EMBOSS FAQ (Frequently Asked Questions)

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Q) I have an AMD64/Opteron/EM64T system. How do I prevent the compiled programs giving segmentation faults?

A) Start with a fresh extraction of the EMBOSS source and, before configuring, type (for all the above systems):

   setenv CC "cc -D__amd64__"           [csh/tcsh shells]  or
   export CC="cc -D__amd64__"           [bash/sh]

Note that the above is case sensitive, there is only one space character between the quotes and that there are 4 underscores in total (two each side of the amd64).

Q) I have a Linux system and compilation ends prematurely saying that it can't find the -lX11 libraries ... but I know I have X11 installed.

A) You may well have the X11 server installed but you haven't installed the X11 development files. For example, on RPM distributions, you need to install:

     xorg-x11-devel           (xorg-based X11 distros) or
     XFree86-devel            (XFree86-based X11 distros)

Q) I'm trying to compile EMBOSS with the PNG support

A) If you have gd-1.7.3, zlib-1.1.3 and libpng-1.0.5 or greater then the normal configure/compile should work! However, due to gd no longer supporting gif format then you may need to install gd, zlib and libpng locally.

You can unpack the tar.gz files in any directory, and install them in a common area.

By default everything (including EMBOSS) installs in /usr/local but in the examples below we use /home/joe/local

Note: gd does not use a ./configure script, and will fail at the "make install" stage if the installation directory does not have a /bin subdirectory. You can create this directory (e.g. /home/joe/local/bin) if it does not already exist.

To install, pick up the sources (jpeg is optional) and then:

   gunzip -c zlib-1.1.4.tar.gz   | tar xf -
   gunzip -c libpng-1.2.5.tar.gz | tar xf -
   gunzip -c jpegsrc.v6b.tar.gz | tar xf -
   gunzip -c gd-2.0.9.tar.gz     | tar xf -

   ln -s zlib-1.1.4   zlib
   ln -s jpeg-6b jpeg
   ln -s libpng-1.2.5 libpng
   ln -s gd-2.0.9     gd

If these directories do not exist, "make install" for jpeg will need them:

   mkdir /home/joe/local/bin
   mkdir /home/joe/local/man
   mkdir /home/joe/local/man/man1

   cd zlib
   ./configure --prefix=/home/joe/local
   make
   make install
   cd ..

   cd jpeg
   ./configure --prefix=/home/joe/local
   make
   make test
   make install
   cd ..

   cd libpng
   ./configure --prefix=/home/joe/local

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EMBOSS FAQ (Frequently Asked Questions)