1.4. Compiling EMBOSS

After you have configured EMBOSS then the compilation stage consists of typing only one command:


This should be done in the same directory from which you invoked the configure command. Most operating systems come complete with a suitable make program. If the make command is not found then install it from your distribution DVD/CDs or install the GNU make application (recommended) from a freeware site or compile it from its source code (available from http://www.gnu.org/gnu/make/). Linux and MacOSX distributions come complete with GNU make.

You will see hundreds of lines scroll up your screen as compilation progresses. The EMBOSS libraries (plplot, ajax [this is composed of several sub-libraries] and nucleus) will be compiled first, followed by the applications themselves. Compilation times will vary according to the power of your processor. On a 3GHz processor it will typically take less than a handful of minutes.

If you have a multi-processor machine then you can speed up the compilation by specifying how many processors to use. e.g.

make -j 4

will specify the use of four processors (or two processors with hyperthreading enabled).

After compilation has completed successfully you will see something similar to the following at the bottom of your screen.

Making all in utils
make[2]: Entering directory `/usr/local/src/EMBOSS-6.1.0/jemboss/utils'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/usr/local/src/EMBOSS-6.1.0/jemboss/utils'
make[2]: Entering directory `/usr/local/src/EMBOSS-6.1.0/jemboss'
Not compiling Jemboss
make[2]: Leaving directory `/usr/local/src/EMBOSS-6.1.0/jemboss'
make[1]: Leaving directory `/usr/local/src/EMBOSS-6.1.0/jemboss'
make[1]: Entering directory `/usr/local/src/EMBOSS-6.1.0'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/usr/local/src/EMBOSS-6.1.0'

1.4.1. Reporting Compilation Errors

If the compilation failed prematurely then recheck the platform-specific notes (Section 1.7, “EMBOSS Installation: Platform-specific Concerns”) for your operating system to make sure you have all the prerequisites installed; then reconfigure and try again assuming you spotted a mistake. If all else fails then email emboss-bug@emboss.open-bio.org for help including:

  • The output from the configure command.

  • The screen output from the make command (not just the last few lines).

  • The config.status file.

  • The config.log file.

You can capture the output from (e.g.) the make command using one of:

make >&! make.out [csh shells]
make > make.out 2>&1 [sh shells]

Use the same method for reporting the output of the configure command.