From tony.travis at abdn.ac.uk Sat Jan 17 10:15:09 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Sat, 17 Jan 2015 15:15:09 +0000 Subject: [Bio-linux-dev] Ubuntu installer bug Message-ID: <54BA7C7D.8000703@abdn.ac.uk> Hi, Tim. I've accidentally overwritten the Windows 8 installation on my colleague's UEFI Acer laptop because of a bug in the Bio-Linux/Ubuntu "Ubiquity" installer: https://bugs.launchpad.net/ubuntu/+source/ubiquity/+bug/1265192 I booted from the Bio-Linux 8.0.5 .iso, but Windows 8 was not detected and I was not offered the option of installing Linux alongside Windows 8. So, I resized the main Windows 8 partition using "gparted" and then installed Bio-Linux from the "Something else" option in the installer GUI. Bio-Linux booted from the hard disk OK, but Windows 8 did not boot from the Windows loader option in the GRUB menu. Eventually, after changing the UEFI boot options, I was able to boot Windows again, but not Bio-Linux. After several reboots, I could no longer boot Bio-Linux. Apparently, Windows 8 detects the changes Ubiquity makes as 'corruption' and 'repairs' them from a copy of its own files. I decided to re-install Bio-Lunux to see if I could find out how to make the Ubiquity boot persistent, but this time the installer detected Ubuntu already installed and one option it offered was to "re-install" Ubuntu. I selected this option expecting to be told what it was going to do and then asked if I wanted to continue. However, the Ubiquity installer IMMEDIATELY overwrote the entire hard disk, destroying the Windows 8 installation completely. I've salvaged what I can from the laptop's hard disk using "testdisk/photorec", but this is my colleague's laptop and we didn't make a Windows 8 recovery USB-stick before installing Linux so I'll have to contact Acer support to see if they can help! This is the first time I've ever had problems installing Bio-Linux, but UEFI has seriously complicated matters :-( Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Mon Jan 19 06:34:20 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 19 Jan 2015 11:34:20 +0000 Subject: [Bio-linux-dev] Ubuntu installer bug In-Reply-To: <54BA7C7D.8000703@abdn.ac.uk> References: <54BA7C7D.8000703@abdn.ac.uk> Message-ID: <1421667260.14602.42.camel@wllt1771.nerc-wallingford.ac.uk> Hi Tony, This is particularly galling as I've actually been tracking the bug you linked to and applied the patch (see comment 55) on Bio-Linux some time ago. It appears that when I updated the ISO to 8.0.5 I got a new version of Ubiquity that clobbered my manual patch but didn't actually fix the bug. I've now updated the Ubiquity package to 2.18.8.3 and I'm rolling a 8.0.5.1 ISO for the website, so hopefully that fixes it for future users. As an aside, I attempted to install dual-boot on my new new personal laptop (a Yoga 2 Pro) over the weekend and completely trashed Windows without the help of this bug, so I'd agree that yes UEFI really is making it hard to get things working. At least for me the resolution was simple - leave Windows off. Hopefully you can get your colleague's laptop fixed too. Cheers, TIM On Sat, 2015-01-17 at 15:15 +0000, Tony Travis wrote: > Hi, Tim. > > I've accidentally overwritten the Windows 8 installation on my > colleague's UEFI Acer laptop because of a bug in the Bio-Linux/Ubuntu > "Ubiquity" installer: > > https://bugs.launchpad.net/ubuntu/+source/ubiquity/+bug/1265192 > > I booted from the Bio-Linux 8.0.5 .iso, but Windows 8 was not detected > and I was not offered the option of installing Linux alongside Windows > 8. So, I resized the main Windows 8 partition using "gparted" and then > installed Bio-Linux from the "Something else" option in the installer > GUI. Bio-Linux booted from the hard disk OK, but Windows 8 did not boot > from the Windows loader option in the GRUB menu. Eventually, after > changing the UEFI boot options, I was able to boot Windows again, but > not Bio-Linux. After several reboots, I could no longer boot Bio-Linux. > Apparently, Windows 8 detects the changes Ubiquity makes as 'corruption' > and 'repairs' them from a copy of its own files. > > I decided to re-install Bio-Lunux to see if I could find out how to make > the Ubiquity boot persistent, but this time the installer detected > Ubuntu already installed and one option it offered was to "re-install" > Ubuntu. I selected this option expecting to be told what it was going to > do and then asked if I wanted to continue. However, the Ubiquity > installer IMMEDIATELY overwrote the entire hard disk, destroying the > Windows 8 installation completely. I've salvaged what I can from the > laptop's hard disk using "testdisk/photorec", but this is my colleague's > laptop and we didn't make a Windows 8 recovery USB-stick before > installing Linux so I'll have to contact Acer support to see if they can > help! > > This is the first time I've ever had problems installing Bio-Linux, but > UEFI has seriously complicated matters :-( > > Bye, > > Tony. > > -- > Dr. A.J.Travis, University of Aberdeen, Institute of Biological and > Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen > AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 > http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis > > > > The University of Aberdeen is a charity registered in Scotland, No SC013683. > Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From tony.travis at abdn.ac.uk Tue Jan 20 06:45:36 2015 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Tue, 20 Jan 2015 11:45:36 +0000 Subject: [Bio-linux-dev] Installing Bio-Linux on old Sun Server In-Reply-To: References: Message-ID: <54BE3FE0.5080007@abdn.ac.uk> On 20/01/15 11:25, Mahendra Modi wrote: > Dear Tony & Tim. > > I have a old Sun Fire X4440 server with 4 x quad-core Opteron CPU and 48 > GB RAM. I am trying to install Bio-linux on it. However after the > Try/install option, the screen goes blank. I am presuming that the video > adapter (ASPEED AST2000) is not compatible and as such Bio-linux is not > being able to get itself displayed. Do you think this may be the case > and if so can you suggest a workaround? Hi, Mahendra. When you boot from the USB-stick, press the [space] bar as soon as you see the boot screen. Choose the language, then, press [F6] followed by [Esc] and change the kernel options. In particular, delete the "quiet" and "splash" and add "nomodeset". You will also need to change these options on the installed Bio-Linux. HTH, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tony.travis at minke-informatics.co.uk Fri Jan 30 09:47:59 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 30 Jan 2015 14:47:59 +0000 Subject: [Bio-linux-dev] Jemboss not launching from MATE Message-ID: <54CB999F.1070003@minke-informatics.co.uk> Hi, Tim. The MATE/Gnome menu "Jemboss" tries to launch: /usr/bin/jemboss However, "Jemboss" is now launched from: /usr/bin/runJemboss.sh I've put in a link: /usr/bin/jemboss -> runJemboss.sh Now working properly on a remote MATE desktop. HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk