[COOT] problem in coot installation in ubuntu

[Rimi]

Hi all,
  I am new to coot. Recently I tried to install coot in my ubuntu
gutsy. But it can not find mmdb library somehow. Below is the message

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
checking for library containing strerror... none required
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ANSI C... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ANSI C... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for a sed that does not truncate output... /bin/sed
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking how to run the C++ preprocessor... g++ -E
checking for g77... g77
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether g77 accepts -g... yes
checking the maximum length of command line arguments... 32768
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... ranlib
checking for strip... strip
checking if gcc static flag  works... yes
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc supports -c -o file.o... yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC
checking if g++ PIC flag -fPIC works... yes
checking if g++ supports -c -o file.o... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g77 option to produce PIC... -fPIC
checking if g77 PIC flag -fPIC works... yes
checking if g77 supports -c -o file.o... yes
checking whether the g77 linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking for ranlib... (cached) ranlib
checking sys/stdtypes.h usability... no
checking sys/stdty

Re: [COOT] problem in coot installation in ubuntu

[Kevin Cowtan]

Hi!

Firstly, do you need to build coot at all? There are binary packages 
which work just fine on Gutsy. You can install them wherever you want on 
your system, and they should just work.


Secondly, if for some reason you do want to build your own (you want to 
make changes to the code???), then are you using the 
build-it-gtk2-simple script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of messing 
around with dependencies. With this script it is usually pretty easy.


Kevin

Rimi wrote:

Hi all,
  I am new to coot. Recently I tried to install coot in my ubuntu
gutsy. But it can not find mmdb library somehow. Below is the message

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Since Ubuntu has gotten to be popular (for good reason, IMO), it might be
useful to have an official (or at least semi-official) debian package whose
installation would guarantee all the dependencies also get installed.  I've
tried to do it in a half-arsed sort of way, but lately have dropped the ball
(sorry).
On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan <[EMAIL PROTECTED]>wrote:

> Hi!
>
> Firstly, do you need to build coot at all? There are binary packages which
> work just fine on Gutsy. You can install them wherever you want on your
> system, and they should just work.
>
> Secondly, if for some reason you do want to build your own (you want to
> make changes to the code???), then are you using the build-it-gtk2-simple
> script?
>
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
> Building coot without this script requires days or weeks of messing around
> with dependencies. With this script it is usually pretty easy.
>
> Kevin
>
>
> Rimi wrote:
>
>> Hi all,
>>  I am new to coot. Recently I tried to install coot in my ubuntu
>> gutsy. But it can not find mmdb library somehow. Below is the message
>>
>


-- 
-


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

Please reply to:  [EMAIL PROTECTED]

Re: [COOT] problem in coot installation in ubuntu

[Tim Fenn]

On Wed, 12 Nov 2008 09:03:34 + Kevin Cowtan
<[EMAIL PROTECTED]> wrote:

> 
> Secondly, if for some reason you do want to build your own (you want
> to make changes to the code???), then are you using the 
> build-it-gtk2-simple script?
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
> Building coot without this script requires days or weeks of messing 
> around with dependencies. With this script it is usually pretty easy.
> 

Why does coot require a 3000 line hand written shell script to set up
the build process?

-Tim

-- 
-

Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
Stanford, CA  94305-5432
Phone:  (650) 736-1714
FAX:  (650) 736-1961

-

Re: [COOT] problem in coot installation in ubuntu

[Kevin Cowtan]

Tim Fenn wrote:

Why does coot require a 3000 line hand written shell script to set up
the build process?


Well, if you look at the script (which I guess you have), then I think 
you already have the answer... which suggests to me that I have 
misunderstood the question. Maybe the question you are actually asking 
is not the one which is obtained by a simple surface reading of your 
message. Could you clarify perhaps?


Thanks,
Kevin

Re: [COOT] problem in coot installation in ubuntu

[Tim Fenn]

On Thu, 13 Nov 2008 09:58:20 + Kevin Cowtan
<[EMAIL PROTECTED]> wrote:

> Tim Fenn wrote:
> > Why does coot require a 3000 line hand written shell script to set
> > up the build process?
> 
> Well, if you look at the script (which I guess you have), then I
> think you already have the answer... which suggests to me that I have 
> misunderstood the question. Maybe the question you are actually
> asking is not the one which is obtained by a simple surface reading
> of your message. Could you clarify perhaps?
> 

It was rhetorical - why not just use autoconf to do all the dirty work?

Also, is the idea to migrate all of the scripting away from guile and
towards python, or update the guile dependencies (as it seems goosh is
part of the os process module now, guile-gtk is deprecated in favor of
guile-gnome, guile net-http and guile-gui look unsupported...)?  I'd
like to begin preparing a rpm for fedora (now that most of the
dependencies are part of the distributions), but their peer review
process might screen out unsupported deps...

Regards,
Tim

-- 
-

Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
Stanford, CA  94305-5432
Phone:  (650) 736-1714
FAX:  (650) 736-1961

-

Re: [COOT] problem in coot installation in ubuntu

[Lynn F. Ten Eyck]

Having tried various forms of building Coot, and looked at several  
Linux and OS X system variants, I can assure you that an autoconf  
build would fail most of the time due to missing dependencies.  Coot  
not only uses a lot of packages, it needs specific versions of many of  
these packages.  This means that an autoconfigure version has to have  
a LARGE number of "--with-XXX=path" directives for those cases in  
which Coot need a version of a package that is either newer or older  
than that provided by the distro.


The build script has its own problems, since Paul doesn't have a  
sourceforge-like build farm.  It's still better than the alternatives  
at this time.


Lynn Ten Eyck
On 14 Nov 2008, at 00:02, Tim Fenn wrote:


On Thu, 13 Nov 2008 09:58:20 + Kevin Cowtan
<[EMAIL PROTECTED]> wrote:


Tim Fenn wrote:

Why does coot require a 3000 line hand written shell script to set
up the build process?


Well, if you look at the script (which I guess you have), then I
think you already have the answer... which suggests to me that I have
misunderstood the question. Maybe the question you are actually
asking is not the one which is obtained by a simple surface reading
of your message. Could you clarify perhaps?



It was rhetorical - why not just use autoconf to do all the dirty  
work?


Also, is the idea to migrate all of the scripting away from guile and
towards python, or update the guile dependencies (as it seems goosh is
part of the os process module now, guile-gtk is deprecated in favor of
guile-gnome, guile net-http and guile-gui look unsupported...)?  I'd
like to begin preparing a rpm for fedora (now that most of the
dependencies are part of the distributions), but their peer review
process might screen out unsupported deps...

Regards,
Tim

--
-

   Tim Fenn
   [EMAIL PROTECTED]
   Stanford University, School of Medicine
   James H. Clark Center
   318 Campus Drive, Room E300
   Stanford, CA  94305-5432
   Phone:  (650) 736-1714
   FAX:  (650) 736-1961

-

Re: [COOT] problem in coot installation in ubuntu

[Mark Brooks]

Hi,

It may be useful to have a 'contrib' section for the Coot binary download
web page (or even some unofficial web page), so that we have more options of
binaries to test. For example, upon upgrading to Ubuntu Hardy Heron, Coot
stopped working, for reasons beyond my understanding, but worked when
recompiled. (Which was very easy using the build-it-gtk2-simple script BTW).
To have a central repository of tested binaries could be very handy, to
avoid having to do this.

The Coot developers and yourself (Bill) have done an enormous amount to
furnish us with working, tested programs,  but perhaps one or two more
updated binaries contributed by users  would be useful, especially for newer
releases of the myriad Linux flavours.

I think for the Coot developers to start providing .deb, .rpm and Gentoo
packages for every update is too onerous, especially when .tar.gz files work
OK. Just my opinion.

Which Ubuntu are you on Bill, and which binary are you using? Are these on
your debian web site? I guess I may be able to give a Hardy Heron binary if
need be.

Thanks for your .debs though, I use them all the time.

Mark

2008/11/12 William G. Scott <[EMAIL PROTECTED]>

> Since Ubuntu has gotten to be popular (for good reason, IMO), it might be
> useful to have an official (or at least semi-official) debian package whose
> installation would guarantee all the dependencies also get installed.  I've
> tried to do it in a half-arsed sort of way, but lately have dropped the ball
> (sorry).
>
> On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan <[EMAIL PROTECTED]>wrote:
>
>> Hi!
>>
>> Firstly, do you need to build coot at all? There are binary packages which
>> work just fine on Gutsy. You can install them wherever you want on your
>> system, and they should just work.
>>
>> Secondly, if for some reason you do want to build your own (you want to
>> make changes to the code???), then are you using the build-it-gtk2-simple
>> script?
>>
>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
>> Building coot without this script requires days or weeks of messing around
>> with dependencies. With this script it is usually pretty easy.
>>
>> Kevin
>>
>>
>> Rimi wrote:
>>
>>> Hi all,
>>>  I am new to coot. Recently I tried to install coot in my ubuntu
>>> gutsy. But it can not find mmdb library somehow. Below is the message
>>>
>>
>
>
> --
> -
>
>
> William G. Scott
>
> contact info:  
> http://chemistry.ucsc.edu/~wgscott
>
> Please reply to:  [EMAIL PROTECTED]
>
>
>
>


-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Hi Mark et al:

The last coot I compiled on Ubuntu Hardy was coot-0.5-pre-1- 
revision-1003.  I've been a bit distracted with other obligations. The  
last one I made into a debian package and put on our server was a
0.4-pre-2release, so I apologize. I keep the OS X fink debian  
packages much more up to date and have tried to maintain those,  
officially (via fink), to a much higher standard.


I don't fully understand the linux debian packaging requirements  
nearly well enough, but should probably take the time to do so, and to  
create standard-compliant debian packages for coot and its  
dependencies and then figure out how to get these things into the  
official distribution system.  I guess if someone else out there with  
the competence and time can do for Debian/Ubuntu what Donnie Berkholz  
has done for Gentoo, it would be helpful.  What is needed are properly  
created debian packages for clipper, mmdb, gpp4, ssm, coot, and a few  
of the other misc dependencies that aren't present in a standard linux  
distribution.


Once you have that, you can use the program alien to convert to rpm,  
etc.


My main limitations are knowledge, time, only one PC running only one  
version of ubuntu, and more specifically getting a complete listing of  
dependencies so that package installation for the end-user is truly  
seamless.  This has been my goal with OSX/fink, and I've invested most  
of my time and effort into that. Linux should actually be much easier,  
but I don't know it nearly as well. I've also now just been put into a  
tailspin by our main funding agency, so I will now have to prioritize  
further, or find something else to do for a living.


Peace and joy,

Bill




On Nov 15, 2008, at 3:32 AM, Mark Brooks wrote:


Hi,

It may be useful to have a 'contrib' section for the Coot binary  
download
web page (or even some unofficial web page), so that we have more  
options of
binaries to test. For example, upon upgrading to Ubuntu Hardy Heron,  
Coot

stopped working, for reasons beyond my understanding, but worked when
recompiled. (Which was very easy using the build-it-gtk2-simple  
script BTW).
To have a central repository of tested binaries could be very handy,  
to

avoid having to do this.

The Coot developers and yourself (Bill) have done an enormous amount  
to

furnish us with working, tested programs,  but perhaps one or two more
updated binaries contributed by users  would be useful, especially  
for newer

releases of the myriad Linux flavours.

I think for the Coot developers to start providing .deb, .rpm and  
Gentoo
packages for every update is too onerous, especially when .tar.gz  
files work

OK. Just my opinion.

Which Ubuntu are you on Bill, and which binary are you using? Are  
these on
your debian web site? I guess I may be able to give a Hardy Heron  
binary if

need be.

Thanks for your .debs though, I use them all the time.

Mark

2008/11/12 William G. Scott <[EMAIL PROTECTED]>

Since Ubuntu has gotten to be popular (for good reason, IMO), it  
might be
useful to have an official (or at least semi-official) debian  
package whose
installation would guarantee all the dependencies also get  
installed.  I've
tried to do it in a half-arsed sort of way, but lately have dropped  
the ball

(sorry).

On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan  
<[EMAIL PROTECTED]>wrote:



Hi!

Firstly, do you need to build coot at all? There are binary  
packages which
work just fine on Gutsy. You can install them wherever you want on  
your

system, and they should just work.

Secondly, if for some reason you do want to build your own (you  
want to
make changes to the code???), then are you using the build-it-gtk2- 
simple

script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of  
messing around

with dependencies. With this script it is usually pretty easy.

Kevin


Rimi wrote:


Hi all,
I am new to coot. Recently I tried to install coot in my  
ubuntu
gutsy. But it can not find mmdb library somehow. Below is the  
message







--
-


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott


Please reply to:  [EMAIL PROTECTED]







--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[Paul Emsley]

It was rhetorical - why not just use autoconf to do all the dirty work?


Like Lynn Ten Eyck says, autoconf configures dependences, it doesn't 
build them (AFAICS, anyway).



Also, is the idea to migrate all of the scripting away from guile and
towards python, 


No.


or update the guile dependencies (as it seems goosh is
part of the os process module now, 


OK, Noted.


guile-gtk is deprecated in favor of
guile-gnome, 


I've not heard that.


guile net-http and guile-gui look unsupported...)?


Yes, they are tiny packages that could easily subsumed into Coot itself 
for ease of packaging (as Bill Scott once suggested).  Not done, no-one 
complained enough.



 I'd
like to begin preparing a rpm for fedora (now that most of the
dependencies are part of the distributions),


Good going!  MATSUURA Takanori and Adam Huffman said they'd like to do 
something similar.



but their peer review
process might screen out unsupported deps...


Hmm... Fingers crossed we'll get the mmdb license issues sorted soon.

Paul.

Re: [COOT] problem in coot installation in ubuntu

[Paul Emsley]

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on 
crystallographic libs for Ubuntu, e.g.:


https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:

Hi,

It may be useful to have a 'contrib' section for the Coot binary 
download web page (or even some unofficial web page), so that we have 
more options of binaries to test. For example, upon upgrading to Ubuntu 
Hardy Heron, Coot stopped working, for reasons beyond my understanding, 
but worked when recompiled. (Which was very easy using the 
build-it-gtk2-simple script BTW). To have a central repository of tested 
binaries could be very handy, to avoid having to do this.


The Coot developers and yourself (Bill) have done an enormous amount to 
furnish us with working, tested programs,  but perhaps one or two more 
updated binaries contributed by users  would be useful, especially for 
newer releases of the myriad Linux flavours.


I think for the Coot developers to start providing .deb, .rpm and Gentoo 
packages for every update is too onerous, especially when .tar.gz files 
work OK. Just my opinion.


Which Ubuntu are you on Bill, and which binary are you using? Are these 
on your debian web site? I guess I may be able to give a Hardy Heron 
binary if need be.


Thanks for your .debs though, I use them all the time.

Mark

2008/11/12 William G. Scott <[EMAIL PROTECTED] 
>


Since Ubuntu has gotten to be popular (for good reason, IMO), it
might be useful to have an official (or at least semi-official)
debian package whose installation would guarantee all the
dependencies also get installed.  I've tried to do it in a
half-arsed sort of way, but lately have dropped the ball (sorry). 


On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
<[EMAIL PROTECTED] > wrote:

Hi!

Firstly, do you need to build coot at all? There are binary
packages which work just fine on Gutsy. You can install them
wherever you want on your system, and they should just work.

Secondly, if for some reason you do want to build your own (you
want to make changes to the code???), then are you using the
build-it-gtk2-simple script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of
messing around with dependencies. With this script it is usually
pretty easy.

Kevin


Rimi wrote:

Hi all,
 I am new to coot. Recently I tried to install coot
in my ubuntu
gutsy. But it can not find mmdb library somehow. Below is
the message




-- 
-



William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott


Please reply to:  [EMAIL PROTECTED]







--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[Donnie Berkholz]

On 02:16 Sun 16 Nov , Paul Emsley wrote:
>> It was rhetorical - why not just use autoconf to do all the dirty 
>> work?
>
> Like Lynn Ten Eyck says, autoconf configures dependences, it doesn't 
> build them (AFAICS, anyway).

Well, autoconf does have a command to kick off another configure script 
as a child, so this can be done.

The (superior, I think) approach that we're using for a similar 
situation is based on GARNOME, a way of getting bleeding-edge GNOME. 
Take a look at 
http://oregonstate.edu/~benisong/software/releases/burrow-installer-1.4.tar.gz 
-- it's basically an easy way of building any required dependencies. 
Certainly looks a lot simpler than the existing script.

In our case, it's a total of ~1300 lines, but around 1000 of those are 
taken directly from GARNOME.

-- 
Thanks,
Donnie

Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com


pgpD0nTFd9r10.pgp
Description: PGP signature

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

That's great.  In the short term, highly unofficial/unauthorized/ 
zeroth-order coot and dependencies for i386 linux:


debians:




rpms (made via alien from above):




These include mmdb, ssm, gpp4, fftw (in the form required for clipper  
and coot), clipper, coot, which will install into /usr/local/xtal


and then the various guile-type dependencies, which will install into / 
usr



On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on  
crystallographic libs for Ubuntu, e.g.:


https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:

Hi,
It may be useful to have a 'contrib' section for the Coot binary  
download web page (or even some unofficial web page), so that we  
have more options of binaries to test. For example, upon upgrading  
to Ubuntu Hardy Heron, Coot stopped working, for reasons beyond my  
understanding, but worked when recompiled. (Which was very easy  
using the build-it-gtk2-simple script BTW). To have a central  
repository of tested binaries could be very handy, to avoid having  
to do this.
The Coot developers and yourself (Bill) have done an enormous  
amount to furnish us with working, tested programs,  but perhaps  
one or two more updated binaries contributed by users  would be  
useful, especially for newer releases of the myriad Linux flavours.
I think for the Coot developers to start providing .deb, .rpm and  
Gentoo packages for every update is too onerous, especially  
when .tar.gz files work OK. Just my opinion.
Which Ubuntu are you on Bill, and which binary are you using? Are  
these on your debian web site? I guess I may be able to give a  
Hardy Heron binary if need be.

Thanks for your .debs though, I use them all the time.
Mark
2008/11/12 William G. Scott <[EMAIL PROTECTED] >

   Since Ubuntu has gotten to be popular (for good reason, IMO), it
   might be useful to have an official (or at least semi-official)
   debian package whose installation would guarantee all the
   dependencies also get installed.  I've tried to do it in a
   half-arsed sort of way, but lately have dropped the ball  
(sorry). On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan

   <[EMAIL PROTECTED] > wrote:
   Hi!
   Firstly, do you need to build coot at all? There are binary
   packages which work just fine on Gutsy. You can install them
   wherever you want on your system, and they should just work.
   Secondly, if for some reason you do want to build your own  
(you

   want to make changes to the code???), then are you using the
   build-it-gtk2-simple script?
   
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
   Building coot without this script requires days or weeks of
   messing around with dependencies. With this script it is  
usually

   pretty easy.
   Kevin
   Rimi wrote:
   Hi all,
I am new to coot. Recently I tried to install  
coot

   in my ubuntu
   gutsy. But it can not find mmdb library somehow. Below is
   the message
   --  
-

   William G. Scott
   contact info:  http://chemistry.ucsc.edu/~wgscott
   
   Please reply to:  [EMAIL PROTECTED]
   
--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[Mark Brooks]

Astounding!

Thanks to all involved.

Mark

2008/11/16 William G. Scott <[EMAIL PROTECTED]>

> That's great.  In the short term, highly
> unofficial/unauthorized/zeroth-order coot and dependencies for i386 linux:
>
> debians:
>
> <
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files
> >
>
> rpms (made via alien from above):
>
> <
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages
> >
>
> These include mmdb, ssm, gpp4, fftw (in the form required for clipper and
> coot), clipper, coot, which will install into /usr/local/xtal
>
> and then the various guile-type dependencies, which will install into /usr
>
>
>
> On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:
>
>  FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on
>> crystallographic libs for Ubuntu, e.g.:
>>
>> https://launchpad.net/ubuntu/+source/clipper
>> https://launchpad.net/ubuntu/+source/mmdb
>>
>> When he gets round to Coot I'm keen to help make his life easier.
>>
>> Regards,
>>
>> Paul.
>>
>>
>> Mark Brooks wrote:
>>
>>> Hi,
>>> It may be useful to have a 'contrib' section for the Coot binary download
>>> web page (or even some unofficial web page), so that we have more options of
>>> binaries to test. For example, upon upgrading to Ubuntu Hardy Heron, Coot
>>> stopped working, for reasons beyond my understanding, but worked when
>>> recompiled. (Which was very easy using the build-it-gtk2-simple script BTW).
>>> To have a central repository of tested binaries could be very handy, to
>>> avoid having to do this.
>>> The Coot developers and yourself (Bill) have done an enormous amount to
>>> furnish us with working, tested programs,  but perhaps one or two more
>>> updated binaries contributed by users  would be useful, especially for newer
>>> releases of the myriad Linux flavours.
>>> I think for the Coot developers to start providing .deb, .rpm and Gentoo
>>> packages for every update is too onerous, especially when .tar.gz files work
>>> OK. Just my opinion.
>>> Which Ubuntu are you on Bill, and which binary are you using? Are these
>>> on your debian web site? I guess I may be able to give a Hardy Heron binary
>>> if need be.
>>> Thanks for your .debs though, I use them all the time.
>>> Mark
>>> 2008/11/12 William G. Scott <[EMAIL PROTECTED] >> [EMAIL PROTECTED]>>
>>>   Since Ubuntu has gotten to be popular (for good reason, IMO), it
>>>   might be useful to have an official (or at least semi-official)
>>>   debian package whose installation would guarantee all the
>>>   dependencies also get installed.  I've tried to do it in a
>>>   half-arsed sort of way, but lately have dropped the ball (sorry).
>>> On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
>>>   <[EMAIL PROTECTED] > wrote:
>>>   Hi!
>>>   Firstly, do you need to build coot at all? There are binary
>>>   packages which work just fine on Gutsy. You can install them
>>>   wherever you want on your system, and they should just work.
>>>   Secondly, if for some reason you do want to build your own (you
>>>   want to make changes to the code???), then are you using the
>>>   build-it-gtk2-simple script?
>>>
>>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
>>>   Building coot without this script requires days or weeks of
>>>   messing around with dependencies. With this script it is usually
>>>   pretty easy.
>>>   Kevin
>>>   Rimi wrote:
>>>   Hi all,
>>>I am new to coot. Recently I tried to install coot
>>>   in my ubuntu
>>>   gutsy. But it can not find mmdb library somehow. Below is
>>>   the message
>>>   --
>>> -
>>>   William G. Scott
>>>   contact info:  
>>> http://chemistry.ucsc.edu/~wgscott
>>>   
>>>   Please reply to:  [EMAIL PROTECTED]
>>>   
>>> --
>>> Mark BROOKS
>>> Telephone: 0169157968
>>> Fax: 0169853715
>>> Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
>>> UMR8619 - Bât 430 - Université de Paris-Sud
>>> 91405 Orsay CEDEX
>>> Skype: markabrooks
>>>
>>


-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[Mark Brooks]

Hi,

I just tested it on a freshly installed system for a student; it works very
well on Ubuntu Hardy.

I'm not sure why "nxnode" is a dependency of the Coot .deb though! (Although
that doesn't bother me too much- I would advise anyone to use NX ).

Thanks again,

Mark

2008/11/16 William G. Scott <[EMAIL PROTECTED]>

> That's great.  In the short term, highly
> unofficial/unauthorized/zeroth-order coot and dependencies for i386 linux:
>
> debians:
>
> <
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files
> >
>
> rpms (made via alien from above):
>
> <
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages
> >
>
> These include mmdb, ssm, gpp4, fftw (in the form required for clipper and
> coot), clipper, coot, which will install into /usr/local/xtal
>
> and then the various guile-type dependencies, which will install into /usr
>
>
>
> On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:
>
>  FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on
>> crystallographic libs for Ubuntu, e.g.:
>>
>> https://launchpad.net/ubuntu/+source/clipper
>> https://launchpad.net/ubuntu/+source/mmdb
>>
>> When he gets round to Coot I'm keen to help make his life easier.
>>
>> Regards,
>>
>> Paul.
>>
>>
>> Mark Brooks wrote:
>>
>>> Hi,
>>> It may be useful to have a 'contrib' section for the Coot binary download
>>> web page (or even some unofficial web page), so that we have more options of
>>> binaries to test. For example, upon upgrading to Ubuntu Hardy Heron, Coot
>>> stopped working, for reasons beyond my understanding, but worked when
>>> recompiled. (Which was very easy using the build-it-gtk2-simple script BTW).
>>> To have a central repository of tested binaries could be very handy, to
>>> avoid having to do this.
>>> The Coot developers and yourself (Bill) have done an enormous amount to
>>> furnish us with working, tested programs,  but perhaps one or two more
>>> updated binaries contributed by users  would be useful, especially for newer
>>> releases of the myriad Linux flavours.
>>> I think for the Coot developers to start providing .deb, .rpm and Gentoo
>>> packages for every update is too onerous, especially when .tar.gz files work
>>> OK. Just my opinion.
>>> Which Ubuntu are you on Bill, and which binary are you using? Are these
>>> on your debian web site? I guess I may be able to give a Hardy Heron binary
>>> if need be.
>>> Thanks for your .debs though, I use them all the time.
>>> Mark
>>> 2008/11/12 William G. Scott <[EMAIL PROTECTED] >> [EMAIL PROTECTED]>>
>>>   Since Ubuntu has gotten to be popular (for good reason, IMO), it
>>>   might be useful to have an official (or at least semi-official)
>>>   debian package whose installation would guarantee all the
>>>   dependencies also get installed.  I've tried to do it in a
>>>   half-arsed sort of way, but lately have dropped the ball (sorry).
>>> On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
>>>   <[EMAIL PROTECTED] > wrote:
>>>   Hi!
>>>   Firstly, do you need to build coot at all? There are binary
>>>   packages which work just fine on Gutsy. You can install them
>>>   wherever you want on your system, and they should just work.
>>>   Secondly, if for some reason you do want to build your own (you
>>>   want to make changes to the code???), then are you using the
>>>   build-it-gtk2-simple script?
>>>
>>> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
>>>   Building coot without this script requires days or weeks of
>>>   messing around with dependencies. With this script it is usually
>>>   pretty easy.
>>>   Kevin
>>>   Rimi wrote:
>>>   Hi all,
>>>I am new to coot. Recently I tried to install coot
>>>   in my ubuntu
>>>   gutsy. But it can not find mmdb library somehow. Below is
>>>   the message
>>>   --
>>> -
>>>   William G. Scott
>>>   contact info:  
>>> http://chemistry.ucsc.edu/~wgscott
>>>   
>>>   Please reply to:  [EMAIL PROTECTED]
>>>   
>>> --
>>> Mark BROOKS
>>> Telephone: 0169157968
>>> Fax: 0169853715
>>> Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
>>> UMR8619 - Bât 430 - Université de Paris-Sud
>>> 91405 Orsay CEDEX
>>> Skype: markabrooks
>>>
>>


-- 
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Woops.  I didn't see that.  I auto-generated the list of dependencies  
from the output of ldd on the coot binary, upon which I then used dpgk  
-S to find the corresponding packages. For some reason it generated  
this falsely (the library is also present, but ldd does not report  
coot linking anything with NX in the path).


Sorry, I will edit this out.

Thanks for testing.

Bill



On Nov 17, 2008, at 3:16 AM, Mark Brooks wrote:


Hi,

I just tested it on a freshly installed system for a student; it  
works very

well on Ubuntu Hardy.

I'm not sure why "nxnode" is a dependency of the Coot .deb though!  
(Although

that doesn't bother me too much- I would advise anyone to use NX ).

Thanks again,

Mark

2008/11/16 William G. Scott <[EMAIL PROTECTED]>


That's great.  In the short term, highly
unofficial/unauthorized/zeroth-order coot and dependencies for i386  
linux:


debians:

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files




rpms (made via alien from above):

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages




These include mmdb, ssm, gpp4, fftw (in the form required for  
clipper and

coot), clipper, coot, which will install into /usr/local/xtal

and then the various guile-type dependencies, which will install  
into /usr




On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on

crystallographic libs for Ubuntu, e.g.:

https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:


Hi,
It may be useful to have a 'contrib' section for the Coot binary  
download
web page (or even some unofficial web page), so that we have more  
options of
binaries to test. For example, upon upgrading to Ubuntu Hardy  
Heron, Coot
stopped working, for reasons beyond my understanding, but worked  
when
recompiled. (Which was very easy using the build-it-gtk2-simple  
script BTW).
To have a central repository of tested binaries could be very  
handy, to

avoid having to do this.
The Coot developers and yourself (Bill) have done an enormous  
amount to
furnish us with working, tested programs,  but perhaps one or two  
more
updated binaries contributed by users  would be useful,  
especially for newer

releases of the myriad Linux flavours.
I think for the Coot developers to start providing .deb, .rpm and  
Gentoo
packages for every update is too onerous, especially when .tar.gz  
files work

OK. Just my opinion.
Which Ubuntu are you on Bill, and which binary are you using? Are  
these
on your debian web site? I guess I may be able to give a Hardy  
Heron binary

if need be.
Thanks for your .debs though, I use them all the time.
Mark
2008/11/12 William G. Scott <[EMAIL PROTECTED] >
 Since Ubuntu has gotten to be popular (for good reason, IMO), it
 might be useful to have an official (or at least semi-official)
 debian package whose installation would guarantee all the
 dependencies also get installed.  I've tried to do it in a
 half-arsed sort of way, but lately have dropped the ball (sorry).
On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
 <[EMAIL PROTECTED] > wrote:
 Hi!
 Firstly, do you need to build coot at all? There are binary
 packages which work just fine on Gutsy. You can install them
 wherever you want on your system, and they should just work.
 Secondly, if for some reason you do want to build your own  
(you

 want to make changes to the code???), then are you using the
 build-it-gtk2-simple script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
 Building coot without this script requires days or weeks of
 messing around with dependencies. With this script it is  
usually

 pretty easy.
 Kevin
 Rimi wrote:
 Hi all,
  I am new to coot. Recently I tried to install  
coot

 in my ubuntu
 gutsy. But it can not find mmdb library somehow. Below is
 the message
 --
-
 William G. Scott
 contact info:  http://chemistry.ucsc.edu/~wgscott

 
 Please reply to:  [EMAIL PROTECTED]
 
--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks






--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Oh, in case anyone is wondering how I did this (and how I screwed it  
up), the correct command should have been:


dpkg -S $(  ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $3}'  
| sort -u | grep -v \(  )| cut -f 1 -d ":" | sort -u | perl -pi -e 's| 
\n|\, |g' >| dependencies.txt


whereas I first used

dpkg -S $(  ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $1}'  
| sort -u | grep -v \(  )| cut -f 1 -d ":" | sort -u | perl -pi -e 's| 
\n|\, |g' >| dependencies.txt


My bad.  I needed the third column of the output of ldd to get the  
full path of the dynamic library. The first column only reports the  
name of the file, and then it wrongly assumed it was in my NX  
directory (it wasn't). Coot was properly linked. The list of  
dependencies in the debian file was wrong. Fixed now.   
( coot_0.5-2_i386.deb ).  Again, thanks for catching this.


Bill



On Nov 17, 2008, at 6:57 AM, William G. Scott wrote:

Woops.  I didn't see that.  I auto-generated the list of  
dependencies from the output of ldd on the coot binary, upon which I  
then used dpgk -S to find the corresponding packages. For some  
reason it generated this falsely (the library is also present, but  
ldd does not report coot linking anything with NX in the path).


Sorry, I will edit this out.

Thanks for testing.

Bill



On Nov 17, 2008, at 3:16 AM, Mark Brooks wrote:


Hi,

I just tested it on a freshly installed system for a student; it  
works very

well on Ubuntu Hardy.

I'm not sure why "nxnode" is a dependency of the Coot .deb though!  
(Although

that doesn't bother me too much- I would advise anyone to use NX ).

Thanks again,

Mark

2008/11/16 William G. Scott <[EMAIL PROTECTED]>


That's great.  In the short term, highly
unofficial/unauthorized/zeroth-order coot and dependencies for  
i386 linux:


debians:

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files




rpms (made via alien from above):

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages




These include mmdb, ssm, gpp4, fftw (in the form required for  
clipper and

coot), clipper, coot, which will install into /usr/local/xtal

and then the various guile-type dependencies, which will install  
into /usr




On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on

crystallographic libs for Ubuntu, e.g.:

https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:


Hi,
It may be useful to have a 'contrib' section for the Coot binary  
download
web page (or even some unofficial web page), so that we have  
more options of
binaries to test. For example, upon upgrading to Ubuntu Hardy  
Heron, Coot
stopped working, for reasons beyond my understanding, but worked  
when
recompiled. (Which was very easy using the build-it-gtk2-simple  
script BTW).
To have a central repository of tested binaries could be very  
handy, to

avoid having to do this.
The Coot developers and yourself (Bill) have done an enormous  
amount to
furnish us with working, tested programs,  but perhaps one or  
two more
updated binaries contributed by users  would be useful,  
especially for newer

releases of the myriad Linux flavours.
I think for the Coot developers to start providing .deb, .rpm  
and Gentoo
packages for every update is too onerous, especially  
when .tar.gz files work

OK. Just my opinion.
Which Ubuntu are you on Bill, and which binary are you using?  
Are these
on your debian web site? I guess I may be able to give a Hardy  
Heron binary

if need be.
Thanks for your .debs though, I use them all the time.
Mark
2008/11/12 William G. Scott <[EMAIL PROTECTED] >
Since Ubuntu has gotten to be popular (for good reason, IMO), it
might be useful to have an official (or at least semi-official)
debian package whose installation would guarantee all the
dependencies also get installed.  I've tried to do it in a
half-arsed sort of way, but lately have dropped the ball (sorry).
On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
<[EMAIL PROTECTED] > wrote:
Hi!
Firstly, do you need to build coot at all? There are binary
packages which work just fine on Gutsy. You can install them
wherever you want on your system, and they should just work.
Secondly, if for some reason you do want to build your own  
(you

want to make changes to the code???), then are you using the
build-it-gtk2-simple script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of
messing around with dependencies. With this script it is  
usually

pretty easy.
Kevin
Rimi wrote:
Hi all,
 I am new to coot. Recently I tried to inst

Re: [COOT] problem in coot installation in ubuntu

[Tim Fenn]

On Sun, 16 Nov 2008 02:16:01 + Paul Emsley
<[EMAIL PROTECTED]> wrote:

> 
> > guile net-http and guile-gui look unsupported...)?
> 
> Yes, they are tiny packages that could easily subsumed into Coot
> itself for ease of packaging (as Bill Scott once suggested).  Not
> done, no-one complained enough.
> 

The reason I bring up the guile dependencies in particular is they're
the only tricky part in getting rpms made, since without an upstream,
they're unlikely to get accepted.  Otherwise I'd be happy to contribute
those as well to fedora.

> >  I'd
> > like to begin preparing a rpm for fedora (now that most of the
> > dependencies are part of the distributions),
> 
> Good going!  MATSUURA Takanori and Adam Huffman said they'd like to
> do something similar.
> 

gpp4/mmdb/ssm and clipper are already available, or will be soon:

https://bugzilla.redhat.com/show_bug.cgi?id=435015
https://bugzilla.redhat.com/show_bug.cgi?id=435016
https://bugzilla.redhat.com/show_bug.cgi?id=435017
https://bugzilla.redhat.com/show_bug.cgi?id=435018

most of these packages are patched to include pkgconfig support, which
I'm attempting to get upstream to include (so the mmdb/mmdb-ssm and
clipper m4 macros can be dropped in favor of PKG_CHECK_MODULES).

and I've started the process for the refmac ligand dictionary and coot:

https://bugzilla.redhat.com/show_bug.cgi?id=472149
https://bugzilla.redhat.com/show_bug.cgi?id=472150

The coot submission does not include the guile dependencies (at the
moment, if the deps are updated to supported versions or included with
coot, that can change).

I also noticed several macros (such as guile-gtk.m4, mmdb.m4,
mmdb-ssm.m4) assume /lib is the proper library location - this
might result in 32 and 64 bit library clashes during a build.  Why not
let the linker define them (using AC_CHECK_LIB perhaps)?  I can write a
few patches, if you'd like.

-tim

-- 
-

Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
Stanford, CA  94305-5432
Phone:  (650) 736-1714
FAX:  (650) 736-1961

-

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

On Nov 18, 2008, at 6:26 PM, Tim Fenn wrote:


The reason I bring up the guile dependencies in particular is they're
the only tricky part in getting rpms made, since without an upstream,
they're unlikely to get accepted.  Otherwise I'd be happy to  
contribute

those as well to fedora.



Create a distraction and sneak them in.

http://diablo.ucsc.edu/~wgscott/debian/rpm/coot/dependencies/

But seriously, if they are GPL-ed, why not just stick them in coot's  
scheme directory and be done with it?

Re: [COOT] problem in coot installation in ubuntu

[Tim Fenn]

On Tue, 18 Nov 2008 18:37:07 -0800 "William G. Scott"
<[EMAIL PROTECTED]> wrote:

> 
> On Nov 18, 2008, at 6:26 PM, Tim Fenn wrote:
> 
> > The reason I bring up the guile dependencies in particular is
> > they're the only tricky part in getting rpms made, since without an
> > upstream, they're unlikely to get accepted.  Otherwise I'd be happy
> > to contribute
> > those as well to fedora.
> 
> 
> Create a distraction and sneak them in.
> 
> http://diablo.ucsc.edu/~wgscott/debian/rpm/coot/dependencies/
> 
> But seriously, if they are GPL-ed, why not just stick them in coot's  
> scheme directory and be done with it?

Sure, I'll give that a try, with the exception of guile-gtk (its a
library that doesn't seem to be necessary for most guile functions - is
this correct, paul?).

-tim

-- 
-

Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
Stanford, CA  94305-5432
Phone:  (650) 736-1714
FAX:  (650) 736-1961

-