Hi Hans,
On Mon, Oct 26, 2015 at 4:38 AM, Hans Joachim Desserud <[email protected]> wrote: >>Sorry, but I don't know how to navigate the site very well and didn't > know about "View full publishing history". > > No problem, we've all been there. The link is a bit hidden in the > corner. :P Thanks for your understanding! That page is a bit overwhelming... >>Very much so! I wasn't aware of Ubuntu's policy with new packages > after it's been release. > > To elaborate a bit, once the development cycle starts, packages get > automatically synced from Debian (unless there's some Ubuntu-specific > changes, in which case they need to be manually merged). Then around > halfway through, there's an import freeze and focus on > bugfixes/stabilizing. It is still possibly to request syncs, but towards > the end there's less changes happening. Then once the release is out, > development continues in the next development release, but in certain > cases updates and fixes for severe issues are applied to the packages in > the archive. These are often minimal changes in order to reduce the > potential for introducing new issues. > > For an overview (and more details for each point) you can take a look at > the release schedule for Xenial at > https://wiki.ubuntu.com/XenialXerus/ReleaseSchedule. I see. The cycle makes sense. I guess for those of us not who don't look ahead at upcoming releases, we only find out a program is missing when we finally upgrade when it's finally released. By then, it's a bit too late, isn't it? I guess I should be looking ahead a bit...at least before I upgrade! By the way, I forgot to mention, when I typed "cufflinks", I get this message: $ cufflinks The program 'cufflinks' is currently not installed. You can install it by typing: sudo apt-get install cufflinks That also led me to believe I had somehow upgraded to 15.10 incorrectly [i.e., missing repository, etc.]. Shall I file a bug report with the command-not-found package? >>I will try building it from source myself with Boost 1.59, then. > > Cool. It would be really nice if you could post a comment on how it > goes. Presumably, Ubuntu/Debian will want to package a newer version of > boost at some point and it would be nice to know whether this package > starts working again or whether additional fixes will be required. I was successful. (I couldn't wait -- I do need to use this program.) The upstream instructions (https://github.com/cole-trapnell-lab/cufflinks) are interesting. Under step #1 of "Installing Boost", it clearly says that only 1.55 or lower is supported. Support is suppose to start from 1.59. I guess someone has complained upstream already to have such a message explicitly stated... Also, * I cloned from Git rather than used the tarball, which was from May 2014. There are two dependencies: eigen and samtools. a) I couldn't get it to work with the libeigen3-dev package. So, I downloaded the eigen source and compiled it according to its instructions. b) samtools made a jump [http://sourceforge.net/projects/samtools/files/samtools/] from 0.1.20 to 1.0 last year. I had to go back to the old version in order to ./configure properly. If the new series is backward compatible source-wise, it might just be a problem with the configure script's parsing of version numbers. Unfortunately, I'm not very good at looking at Autoconf scripts to fix it... So, it works and the instructions upstream may be a year old, but seems still relevant. There is some eigen and samtools redundancy with an Ubuntu system. Maybe someone can figure out what to do with the cufflinks source code... Anyway, I guess someone looking for cufflinks might come across this thread. Maybe the above will be of some help! Thanks Hans for all your help! Ray PS: Now to find out if there are any runtime errors....... :-) -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1509813 Title: Missing package from Wily (15.10)? To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/cufflinks/+bug/1509813/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
