...
Installing new version of config file /etc/pam.d/login ...
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Installing new version of config file /etc/securetty ...
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Setting up ncurses-bin (5.9-10) ...
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Preparing to replace perl-base 5.10.1-17squeeze5 (using .../perl-base_5.14.2-18_amd64.deb) ...
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Setting up perl-base (5.14.2-18) ...
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Selecting previously unselected package libapt-inst1.5:amd64.
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Preparing to replace debian-archive-keyring 2010.08.28+squeeze1 (using .../debian-archive-keyring_2012.4_all.deb) ...
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Setting up libreadline6:amd64 (6.2+dfsg-0.1) ...
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Selecting previously unselected package libapt-pkg4.12:amd64.
dpkg: considering deconfiguration of apt, which would be broken by installation of libapt-pkg4.12:amd64 ...
dpkg: yes, will deconfigure apt (broken by libapt-pkg4.12:amd64)
(Reading database ... 12828 files and directories currently installed.)
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gpg: key B98321F9: "Squeeze Stable Release Key <debian-release at lists.debian.org>" not changed
gpg: key 473041FA: "Debian Archive Automatic Signing Key (6.0/squeeze) <ftpmaster at debian.org>" not changed
gpg: key 65FFB764: "Wheezy Stable Release Key <debian-release at lists.debian.org>" not changed
gpg: key 46925553: "Debian Archive Automatic Signing Key (7.0/wheezy) <ftpmaster at debian.org>" not changed
gpg: Total number processed: 4
gpg: unchanged: 4
gpg: checking the trustdb
gpg: WARNING: digest algorithm MD5 is deprecated
gpg: please see http://www.gnupg.org/faq/weak-digest-algos.html for more information
gpg: no ultimately trusted keys found
(Reading database ... 12786 files and directories currently installed.)
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(Reading database ... 12778 files and directories currently installed.)
Preparing to replace mawk 1.3.3-15 (using .../mawk_1.3.3-17_amd64.deb) ...
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Selecting previously unselected package libgpg-error0:amd64.
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Selecting previously unselected package libtasn1-3:amd64.
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Selecting previously unselected package libgnutls26:amd64.
Unpacking libgnutls26:amd64 (from .../libgnutls26_2.12.20-4_amd64.deb) ...
Preparing to replace libgpm2 1.20.4-3.3 (using .../libgpm2_1.20.4-6_amd64.deb) ...
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Selecting previously unselected package libidn11:amd64.
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Selecting previously unselected package libitm1:amd64.
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Preparing to replace libjpeg62-dev 6b1-1 (using .../libjpeg62-dev_6b1-3_amd64.deb) ...
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Selecting previously unselected package libjpeg8:amd64.
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Selecting previously unselected package libmpc2:amd64.
Unpacking libmpc2:amd64 (from .../libmpc2_0.9-4_amd64.deb) ...
Preparing to replace libpam-runtime 1.1.1-6.1+squeeze1 (using .../libpam-runtime_1.1.3-7.1_all.deb) ...
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Setting up libpam-runtime (1.1.3-7.1) ...
(Reading database ... 12879 files and directories currently installed.)
Preparing to replace xz-utils 5.0.0-2 (using .../xz-utils_5.1.1alpha+20120614-2_amd64.deb) ...
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Setting up xz-utils (5.1.1alpha+20120614-2) ...
update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode
(Reading database ... 12881 files and directories currently installed.)
Preparing to replace vim 2:7.2.445+hg~cb94c42c0e1a-1 (using .../vim_2%3a7.3.547-7_amd64.deb) ...
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Adding 'diversion of /usr/share/vim/vim73/doc/help.txt to /usr/share/vim/vim73/doc/help.txt.vim-tiny by vim-runtime'
Adding 'diversion of /usr/share/vim/vim73/doc/tags to /usr/share/vim/vim73/doc/tags.vim-tiny by vim-runtime'
Unpacking replacement vim-runtime ...
Removing 'diversion of /usr/share/vim/vim72/doc/help.txt to /usr/share/vim/vim72/doc/help.txt.vim-tiny by vim-runtime'
Removing 'diversion of /usr/share/vim/vim72/doc/tags to /usr/share/vim/vim72/doc/tags.vim-tiny by vim-runtime'
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Preparing to replace pbuilder 0.199+nmu1squeeze1 (using .../pbuilder_0.213_all.deb) ...
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Selecting previously unselected package cpp-4.7.
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Preparing to replace eatmydata 26-1~bpo60+1 (using .../eatmydata_26-2_amd64.deb) ...
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Selecting previously unselected package gcc-4.7.
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Preparing to replace gcc 4:4.4.5-1 (using .../gcc_4%3a4.7.2-1_amd64.deb) ...
Removing old gcc doc directory.
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Selecting previously unselected package libstdc++6-4.7-dev.
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Preparing to replace g++ 4:4.4.5-1 (using .../g++_4%3a4.7.2-1_amd64.deb) ...
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Selecting previously unselected package hdf5-helpers.
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Selecting previously unselected package libhdf5-7.
Unpacking libhdf5-7 (from .../libhdf5-7_1.8.8-9.1_amd64.deb) ...
Setting up gcc-4.4-base:amd64 (4.4.7-2) ...
Setting up libgmp10:amd64 (2:5.0.5+dfsg-2) ...
Setting up libmpfr4:amd64 (3.1.0-5) ...
Setting up cpp-4.4 (4.4.7-2) ...
Setting up binutils (2.22-7.1) ...
Setting up libgomp1:amd64 (4.7.2-5) ...
Setting up gcc-4.4 (4.4.7-2) ...
Setting up libc-dev-bin (2.13-38) ...
Setting up linux-libc-dev:amd64 (3.2.35-2) ...
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Setting up libquadmath0:amd64 (4.7.2-5) ...
Setting up libgfortran3:amd64 (4.7.2-5) ...
Setting up make (3.81-8.2) ...
Setting up zlib1g-dev:amd64 (1:1.2.7.dfsg-13) ...
Setting up bzip2 (1.0.6-4) ...
Setting up libclass-isa-perl (0.36-3) ...
Setting up libgdbm3:amd64 (1.8.3-11) ...
Setting up libtext-charwidth-perl (0.04-7+b1) ...
Setting up libtext-iconv-perl (1.7-5) ...
Setting up liblocale-gettext-perl (1.05-7+b1) ...
Setting up libapt-inst1.5:amd64 (0.9.7.7) ...
Setting up apt-utils (0.9.7.7) ...
Setting up mawk (1.3.3-17) ...
Setting up libgpg-error0:amd64 (1.10-3.1) ...
Setting up libgcrypt11:amd64 (1.5.0-3) ...
Setting up libp11-kit0:amd64 (0.12-3) ...
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Setting up libjpeg62-dev:amd64 (6b1-3) ...
Setting up libjpeg8:amd64 (8d-1) ...
Setting up libmpc2:amd64 (0.9-4) ...
Setting up vim-common (2:7.3.547-7) ...
Setting up vim-runtime (2:7.3.547-7) ...
Processing /usr/share/vim/addons/doc
Setting up vim (2:7.3.547-7) ...
Setting up wget (1.13.4-3) ...
Setting up debconf-i18n (1.5.49) ...
Setting up patch (2.6.1-3) ...
Setting up debootstrap (1.0.44) ...
Setting up cowdancer (0.70) ...
Setting up cpp-4.7 (4.7.2-5) ...
Setting up cpp (4:4.7.2-1) ...
Setting up eatmydata (26-2) ...
Setting up gcc-4.7 (4.7.2-5) ...
Setting up gcc (4:4.7.2-1) ...
Setting up hdf5-helpers (1.8.8-9.1) ...
Setting up libhdf5-7 (1.8.8-9.1) ...
Setting up libstdc++6-4.7-dev (4.7.2-5) ...
Setting up g++-4.4 (4.4.7-2) ...
Setting up libswitch-perl (2.16-2) ...
Setting up g++-4.7 (4.7.2-5) ...
Setting up g++ (4:4.7.2-1) ...
Setting up libstdc++6-4.4-dev (4.4.7-2) ...
Setting up perl-modules (5.14.2-18) ...
Setting up perl (5.14.2-18) ...
Setting up libdpkg-perl (1.16.9) ...
Setting up dpkg-dev (1.16.9) ...
Setting up pbuilder (0.213) ...
Installing new version of config file /etc/bash_completion.d/pbuilder ...
Setting up cowbuilder (0.70) ...
Installing new version of config file /etc/bash_completion.d/cowbuilder ...
root at c7test:/# dpkg -l | grep hdf5
ii hdf5-helpers 1.8.8-9.1 amd64 Hierarchical Data Format 5 (HDF5) - Helper tools
ii libhdf5-7 1.8.8-9.1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-serial-1.8.4 1.8.4-patch1-2 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
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c7test:/home/ana# cowbuilder --login
-> Copying COW directory
forking: rm -rf /var/cache/pbuilder/build//cow.28849
forking: cp -al /var/cache/pbuilder/base.cow /var/cache/pbuilder/build//cow.28849
I: removed stale ilistfile /var/cache/pbuilder/build//cow.28849/.ilist
-> Invoking pbuilder
forking: pbuilder login --buildplace /var/cache/pbuilder/build//cow.28849 --no-targz --internal-chrootexec chroot /var/cache/pbuilder/build//cow.28849 cow-shell
W: /root/.pbuilderrc does not exist
I: Running in no-targz mode
I: copying local configuration
I: mounting /proc filesystem
I: mounting /dev/pts filesystem
I: Mounting /var/cache/pbuilder/ccache
I: policy-rc.d already exists
I: Obtaining the cached apt archive contents
I: entering the shell
root at c7test:/# apt-get install libhdf5-openmpi-1.8.4 r-cran-hdf5 --no-install-recommends
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following extra packages will be installed:
adduser defoma file fontconfig fontconfig-config libblas3gf libcairo2 libdatrie1 libexpat1 libfontconfig1 libfreetype6 libgfortran3
libglib2.0-0 libibverbs1 libice6 libjpeg62 liblapack3gf libmagic1 libnewt0.52 libnuma1 libopenmpi1.3 libpango1.0-0 libpango1.0-common
libpaper-utils libpaper1 libpcre3 libpixman-1-0 libpng12-0 libpopt0 libsm6 libthai-data libthai0 libtiff4 libtorque2 libx11-6 libx11-data
libxau6 libxcb-render-util0 libxcb-render0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 r-base-core tcl8.5 tk8.5
ttf-dejavu-core ucf unzip whiptail x11-common xdg-utils zip
Suggested packages:
defoma-doc psfontmgr x-ttcidfont-conf dfontmgr ttf-japanese-gothic ttf-japanese-mincho ttf-thryomanes ttf-baekmuk ttf-arphic-gbsn00lp
ttf-arphic-bsmi00lp ttf-arphic-gkai00mp ttf-arphic-bkai00mp ess r-doc-info r-doc-pdf r-mathlib r-base-html tclreadline gvfs-bin
Recommended packages:
libfont-freetype-perl libglib2.0-data shared-mime-info libfribidi0 r-recommended r-base-dev r-doc-html xterm x-terminal-emulator iceweasel
www-browser x11-utils x11-xserver-utils mime-support
The following NEW packages will be installed:
adduser defoma file fontconfig fontconfig-config libblas3gf libcairo2 libdatrie1 libexpat1 libfontconfig1 libfreetype6 libgfortran3
libglib2.0-0 libhdf5-openmpi-1.8.4 libibverbs1 libice6 libjpeg62 liblapack3gf libmagic1 libnewt0.52 libnuma1 libopenmpi1.3 libpango1.0-0
libpango1.0-common libpaper-utils libpaper1 libpcre3 libpixman-1-0 libpng12-0 libpopt0 libsm6 libthai-data libthai0 libtiff4 libtorque2
libx11-6 libx11-data libxau6 libxcb-render-util0 libxcb-render0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 r-base-core
r-cran-hdf5 tcl8.5 tk8.5 ttf-dejavu-core ucf unzip whiptail x11-common xdg-utils zip
0 upgraded, 58 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/34.1 MB of archives.
After this operation, 82.2 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
Extracting templates from packages: 100%
Preconfiguring packages ...
Selecting previously deselected package adduser.
(Reading database ... 11950 files and directories currently installed.)
Unpacking adduser (from .../adduser_3.112+nmu2_all.deb) ...
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Selecting previously deselected package tcl8.5.
Unpacking tcl8.5 (from .../tcl8.5_8.5.8-2_amd64.deb) ...
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Unpacking tk8.5 (from .../tk8.5_8.5.8-1_amd64.deb) ...
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Unpacking r-base-core (from .../r-base-core_2.11.1-6_amd64.deb) ...
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Selecting previously deselected package libopenmpi1.3.
Unpacking libopenmpi1.3 (from .../libopenmpi1.3_1.4.2-4_amd64.deb) ...
Selecting previously deselected package libhdf5-openmpi-1.8.4.
Unpacking libhdf5-openmpi-1.8.4 (from .../libhdf5-openmpi-1.8.4_1.8.4-patch1-2_amd64.deb) ...
Selecting previously deselected package r-cran-hdf5.
Unpacking r-cran-hdf5 (from .../r-cran-hdf5_1.6.9-2+b1_amd64.deb) ...
Setting up adduser (3.112+nmu2) ...
Setting up libnewt0.52 (0.52.11-1) ...
Setting up libpopt0 (1.16-1) ...
Setting up whiptail (0.52.11-1) ...
Setting up libmagic1 (5.04-5+squeeze2) ...
Setting up file (5.04-5+squeeze2) ...
Setting up libpcre3 (8.02-1.1) ...
Setting up ucf (3.0025+nmu1) ...
Setting up defoma (0.11.11) ...
Setting up libexpat1 (2.0.1-7+squeeze1) ...
Setting up libfreetype6 (2.4.2-2.1+squeeze4) ...
Setting up ttf-dejavu-core (2.31-1) ...
Setting up fontconfig-config (2.8.0-2.1) ...
Setting up libfontconfig1 (2.8.0-2.1) ...
Setting up fontconfig (2.8.0-2.1) ...
Updating font configuration of fontconfig...
Cleaning up category cid..
Cleaning up category truetype..
Cleaning up category type1..
Updating category type1..
Updating category truetype..
Updating category cid..
Cleaning up old fontconfig caches... done.
Regenerating fonts cache... done.
Setting up libgfortran3 (4.4.5-8) ...
Setting up libblas3gf (1.2-8) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3gf to provide /usr/lib/libblas.so.3gf (libblas.so.3gf) in auto mode.
Setting up libpixman-1-0 (0.16.4-1) ...
Setting up libpng12-0 (1.2.44-1+squeeze4) ...
Setting up libxau6 (1:1.0.6-1) ...
Setting up libxdmcp6 (1:1.0.3-2) ...
Setting up libxcb1 (1.6-1) ...
Setting up libx11-data (2:1.3.3-4) ...
Setting up libx11-6 (2:1.3.3-4) ...
Setting up libxcb-render0 (1.6-1) ...
Setting up libxcb-render-util0 (0.3.6-1) ...
Setting up libxrender1 (1:0.9.6-1) ...
Setting up libcairo2 (1.8.10-6) ...
Setting up libdatrie1 (0.2.4-1) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up x11-common (1:7.5+8+squeeze1) ...
Setting up libice6 (2:1.0.6-2) ...
Setting up libjpeg62 (6b1-1) ...
Setting up liblapack3gf (3.2.1-8) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3gf to provide /usr/lib/liblapack.so.3gf (liblapack.so.3gf) in auto mode.
Setting up libnuma1 (2.0.5-1) ...
Setting up libpango1.0-common (1.28.3-1+squeeze2) ...
Cleaning up font configuration of pango...
Updating font configuration of pango...
Cleaning up category xfont..
Updating category xfont..
*** You don't have any defomized font packages.
*** So we are trying to force to generate pangox.aliases...
Setting up libthai-data (0.1.14-2) ...
Setting up libthai0 (0.1.14-2) ...
Setting up libxft2 (2.1.14-2) ...
Setting up libpango1.0-0 (1.28.3-1+squeeze2) ...
Setting up libpaper1 (1.1.24) ...
Creating config file /etc/papersize with new version
Setting up libpaper-utils (1.1.24) ...
Setting up libsm6 (2:1.1.1-1) ...
Setting up libtiff4 (3.9.4-5+squeeze8) ...
Setting up libtorque2 (2.4.8+dfsg-9squeeze1) ...
Setting up libxext6 (2:1.1.2-1) ...
Setting up libxss1 (1:1.2.0-2) ...
Setting up libxt6 (1:1.0.7-1) ...
Setting up zip (3.0-3) ...
Setting up unzip (6.0-4) ...
Setting up xdg-utils (1.0.2+cvs20100307-2) ...
Setting up tcl8.5 (8.5.8-2) ...
update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode.
Setting up tk8.5 (8.5.8-1) ...
update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode.
Setting up r-base-core (2.11.1-6) ...
Setting R_PAPERSIZE_USER default to 'a4'
Creating config file /etc/R/Renviron with new version
Setting up libibverbs1 (1.1.3-2) ...
Setting up libopenmpi1.3 (1.4.2-4) ...
Setting up libhdf5-openmpi-1.8.4 (1.8.4-patch1-2) ...
Setting up r-cran-hdf5 (1.6.9-2+b1) ...
root at c7test:/# dpkg -l | grep hdf5
ii libhdf5-openmpi-1.8.4 1.8.4-patch1-2 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version
ii r-cran-hdf5 1.6.9-2+b1 GNU R package interfacing the NCSA HDF5 library
root at c7test:/# vim /etc/apt/sources.list
root at c7test:/# apt-get update
Ign file: ./ Release.gpg
Ign file:/tmp/Mirror/ ./ Translation-en
Ign file: ./ Release
Ign file: ./ Packages
Hit http://debian squeeze Release.gpg
Ign http://debian/debian/ squeeze/main Translation-en
Get:1 http://debian wheezy Release.gpg [836 B]
Get:2 http://debian/debian/ wheezy/main Translation-en [3870 kB]
Hit http://debian squeeze Release
Get:3 http://debian wheezy Release [223 kB]
Hit http://debian squeeze/main amd64 Packages
Get:4 http://debian wheezy/main amd64 Packages [5872 kB]
Fetched 9966 kB in 1s (6456 kB/s)
Reading package lists... Done
root at c7test:/# apt-get -u dist-upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
The following packages will be REMOVED:
defoma libpango1.0-common
The following NEW packages will be installed:
cpp-4.7 g++-4.7 gcc-4.7 gcc-4.7-base libapt-inst1.5 libapt-pkg4.12 libblas3 libclass-isa-perl libdb5.1 libffi5 libgcrypt11 libgmp10
libgnutls26 libgpg-error0 libhdf5-7 libidn11 libitm1 libjbig0 libjpeg8 liblapack3 liblzma5 libmount1 libmpc2 libp11-kit0
libpam-modules-bin libquadmath0 libsemanage-common libsemanage1 libstdc++6-4.7-dev libswitch-perl libtasn1-3 libtinfo5 libustr-1.0-1
libxcb-shm0 multiarch-support
The following packages will be upgraded:
adduser apt apt-utils base-files base-passwd bash binutils bsdutils bzip2 coreutils cowbuilder cowdancer cpp cpp-4.4 dash debconf
debconf-i18n debian-archive-keyring debianutils debootstrap diffutils dpkg dpkg-dev e2fslibs e2fsprogs eatmydata file findutils fontconfig
fontconfig-config g++ g++-4.4 gcc gcc-4.4 gcc-4.4-base gnupg gpgv grep gzip hostname initscripts insserv libacl1 libattr1 libblas3gf
libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo2 libcomerr2 libdatrie1 libdpkg-perl libexpat1 libfontconfig1
libfreetype6 libgcc1 libgdbm3 libgfortran3 libglib2.0-0 libgomp1 libgpm2 libibverbs1 libice6 libjpeg62 liblapack3gf liblocale-gettext-perl
libmagic1 libmpfr4 libncurses5 libnewt0.52 libnuma1 libopenmpi1.3 libpam-modules libpam-runtime libpam0g libpango1.0-0 libpaper-utils
libpaper1 libpcre3 libpixman-1-0 libpng12-0 libpopt0 libreadline6 libselinux1 libsepol1 libslang2 libsm6 libss2 libstdc++6
libstdc++6-4.4-dev libtext-charwidth-perl libtext-iconv-perl libthai-data libthai0 libtiff4 libtorque2 libusb-0.1-4 libuuid1 libx11-6
libx11-data libxau6 libxcb-render-util0 libxcb-render0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 linux-libc-dev login
lsb-base make mawk mount ncurses-base ncurses-bin passwd patch pbuilder perl perl-base perl-modules r-base-core r-cran-hdf5
readline-common sed sensible-utils sysv-rc sysvinit sysvinit-utils tar tcl8.5 tk8.5 ttf-dejavu-core tzdata ucf unzip util-linux vim
vim-common vim-runtime wget whiptail x11-common xdg-utils xz-utils zip zlib1g
153 upgraded, 35 newly installed, 2 to remove and 0 not upgraded.
Need to get 0 B/145 MB of archives.
After this operation, 63.4 MB of additional disk space will be used.
Do you want to continue [Y/n]? y
WARNING: The following packages cannot be authenticated!
libhdf5-7
Install these packages without verification [y/N]? Y
Extracting templates from packages: 100%
Preconfiguring packages ...
(Reading database ... 14737 files and directories currently installed.)
Preparing to replace libc-dev-bin 2.11.3-4 (using .../libc-dev-bin_2.13-38_amd64.deb) ...
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Setting up gcc-4.7-base (4.7.2-5) ...
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(Reading database ... 14744 files and directories currently installed.)
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Setting up multiarch-support (2.13-38) ...
(Reading database ... 14748 files and directories currently installed.)
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Preparing to replace cpp-4.4 4.4.5-8 (using .../cpp-4.4_4.4.7-2_amd64.deb) ...
Unpacking replacement cpp-4.4 ...
dpkg: considering deconfiguration of gcc-4.4, which would be broken by installation of libgcc1 ...
dpkg: yes, will deconfigure gcc-4.4 (broken by libgcc1).
Preparing to replace libgcc1 1:4.4.5-8 (using .../libgcc1_1%3a4.7.2-5_amd64.deb) ...
De-configuring gcc-4.4 ...
Unpacking replacement libgcc1 ...
Setting up libgcc1 (1:4.7.2-5) ...
(Reading database ... 14760 files and directories currently installed.)
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Unpacking replacement libgomp1 ...
Preparing to replace gcc-4.4 4.4.5-8 (using .../gcc-4.4_4.4.7-2_amd64.deb) ...
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Preparing to replace libstdc++6 4.4.5-8 (using .../libstdc++6_4.7.2-5_amd64.deb) ...
Unpacking replacement libstdc++6 ...
Setting up libstdc++6 (4.7.2-5) ...
(Reading database ... 14760 files and directories currently installed.)
Preparing to replace g++-4.4 4.4.5-8 (using .../g++-4.4_4.4.7-2_amd64.deb) ...
Unpacking replacement g++-4.4 ...
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Unpacking replacement libstdc++6-4.4-dev ...
Selecting previously deselected package libquadmath0.
Unpacking libquadmath0 (from .../libquadmath0_4.7.2-5_amd64.deb) ...
Preparing to replace libgfortran3 4.4.5-8 (using .../libgfortran3_4.7.2-5_amd64.deb) ...
Unpacking replacement libgfortran3 ...
Preparing to replace make 3.81-8 (using .../make_3.81-8.2_amd64.deb) ...
Unpacking replacement make ...
Preparing to replace libc6-dev 2.11.3-4 (using .../libc6-dev_2.13-38_amd64.deb) ...
Unpacking replacement libc6-dev ...
Preparing to replace libc-bin 2.11.3-4 (using .../libc-bin_2.13-38_amd64.deb) ...
Unpacking replacement libc-bin ...
Setting up libc-bin (2.13-38) ...
Installing new version of config file /etc/bindresvport.blacklist ...
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Checking for services that may need to be restarted...
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Setting up libc6 (2.13-38) ...
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W: fontconfig is already removed. It is recommended to run defoma-app purge fontconfig.
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Current default time zone: 'Etc/UTC'
Local time is now: Tue Feb 26 23:13:58 UTC 2013.
Universal Time is now: Tue Feb 26 23:13:58 UTC 2013.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
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guest environment detected: Linking /run to /var/run
guest environment detected: Linking /run/lock to /var/lock
guest environment detected: Linking /dev/shm to /run/shm
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update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
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Setting up readline-common (6.2+dfsg-0.1) ...
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Preparing to replace libreadline6 6.1-3 (using .../libreadline6_6.2+dfsg-0.1_amd64.deb) ...
Unpacking replacement libreadline6:amd64 ...
Setting up libreadline6:amd64 (6.2+dfsg-0.1) ...
(Reading database ... 15466 files and directories currently installed.)
Preparing to replace libusb-0.1-4 2:0.1.12-16 (using .../libusb-0.1-4_2%3a0.1.12-20+nmu1_amd64.deb) ...
Unpacking replacement libusb-0.1-4:amd64 ...
Setting up libusb-0.1-4:amd64 (2:0.1.12-20+nmu1) ...
(Reading database ... 15465 files and directories currently installed.)
Preparing to replace gnupg 1.4.10-4+squeeze1 (using .../gnupg_1.4.12-7_amd64.deb) ...
Unpacking replacement gnupg ...
Setting up gnupg (1.4.12-7) ...
Selecting previously unselected package libapt-pkg4.12:amd64.
dpkg: considering deconfiguration of apt, which would be broken by installation of libapt-pkg4.12:amd64 ...
dpkg: yes, will deconfigure apt (broken by libapt-pkg4.12:amd64)
(Reading database ... 15454 files and directories currently installed.)
Unpacking libapt-pkg4.12:amd64 (from .../libapt-pkg4.12_0.9.7.7_amd64.deb) ...
De-configuring apt ...
Setting up libapt-pkg4.12:amd64 (0.9.7.7) ...
(Reading database ... 15502 files and directories currently installed.)
Preparing to replace apt 0.8.10.3+squeeze1 (using .../archives/apt_0.9.7.7_amd64.deb) ...
Unpacking replacement apt ...
Setting up apt (0.9.7.7) ...
Installing new version of config file /etc/apt/apt.conf.d/01autoremove ...
Installing new version of config file /etc/cron.daily/apt ...
gpg: key B98321F9: "Squeeze Stable Release Key <debian-release at lists.debian.org>" not changed
gpg: key 473041FA: "Debian Archive Automatic Signing Key (6.0/squeeze) <ftpmaster at debian.org>" not changed
gpg: key 65FFB764: "Wheezy Stable Release Key <debian-release at lists.debian.org>" not changed
gpg: key 46925553: "Debian Archive Automatic Signing Key (7.0/wheezy) <ftpmaster at debian.org>" not changed
gpg: Total number processed: 4
gpg: unchanged: 4
gpg: checking the trustdb
gpg: WARNING: digest algorithm MD5 is deprecated
gpg: please see http://www.gnupg.org/faq/weak-digest-algos.html for more information
gpg: no ultimately trusted keys found
(Reading database ... 15412 files and directories currently installed.)
Preparing to replace libncurses5 5.7+20100313-5 (using .../libncurses5_5.9-10_amd64.deb) ...
Unpacking replacement libncurses5:amd64 ...
Setting up libncurses5:amd64 (5.9-10) ...
(Reading database ... 15404 files and directories currently installed.)
Preparing to replace libss2 1.41.12-4stable1 (using .../libss2_1.42.5-1_amd64.deb) ...
Unpacking replacement libss2:amd64 ...
Setting up libss2:amd64 (1.42.5-1) ...
(Reading database ... 15404 files and directories currently installed.)
Preparing to replace libnewt0.52 0.52.11-1 (using .../libnewt0.52_0.52.14-10_amd64.deb) ...
Unpacking replacement libnewt0.52 ...
Preparing to replace libpopt0 1.16-1 (using .../libpopt0_1.16-7_amd64.deb) ...
Unpacking replacement libpopt0:amd64 ...
Preparing to replace mawk 1.3.3-15 (using .../mawk_1.3.3-17_amd64.deb) ...
Unpacking replacement mawk ...
Selecting previously unselected package libgpg-error0:amd64.
Unpacking libgpg-error0:amd64 (from .../libgpg-error0_1.10-3.1_amd64.deb) ...
Selecting previously unselected package libgcrypt11:amd64.
Unpacking libgcrypt11:amd64 (from .../libgcrypt11_1.5.0-3_amd64.deb) ...
Selecting previously unselected package libp11-kit0:amd64.
Unpacking libp11-kit0:amd64 (from .../libp11-kit0_0.12-3_amd64.deb) ...
Selecting previously unselected package libtasn1-3:amd64.
Unpacking libtasn1-3:amd64 (from .../libtasn1-3_2.13-2_amd64.deb) ...
Selecting previously unselected package libgnutls26:amd64.
Unpacking libgnutls26:amd64 (from .../libgnutls26_2.12.20-4_amd64.deb) ...
Preparing to replace libgpm2 1.20.4-3.3 (using .../libgpm2_1.20.4-6_amd64.deb) ...
Unpacking replacement libgpm2:amd64 ...
Selecting previously unselected package libidn11:amd64.
Unpacking libidn11:amd64 (from .../libidn11_1.25-2_amd64.deb) ...
Preparing to replace file 5.04-5+squeeze2 (using .../archives/file_5.11-2_amd64.deb) ...
Unpacking replacement file ...
Preparing to replace libmagic1 5.04-5+squeeze2 (using .../libmagic1_5.11-2_amd64.deb) ...
Unpacking replacement libmagic1:amd64 ...
Preparing to replace x11-common 1:7.5+8+squeeze1 (using .../x11-common_1%3a7.7+1_all.deb) ...
Unpacking replacement x11-common ...
Preparing to replace libice6 2:1.0.6-2 (using .../libice6_2%3a1.0.8-2_amd64.deb) ...
Unpacking replacement libice6:amd64 ...
Selecting previously unselected package libitm1:amd64.
Unpacking libitm1:amd64 (from .../libitm1_4.7.2-5_amd64.deb) ...
Preparing to replace libjpeg62 6b1-1 (using .../libjpeg62_6b1-3_amd64.deb) ...
Unpacking replacement libjpeg62:amd64 ...
Selecting previously unselected package libjpeg8:amd64.
Unpacking libjpeg8:amd64 (from .../libjpeg8_8d-1_amd64.deb) ...
Preparing to replace libpaper1 1.1.24 (using .../libpaper1_1.1.24+nmu2_amd64.deb) ...
Unpacking replacement libpaper1:amd64 ...
Preparing to replace libsm6 2:1.1.1-1 (using .../libsm6_2%3a1.2.1-2_amd64.deb) ...
Unpacking replacement libsm6:amd64 ...
Selecting previously unselected package libjbig0:amd64.
Unpacking libjbig0:amd64 (from .../libjbig0_2.0-2_amd64.deb) ...
Preparing to replace libtiff4 3.9.4-5+squeeze8 (using .../libtiff4_3.9.6-11_amd64.deb) ...
Unpacking replacement libtiff4:amd64 ...
Preparing to replace libxext6 2:1.1.2-1 (using .../libxext6_2%3a1.3.1-2_amd64.deb) ...
Unpacking replacement libxext6:amd64 ...
Preparing to replace libxss1 1:1.2.0-2 (using .../libxss1_1%3a1.2.2-1_amd64.deb) ...
Unpacking replacement libxss1:amd64 ...
Preparing to replace libxt6 1:1.0.7-1 (using .../libxt6_1%3a1.1.3-1_amd64.deb) ...
Unpacking replacement libxt6:amd64 ...
Selecting previously unselected package libmpc2:amd64.
Unpacking libmpc2:amd64 (from .../libmpc2_0.9-4_amd64.deb) ...
Preparing to replace libxcb-render-util0 0.3.6-1 (using .../libxcb-render-util0_0.3.8-1.1_amd64.deb) ...
Unpacking replacement libxcb-render-util0:amd64 ...
Preparing to replace libpam-runtime 1.1.1-6.1+squeeze1 (using .../libpam-runtime_1.1.3-7.1_all.deb) ...
Unpacking replacement libpam-runtime ...
Setting up libpam-runtime (1.1.3-7.1) ...
(Reading database ... 15528 files and directories currently installed.)
Preparing to replace xz-utils 5.0.0-2 (using .../xz-utils_5.1.1alpha+20120614-2_amd64.deb) ...
Unpacking replacement xz-utils ...
Setting up xz-utils (5.1.1alpha+20120614-2) ...
update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode
(Reading database ... 15530 files and directories currently installed.)
Preparing to replace adduser 3.112+nmu2 (using .../adduser_3.113+nmu3_all.deb) ...
Unpacking replacement adduser ...
Preparing to replace vim 2:7.2.445+hg~cb94c42c0e1a-1 (using .../vim_2%3a7.3.547-7_amd64.deb) ...
Unpacking replacement vim ...
Preparing to replace vim-runtime 2:7.2.445+hg~cb94c42c0e1a-1 (using .../vim-runtime_2%3a7.3.547-7_all.deb) ...
Adding 'diversion of /usr/share/vim/vim73/doc/help.txt to /usr/share/vim/vim73/doc/help.txt.vim-tiny by vim-runtime'
Adding 'diversion of /usr/share/vim/vim73/doc/tags to /usr/share/vim/vim73/doc/tags.vim-tiny by vim-runtime'
Unpacking replacement vim-runtime ...
Removing 'diversion of /usr/share/vim/vim72/doc/help.txt to /usr/share/vim/vim72/doc/help.txt.vim-tiny by vim-runtime'
Removing 'diversion of /usr/share/vim/vim72/doc/tags to /usr/share/vim/vim72/doc/tags.vim-tiny by vim-runtime'
Preparing to replace vim-common 2:7.2.445+hg~cb94c42c0e1a-1 (using .../vim-common_2%3a7.3.547-7_amd64.deb) ...
Unpacking replacement vim-common ...
Preparing to replace wget 1.12-2.1 (using .../wget_1.13.4-3_amd64.deb) ...
Unpacking replacement wget ...
Preparing to replace whiptail 0.52.11-1 (using .../whiptail_0.52.14-10_amd64.deb) ...
Unpacking replacement whiptail ...
Preparing to replace debconf-i18n 1.5.36.1 (using .../debconf-i18n_1.5.49_all.deb) ...
Unpacking replacement debconf-i18n ...
Preparing to replace patch 2.6-2 (using .../patch_2.6.1-3_amd64.deb) ...
Unpacking replacement patch ...
Preparing to replace debootstrap 1.0.26+squeeze1 (using .../debootstrap_1.0.44_all.deb) ...
Unpacking replacement debootstrap ...
Preparing to replace dpkg-dev 1.15.8.13 (using .../dpkg-dev_1.16.9_all.deb) ...
Unpacking replacement dpkg-dev ...
Preparing to replace libdpkg-perl 1.15.8.13 (using .../libdpkg-perl_1.16.9_all.deb) ...
Unpacking replacement libdpkg-perl ...
Preparing to replace pbuilder 0.199+nmu1squeeze1 (using .../pbuilder_0.213_all.deb) ...
Unpacking replacement pbuilder ...
Preparing to replace cowdancer 0.62+nmu2 (using .../cowdancer_0.70_amd64.deb) ...
Unpacking replacement cowdancer ...
Preparing to replace cowbuilder 0.62+nmu2 (using .../cowbuilder_0.70_amd64.deb) ...
Unpacking replacement cowbuilder ...
Selecting previously unselected package cpp-4.7.
Unpacking cpp-4.7 (from .../cpp-4.7_4.7.2-5_amd64.deb) ...
Preparing to replace cpp 4:4.4.5-1 (using .../cpp_4%3a4.7.2-1_amd64.deb) ...
Unpacking replacement cpp ...
Preparing to replace eatmydata 26-1~bpo60+1 (using .../eatmydata_26-2_amd64.deb) ...
Unpacking replacement eatmydata ...
Selecting previously unselected package gcc-4.7.
Unpacking gcc-4.7 (from .../gcc-4.7_4.7.2-5_amd64.deb) ...
Preparing to replace gcc 4:4.4.5-1 (using .../gcc_4%3a4.7.2-1_amd64.deb) ...
Removing old gcc doc directory.
Unpacking replacement gcc ...
Selecting previously unselected package libstdc++6-4.7-dev.
Unpacking libstdc++6-4.7-dev (from .../libstdc++6-4.7-dev_4.7.2-5_amd64.deb) ...
Selecting previously unselected package g++-4.7.
Unpacking g++-4.7 (from .../g++-4.7_4.7.2-5_amd64.deb) ...
Preparing to replace g++ 4:4.4.5-1 (using .../g++_4%3a4.7.2-1_amd64.deb) ...
Unpacking replacement g++ ...
Preparing to replace r-base-core 2.11.1-6 (using .../r-base-core_2.15.1-4_amd64.deb) ...
Unpacking replacement r-base-core ...
Preparing to replace liblapack3gf 3.2.1-8 (using .../liblapack3gf_3.4.1-6_all.deb) ...
Unpacking replacement liblapack3gf ...
Preparing to replace libblas3gf 1.2-8 (using .../libblas3gf_1.2.20110419-5_all.deb) ...
Unpacking replacement libblas3gf ...
Selecting previously unselected package libblas3.
Unpacking libblas3 (from .../libblas3_1.2.20110419-5_amd64.deb) ...
update-alternatives: warning: alternative /usr/lib/libblas/libblas.so.3gf (part of link group libblas.so.3gf) doesn't exist; removing from list of alternatives
update-alternatives: warning: /etc/alternatives/libblas.so.3gf is dangling; it will be updated with best choice
Selecting previously unselected package libhdf5-7.
Unpacking libhdf5-7 (from .../libhdf5-7_1.8.8-9.1_amd64.deb) ...
Selecting previously unselected package liblapack3.
Unpacking liblapack3 (from .../liblapack3_3.4.1-6_amd64.deb) ...
update-alternatives: warning: alternative /usr/lib/lapack/liblapack.so.3gf (part of link group liblapack.so.3gf) doesn't exist; removing from list of alternatives
update-alternatives: warning: /etc/alternatives/liblapack.so.3gf is dangling; it will be updated with best choice
Preparing to replace libnuma1 2.0.5-1 (using .../libnuma1_2.0.8~rc4-1_amd64.deb) ...
Unpacking replacement libnuma1 ...
Preparing to replace libpaper-utils 1.1.24 (using .../libpaper-utils_1.1.24+nmu2_amd64.deb) ...
Unpacking replacement libpaper-utils ...
Preparing to replace libtorque2 2.4.8+dfsg-9squeeze1 (using .../libtorque2_2.4.16+dfsg-1_amd64.deb) ...
Unpacking replacement libtorque2 ...
Preparing to replace zip 3.0-3 (using .../archives/zip_3.0-6_amd64.deb) ...
Unpacking replacement zip ...
Preparing to replace unzip 6.0-4 (using .../archives/unzip_6.0-8_amd64.deb) ...
Unpacking replacement unzip ...
Preparing to replace xdg-utils 1.0.2+cvs20100307-2 (using .../xdg-utils_1.1.0~rc1+git20111210-6_all.deb) ...
Unpacking replacement xdg-utils ...
Preparing to replace tcl8.5 8.5.8-2 (using .../tcl8.5_8.5.11-2_amd64.deb) ...
Unpacking replacement tcl8.5 ...
Preparing to replace tk8.5 8.5.8-1 (using .../tk8.5_8.5.11-2_amd64.deb) ...
Unpacking replacement tk8.5 ...
Preparing to replace r-cran-hdf5 1.6.9-2+b1 (using .../r-cran-hdf5_1.6.10-1+b1_amd64.deb) ...
Unpacking replacement r-cran-hdf5 ...
Preparing to replace libibverbs1 1.1.3-2 (using .../libibverbs1_1.1.6-1_amd64.deb) ...
Unpacking replacement libibverbs1 ...
Preparing to replace libopenmpi1.3 1.4.2-4 (using .../libopenmpi1.3_1.4.5-1_amd64.deb) ...
Unpacking replacement libopenmpi1.3 ...
Setting up libc-dev-bin (2.13-38) ...
Setting up gcc-4.4-base:amd64 (4.4.7-2) ...
Setting up libgmp10:amd64 (2:5.0.5+dfsg-2) ...
Setting up libmpfr4:amd64 (3.1.0-5) ...
Setting up cpp-4.4 (4.4.7-2) ...
Setting up libgomp1:amd64 (4.7.2-5) ...
Setting up binutils (2.22-7.1) ...
Setting up gcc-4.4 (4.4.7-2) ...
Setting up linux-libc-dev:amd64 (3.2.35-2) ...
Setting up libc6-dev:amd64 (2.13-38) ...
Setting up libquadmath0:amd64 (4.7.2-5) ...
Setting up libgfortran3:amd64 (4.7.2-5) ...
Setting up make (3.81-8.2) ...
Setting up libexpat1:amd64 (2.1.0-1) ...
Setting up libfreetype6:amd64 (2.4.9-1.1) ...
Setting up ucf (3.0025+nmu3) ...
Setting up ttf-dejavu-core (2.33-3) ...
Setting up fontconfig-config (2.9.0-7.1) ...
Installing new version of config file /etc/fonts/conf.avail/65-nonlatin.conf ...
Installing new version of config file /etc/fonts/conf.avail/45-latin.conf ...
Installing new version of config file /etc/fonts/conf.avail/40-nonlatin.conf ...
Installing new version of config file /etc/fonts/conf.avail/30-urw-aliases.conf ...
Installing new version of config file /etc/fonts/conf.avail/30-metric-aliases.conf ...
Installing new version of config file /etc/fonts/fonts.dtd ...
Setting up libfontconfig1:amd64 (2.9.0-7.1) ...
Setting up libpixman-1-0:amd64 (0.26.0-4) ...
Setting up libpng12-0:amd64 (1.2.49-1) ...
Setting up libxau6:amd64 (1:1.0.7-1) ...
Setting up libxdmcp6:amd64 (1:1.1.1-1) ...
Setting up libxcb1:amd64 (1.8.1-2) ...
Setting up libx11-data (2:1.5.0-1) ...
Setting up libx11-6:amd64 (2:1.5.0-1) ...
Setting up libxcb-render0:amd64 (1.8.1-2) ...
Setting up libxcb-shm0:amd64 (1.8.1-2) ...
Setting up libxrender1:amd64 (1:0.9.7-1) ...
Setting up libcairo2:amd64 (1.12.2-3) ...
Setting up libffi5:amd64 (3.0.10-3) ...
Setting up libpcre3:amd64 (1:8.30-5) ...
Setting up libglib2.0-0:amd64 (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libthai-data (0.1.18-2) ...
Setting up libdatrie1:amd64 (0.2.5-3) ...
Setting up libthai0:amd64 (0.1.18-2) ...
Setting up libxft2:amd64 (2.3.1-1) ...
Setting up fontconfig (2.9.0-7.1) ...
Regenerating fonts cache... done.
Setting up libpango1.0-0:amd64 (1.30.0-1) ...
Setting up bzip2 (1.0.6-4) ...
Setting up libclass-isa-perl (0.36-3) ...
Setting up libgdbm3:amd64 (1.8.3-11) ...
Setting up libtext-iconv-perl (1.7-5) ...
Setting up libtext-charwidth-perl (0.04-7+b1) ...
Setting up liblocale-gettext-perl (1.05-7+b1) ...
Setting up libapt-inst1.5:amd64 (0.9.7.7) ...
Setting up apt-utils (0.9.7.7) ...
Setting up libnewt0.52 (0.52.14-10) ...
Setting up libpopt0:amd64 (1.16-7) ...
Setting up mawk (1.3.3-17) ...
Setting up libgpg-error0:amd64 (1.10-3.1) ...
Setting up libgcrypt11:amd64 (1.5.0-3) ...
Setting up libp11-kit0:amd64 (0.12-3) ...
Setting up libtasn1-3:amd64 (2.13-2) ...
Setting up libgnutls26:amd64 (2.12.20-4) ...
Setting up libgpm2:amd64 (1.20.4-6) ...
Setting up libidn11:amd64 (1.25-2) ...
Setting up libmagic1:amd64 (5.11-2) ...
Setting up file (5.11-2) ...
Setting up x11-common (1:7.7+1) ...
Installing new version of config file /etc/init.d/x11-common ...
Installing new version of config file /etc/X11/Xsession.d/50x11-common_determine-startup ...
[ ok ] Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix.
Setting up libice6:amd64 (2:1.0.8-2) ...
Setting up libitm1:amd64 (4.7.2-5) ...
Setting up libjpeg62:amd64 (6b1-3) ...
Setting up libjpeg8:amd64 (8d-1) ...
Setting up libpaper1:amd64 (1.1.24+nmu2) ...
Setting up libsm6:amd64 (2:1.2.1-2) ...
Setting up libjbig0:amd64 (2.0-2) ...
Setting up libtiff4:amd64 (3.9.6-11) ...
Setting up libxext6:amd64 (2:1.3.1-2) ...
Setting up libxss1:amd64 (1:1.2.2-1) ...
Setting up libxt6:amd64 (1:1.1.3-1) ...
Setting up libmpc2:amd64 (0.9-4) ...
Setting up libxcb-render-util0:amd64 (0.3.8-1.1) ...
Setting up adduser (3.113+nmu3) ...
Installing new version of config file /etc/deluser.conf ...
Setting up vim-common (2:7.3.547-7) ...
Setting up vim-runtime (2:7.3.547-7) ...
Processing /usr/share/vim/addons/doc
Setting up vim (2:7.3.547-7) ...
Setting up wget (1.13.4-3) ...
Setting up whiptail (0.52.14-10) ...
Setting up debconf-i18n (1.5.49) ...
Setting up patch (2.6.1-3) ...
Setting up debootstrap (1.0.44) ...
Setting up cowdancer (0.70) ...
Setting up cpp-4.7 (4.7.2-5) ...
Setting up cpp (4:4.7.2-1) ...
Setting up eatmydata (26-2) ...
Setting up gcc-4.7 (4.7.2-5) ...
Setting up gcc (4:4.7.2-1) ...
Setting up zip (3.0-6) ...
Setting up unzip (6.0-8) ...
Setting up libpaper-utils (1.1.24+nmu2) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-6) ...
Setting up libblas3 (1.2.20110419-5) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up liblapack3 (3.4.1-6) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up tcl8.5 (8.5.11-2) ...
Setting up tk8.5 (8.5.11-2) ...
Setting up r-base-core (2.15.1-4) ...
Installing new version of config file /etc/bash_completion.d/R ...
Installing new version of config file /etc/R/Makeconf ...
Installing new version of config file /etc/R/ldpaths ...
Installing new version of config file /etc/R/repositories ...
Setting R_PAPERSIZE_USER default to 'a4'
Replacing config file /etc/R/Renviron with new version
Setting up liblapack3gf (3.4.1-6) ...
Setting up libblas3gf (1.2.20110419-5) ...
Setting up libhdf5-7 (1.8.8-9.1) ...
Setting up libnuma1 (2.0.8~rc4-1) ...
Setting up libtorque2 (2.4.16+dfsg-1) ...
Setting up r-cran-hdf5 (1.6.10-1+b1) ...
Setting up libibverbs1 (1.1.6-1) ...
Setting up libopenmpi1.3 (1.4.5-1) ...
Setting up libstdc++6-4.7-dev (4.7.2-5) ...
Setting up g++-4.4 (4.4.7-2) ...
Setting up libswitch-perl (2.16-2) ...
Setting up g++-4.7 (4.7.2-5) ...
Setting up g++ (4:4.7.2-1) ...
Setting up libstdc++6-4.4-dev (4.4.7-2) ...
Setting up perl-modules (5.14.2-18) ...
Setting up perl (5.14.2-18) ...
Setting up libdpkg-perl (1.16.9) ...
Setting up dpkg-dev (1.16.9) ...
Setting up pbuilder (0.213) ...
Installing new version of config file /etc/bash_completion.d/pbuilder ...
Setting up cowbuilder (0.70) ...
Installing new version of config file /etc/bash_completion.d/cowbuilder ...
root at c7test:/#
root at c7test:/# dpkg -l | grep hdf5
ii libhdf5-7 1.8.8-9.1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-openmpi-1.8.4 1.8.4-patch1-2 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version
ii r-cran-hdf5 1.6.10-1+b1 amd64 GNU R package interfacing the NCSA HDF5 library
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