[Bio-linux-dev] Bio-Linux upgrade problems
Tony Travis
tony.travis at ed.ac.uk
Mon Jun 3 14:41:15 EDT 2013
On 03/06/13 15:59, Tim Booth wrote:
> [...]
> Regarding the 3.5 series kernel, this is already the default in the
> latest Bio-Linux ISO, but it is not the default if you upgrade from BL6
> - you get 3.2 the same as other Ubuntu upgraders. My logic is that the
> new kernel is most useful for those with new hardware and thus not
> relevant to most upgraders. (I'm using 3.2 until I see a good reason
> not to - it never seems to crash on my laptop and everything works)
Hi, Tim.
I checked again because I was sure that you had based Bio-Linux 7.0.6 on
Ubuntu 12.04.1 LTS, from what I read in your 7.0.6 iso's .disk/info:
> ajt at beluga:~/Downloads/iso$ sudo mount -o ro,loop bio-linux-7.0.6.iso /mnt
> ajt at beluga:~/Downloads/iso$ cd /mnt/.disk
> ajt at beluga:/mnt/.disk$ ls
> base_installable casper-uuid-generic cd_type info release_notes_url
> ajt at beluga:/mnt/.disk$ cat info
> Bio-Linux 7 based on Ubuntu 12.04.1 LTS "Precise Pangolin" - Release amd64 (20120823.1)
As far as I can see, Bio-Linux 7.0.6 *is* based on 12.04.1 LTS, but with
the 3.5 kernel package installed. This is the cause of some of my
problems, because the X.org stack from 12.04.1 LTS is not compatible
with some of the drivers in the X.org stack from 12.04.2 LTS...
I've compared the package inventories of Ubuntu 12.04.1 and 12.04.2 LTS,
and the main difference (apart from the quantal kernel) is the X.org
stack. However, only the quantal kernel is present in Bio-Linux 7.0.6.
The other 12.04.2 LTS quantal packages and dependencies are missing:
> ajt at beluga:~/src/dpkg-util/dpkg-dsel$ fgrep quantal bio-linux-7.0.6-filesystem.manifest
> linux-image-generic-lts-quantal 3.5.0.26.33
These desktop 'selections' are based on the casper filesystem manifests
on the iso, with the packages from filesystem.manifest-removed and
should represent the output from "dpkg --get-selections" on a newly
installed instance. The attached Makefile and dpkg-audit script are what
I'm using to check the package inventories of upgraded systems.
I'll audit the package inventory on a running instance of Bio-Linux
7.0.6 under VirtualBox and let you know what I find. BTW, there are some
duplicate entries in your Bio-Linux 7.0.6 filesystem.manifest.
HTH,
Tony.
> ajt at beluga:~/src/dpkg-util/dpkg-dsel$ diff ubuntu-12.04.1-desktop.sel ubuntu-12.04.2-desktop.sel
> 454a455
>> libdrm-nouveau2 install
> 487a489
>> libframe6 install
> 512a515
>> libgeis1 install
> 518,520c521,523
> < libgl1-mesa-dri install
> < libgl1-mesa-glx install
> < libglapi-mesa install
> ---
>> libgl1-mesa-dri-lts-quantal install
>> libgl1-mesa-glx-lts-quantal install
>> libglapi-mesa-lts-quantal install
> 553a557
>> libgrail5 install
> 595,596d598
> < libidl0 install
> < libidl-common install
> 636c638
> < libllvm3.0 install
> ---
>> libllvm3.1 install
> 693d694
> < liborbit2 install
> 856,859d856
> < libutouch-evemu1 install
> < libutouch-frame1 install
> < libutouch-geis1 install
> < libutouch-grail1 install
> 894c891
> < libxatracker1 install
> ---
>> libxatracker1-lts-quantal install
> 921a919
>> libxrandr-ltsq2 install
> 939,944c937,942
> < linux-generic install
> < linux-headers-3.2.0-29 install
> < linux-headers-3.2.0-29-generic install
> < linux-headers-generic install
> < linux-image-3.2.0-29-generic install
> < linux-image-generic install
> ---
>> linux-generic-lts-quantal install
>> linux-headers-3.5.0-23 install
>> linux-headers-3.5.0-23-generic install
>> linux-headers-generic-lts-quantal install
>> linux-image-3.5.0-23-generic install
>> linux-image-generic-lts-quantal install
> 1297a1296
>> x11-xserver-utils-lts-quantal install
> 1317,1346c1316,1346
> < xserver-xorg install
> < xserver-xorg-core install
> < xserver-xorg-input-all install
> < xserver-xorg-input-evdev install
> < xserver-xorg-input-mouse install
> < xserver-xorg-input-synaptics install
> < xserver-xorg-input-vmmouse install
> < xserver-xorg-input-wacom install
> < xserver-xorg-video-all install
> < xserver-xorg-video-ati install
> < xserver-xorg-video-cirrus install
> < xserver-xorg-video-fbdev install
> < xserver-xorg-video-intel install
> < xserver-xorg-video-mach64 install
> < xserver-xorg-video-mga install
> < xserver-xorg-video-neomagic install
> < xserver-xorg-video-nouveau install
> < xserver-xorg-video-openchrome install
> < xserver-xorg-video-qxl install
> < xserver-xorg-video-r128 install
> < xserver-xorg-video-radeon install
> < xserver-xorg-video-s3 install
> < xserver-xorg-video-savage install
> < xserver-xorg-video-siliconmotion install
> < xserver-xorg-video-sis install
> < xserver-xorg-video-sisusb install
> < xserver-xorg-video-tdfx install
> < xserver-xorg-video-trident install
> < xserver-xorg-video-vesa install
> < xserver-xorg-video-vmware install
> ---
>> xserver-common-lts-quantal install
>> xserver-xorg-core-lts-quantal install
>> xserver-xorg-input-all-lts-quantal install
>> xserver-xorg-input-evdev-lts-quantal install
>> xserver-xorg-input-mouse-lts-quantal install
>> xserver-xorg-input-synaptics-lts-quantal install
>> xserver-xorg-input-vmmouse-lts-quantal install
>> xserver-xorg-input-wacom-lts-quantal install
>> xserver-xorg-lts-quantal install
>> xserver-xorg-video-all-lts-quantal install
>> xserver-xorg-video-ati-lts-quantal install
>> xserver-xorg-video-cirrus-lts-quantal install
>> xserver-xorg-video-fbdev-lts-quantal install
>> xserver-xorg-video-intel-lts-quantal install
>> xserver-xorg-video-mach64-lts-quantal install
>> xserver-xorg-video-mga-lts-quantal install
>> xserver-xorg-video-modesetting-lts-quantal install
>> xserver-xorg-video-neomagic-lts-quantal install
>> xserver-xorg-video-nouveau-lts-quantal install
>> xserver-xorg-video-openchrome-lts-quantal install
>> xserver-xorg-video-r128-lts-quantal install
>> xserver-xorg-video-radeon-lts-quantal install
>> xserver-xorg-video-s3-lts-quantal install
>> xserver-xorg-video-savage-lts-quantal install
>> xserver-xorg-video-siliconmotion-lts-quantal install
>> xserver-xorg-video-sis-lts-quantal install
>> xserver-xorg-video-sisusb-lts-quantal install
>> xserver-xorg-video-tdfx-lts-quantal install
>> xserver-xorg-video-trident-lts-quantal install
>> xserver-xorg-video-vesa-lts-quantal install
>> xserver-xorg-video-vmware-lts-quantal install
-------------- next part --------------
# @(#)Makefile 2013-06-03 A.J.Travis
#
# Create a dselect-upgrade 'selections' file from Ubuntu to Bio-Linux
#
PREFIX=/usr/local
SCRIPT=dpkg-dsel
SELECT=ubuntu-12.04.1-desktop.sel ubuntu-12.04.2-desktop.sel bio-linux-7.0.6-desktop.sel
all: $(SCRIPT) $(SELECT)
install: $(SCRIPT) $(SELECT)
install -Dp $(SCRIPT) $(PREFIX)/bin/
install -Dp $(SELECT) $(PREFIX)/share/dpkg-dsel/
clean:
rm -f $(BIOLINUX)-filesystem.manifest-desktop
clobber: clean
rm -f $(SELECT)
.SECONDARY:
%-filesystem.manifest-desktop: %-filesystem.manifest %-filesystem.manifest-remove
sort $*-filesystem.manifest | uniq | grep -vf $*-filesystem.manifest-remove > $@
%-desktop.sel: %-filesystem.manifest-desktop
awk '{ printf("%-48sinstall\n", $$1) }' $< > $@
-------------- next part --------------
#!/usr/bin/perl -w
#@(#)dpkg-audit.pl 2013-05-24 A.J.Travis
#
# Audit installed packages against distribution manifest
#
open( LIST, "<$ARGV[0]" ) || die "can't open $ARGV[0]";
open( DPKG, "dpkg --get-selections |" )
|| die "can't run dpkg";
open( OUT, "| unexpand -a | sort" ) || die "can't run sort";
# read manifest
while (<LIST>) {
chomp;
( $name, $sel ) = split;
$pkg{$name} = $sel;
}
close LIST;
# read selections
while (<DPKG>) {
chomp;
( $name, $sel ) = split;
if ( !defined $pkg{$name} ) {
if ( $sel eq "install" ) {
$pkg{$name} = "deinstall";
}
}
else {
if ( $pkg{$name} eq $sel ) {
delete $pkg{$name};
}
}
}
close DPKG;
# write updated selections
while ( ( $name, $sel ) = each %pkg ) {
printf OUT "%-48s%s\n", $name, $sel;
}
close OUT;
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