[EMBOSS] problems installing EMBOSS under Cygwin

[Jon Ison]

Hi Andreas

I don't think you got a reply to this.  I've had a trawl through the
messages to the EMBOSS lists ... perhaps some of the following will
help (I'm no expert on cygwin) ?  A port of EMBOSS 3 to windows will
be made available soonish - so you'll never need to use cygwin again.

Cheers

Jon



1. Apply all the fixes from:
ftp://emboss.open-bio.org/pub/EMBOSS/fixes/

2. Update cygwin
Problems can arise from using older versions of cygwin, or selective
("pick and choose") installations of cygwin.

Download a new, completely fresh copy of cygwin (the cygwin updating
mechanism has proved unsatisfactory) and accept the default packages;
best to get a pretty complete set of cygwin packages.

If you decide to install a fresh copy then be sure to delete any cygwin
registry entries after deleting the cygwin directory: see (1) DELETING
CYGWIN below (email emboss-bug if the registry fixing script cygtidy.reg
is not available on the website).
Your cygwin installation directory should be around 1.5 - 2Gb in size.

3. Read the instructions on the web, but see the corrections (1) to
that text, which haven't made it onto the website yet:
http://emboss.sourceforge.net/download/cygwin.html

The instructions imply that --without-x is essential, whereas X windows
works fine as long as you've installed it under cygwin. It also suggests
using CFLAGS=-s to the configure, presumably to strip the binaries. This
should not be required as the latest cygwin distributions automatically
strip the binaries.



(1) CORRECTIONS / ADDITIONS

1) install cygwin (http://www.cygwin.com). That's surely possible to
compile without it, but it's making everything easier. You'll have to
install the base part plus the devel/make and devel/gcc
packages. Before installing, see the first line of 2). Then you'll
have a linux-like command-line with tools like gcc and make. The paths
are then made according to the place where you installed cygwin (ex:
c\cygwin becomes /).

Notes from the EMBOSS developers: We recommend doing a full cygwin
installation or problems may arise with creating the DLLs.


3) quit and restart the cygwin bash (you'll start in your
"FirstName_LastName" directory, you can delete "FirstName LastName"),
download the EMBOSS package and cd to the place where you uncompressed
it. Follow the usual procedure:

./configure --without-x CFLAGS=-s
make
make install

--without-x because at one point the X11 library is required (even if
useless) and without this flag the compilation would stop. CFLAGS=-s
to make the binaries smaller.

Notes from the EMBOSS developers: If you have done a reasonably full
cygwin installation then you can leave out the --without-x switch. X
will work perfectly well if installed. Also, with later cygwin
installations, you can omit the CFLAGS=-s switch. We also recommend
providing a prefix switch to install EMBOSS in a specified
location. The configuration then becomes:

./configure --prefix=/usr/local/emboss
make
make install

After installation make sure that /usr/local/emboss/bin is in your PATH.

DELETING CYGWIN
To delete cygwin you should drag your cygwin installation directory to
the recycle bin. Then delete any cygwin entries from the 'start'
menu. You should then download the file cygtidy.reg and double-click
it to remove any cygwin registry entries.




> Hi, I download Emboss package and tried to install it under cygwin. I
> keep getting the error message cc1.exe - Entry Point not found The
> procedure entry point_impure_ptr could not be located in the dynamic
> link library cygwin1.dll when I try to run the: "./configure --without-x
> CFLAGS=-s" command. I am using:
> cygwin: 1.5.19-4
> gcc: 3.4.4-1
> It seems that my cygwin installation might not have worked, i.e. there
> is an incompatibility issue between GCC and Cygwin. Any suggestions?
> Thanks a lot
> Andreas
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