'Manually' probably means not using a package manager - either with the configure/make dance, or with a binary installer like Google Earth used for a long time. In those cases, you still need to sort out dependencies manually.
apt-get install <something-in-repository-or-ppa-you-added>
dpkg -i <some-random-deb-you-downloaded>
But a quick apt-get -f install after I get those errors sorts it out.
Random downloading of debs from Web sites could lead to a situation where a different version of a dependency is needed. "foo needs libnaff-ubuntu345 but libnaff-ubuntu345 is not going to be installed" type errors result.