From b.harrison at louisville.edu Sun Apr 3 13:17:10 2016 From: b.harrison at louisville.edu (b.harrison at louisville.edu) Date: Sun, 3 Apr 2016 17:17:10 +0000 Subject: [Bio-linux-devel] Bug in upgrade8.sh, please help to fix. Message-ID: There is a bug in upgrade8.sh: It tries to install google chrome from an old PPA that does not now exist. Google removed this PPA. Unfortunately, this problem causes the whole update script to fail. Could you please update the script with the working chrome PPA. It would do it myself, but the script is greek to me. Great work with biolinux!! Ben -------------- next part -------------- An HTML attachment was scrubbed... URL: From gawbul at gmail.com Mon Apr 4 09:18:40 2016 From: gawbul at gmail.com (Steve Moss) Date: Mon, 4 Apr 2016 14:18:40 +0100 Subject: [Bio-linux-devel] Bug in upgrade8.sh, please help to fix. In-Reply-To: References: Message-ID: Dear Ben, I think this is to do with them dropping 32-bit support for Linux binaries? Maybe to do with public key verification too? Run the following command to install their public key (or is this already included in the bio-linux-keyring package, anyone)? wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | sudo apt-key add - Then you can manually edit */etc/apt/sources.list.d/google-chrome.list* and replace the line in there with: deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main Then do a sudo apt-get update and try installing again? Should be relatively easy to update these settings in the script? I've submitted a PR - can remove the apt-key add line if it is already in bio-linux-keyring. https://github.com/environmentalomics/build-bio-linux/pull/2 Cheers, Steve --- *Dr. Stephen Moss* e: gawbul at gmail.com www: https://gawbul.github.io On 3 April 2016 at 18:17, wrote: > There is a bug in upgrade8.sh: > > It tries to install google chrome from an old PPA that does not now exist. > Google removed this PPA. > > Unfortunately, this problem causes the whole update script to fail. Could > you please update the script with the working chrome PPA. It would do it > myself, but the script is greek to me. > > Great work with biolinux!! > > Ben > > _______________________________________________ > Bio-Linux-devel mailing list > Bio-Linux-devel at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-devel > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Fri Apr 8 06:37:00 2016 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 8 Apr 2016 11:37:00 +0100 Subject: [Bio-linux-devel] Errors when updating the APT database Message-ID: <570789CC.6090901@minke-informatics.co.uk> Hi, I've just submitted this bug-report: > The i386 version of the Google Chrome directory is searched for by default causing errors when updating the APT database: > > apt update > Ign http://extras.ubuntu.com trusty InRelease > Ign http://nebc.nerc.ac.uk unstable InRelease > Ign http://ppa.launchpad.net precise InRelease > ... > Hit http://security.ubuntu.com trusty-security/multiverse Translation-en > Hit http://security.ubuntu.com trusty-security/restricted Translation-en > Hit http://security.ubuntu.com trusty-security/universe Translation-en > Fetched 4,357 kB in 8s (538 kB/s) > W: Failed to fetch http://dl.google.com/linux/chrome/deb/dists/stable/Release Unable to find expected entry 'main/binary- > i386/Packages' in Release file (Wrong sources.list entry or malformed file) > > E: Some index files failed to download. They have been ignored, or old ones used instead. > > The "google-chrome-stable" package installs an update script that updates the source list: > > /etc/cron.daily/google-chrome > > This script reads "/etc/default/" and updates the APT list once on installation or upgrade, but the package can never be upgraded if the entry is incorrect. The work-around is to 'fake' an upgrade: > > --- ./.old/google-chrome.201602192326 2016-02-19 23:26:34.014962970 +0000 > +++ google-chrome 2016-04-08 11:23:43.857313469 +0100 > @@ -1,2 +1,2 @@ > -repo_add_once="false" > +repo_add_once="true" > repo_reenable_on_distupgrade="true" > > Then, run the update script: > > /etc/cron.daily/google-chrome > > This will correct the APT sources list: > > diff -Naur google-chrome.list.save google-chrome.list > --- google-chrome.list.save 2016-03-22 21:57:14.751417979 +0000 > +++ google-chrome.list 2016-04-08 11:11:01.409333455 +0100 > @@ -1,3 +1,3 @@ > ### THIS FILE IS AUTOMATICALLY CONFIGURED ### > # You may comment out this entry, but any other modifications may be lost. > -deb http://dl.google.com/linux/chrome/deb/ stable main > +deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main > > [The APT sources list could just be edited by hand at present, but Google may change the URL in future] > > 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