A commonly reported error is that the operating system does not recognise any EMBOSS commands e.g. Command not found is reported when typing embossversion. The most common causes are that the compilation failed or that the PATH was incorrectly set. If you are unsure whether the compilation has failed then look for the executables in the bin directory appropriate for your configuration. For example, if you used --prefix=/usr/local/emboss in your configuration then, after the make install look in the /usr/local/emboss/bin directory for the executables. If they are there then check your PATH as described above. If the executables are not there then study the output of the make command carefully, particularly the last few lines, as they should give you some idea why the compilation failed. It may be useful to re-check the prerequisite section of this chapter for your operating system.

Pre-EMBOSS 6.1.0 the most common compilation error was that, in mid-compilation, the compiler stopped and reported that lX11 could not be found. This was always because, whereas the operating system's X11 server files had been installed, the X11 development files hadn't. See the recommendations for X11 in the prerequisites section of this chapter for your operating system if you get this error compiling older versions of EMBOSS. After installing the correct system files you should do a make clean and perform the configure command again.

The most recent distributions of EMBOSS test more extensively for the presence of X11 files and should report their absence during the configuration stage. You therefore should not get the error mentioned in the paragraph above. If you do then please contact the EMBOSS development team emboss-bug@emboss.open-bio.org with details of your operating system and, as a file, the screen output from the configure command.