I don't consider myself a total noob, but compiling and installing software is a pain and problem I cannot overcome. I just want to run down through my understanding of this process with someone more knowledgeable to clear my mind to get to the next level. Many scientific software I need are not distributed as packages. I understand ./configure sets up the compilation variables and checking for dependencies make does the compilation sudo make install puts all the libraries and bins in their places. However it never works. I rarely get out of the a) ./configure stage without entering dependency hell, and if I do, b) sudo make install will probably nuke my box. a) The dependency hell is very frustrating. Sometimes I have the library, but it doesn't like it. Or the library doesn't want to install. Or configure can't find it. Or my distro placed it somewhere it shouldn't be. Or there are two versions in my system. Problem is, I can't understand how to diagnose and therefore fix these problems. What are some good references to learn for someone who doesn't need to become a programmer?b) My understanding is make install will replace some libraries and change settings without my package manager being aware of this. Therefore, some programs won't run, others can't be updated. So, if I don't use make install, and just keep the compiled binary in my user directory with a symbolic link added to the PATH, will I be in the clear? Finally, some philosophical positions. I love free (as in beer and freedom) software, but in my line of work I can't afford to be dogmatic about it - I need the program to install. Also, my box is single user, has tons of free HD so I don't really care about having multiple (dozens) of copies of libraries if that will solve my problems. Space is cheap. I appreciate your help and patience.  G
Installing from source. How to resolve dependencies without destroying the package manager
software installation;make
Most packages will have a <package>-dev (for Debian based) or <package>-devel (for Red Hat based) that will be the libraries needed to link against for building.So, for example if the source says it requires libxml, in Debian based systems you'll find libxml2 and libxml2-dev (use apt-cache search <dependancy> to find them).You'll need the libxml2-dev to build it, and libxml2 to run it.The ./configure step usually supports flags like --with-libxml=/usr/lib/ to point it at the correct libraries (./configure --help should list all of the options). It also usually supports changing the install location with --prefix=$HOME/sw. Using a prefix outside of what your package manager controls is the best way to avoid conflicts with package manager installed software.On Debian & derivatives using a --prefix of /usr/local/ or /opt/local/ should be safe.If a library (or version) you need isn't available from the package manager just download the source and compile it using similar options. Most importantly use a --prefix outside of your package manager and when compiling the software you really want use --with-<library>=/<path/to/installed/library>.